Binding Site Information of Target
| Target General Information | Top | ||||
|---|---|---|---|---|---|
| Target ID | T18904 | Target Info | |||
| Target Name | Lysine-specific demethylase 4A (KDM4A) | ||||
| Synonyms | KIAA0677; Jumonji domain-containing protein 2A; JmjC domain-containing histone demethylation protein 3A; JMJD2A; JMJD2; JHDM3A | ||||
| Target Type | Patented-recorded Target | ||||
| Gene Name | KDM4A | ||||
| Biochemical Class | Paired donor oxygen oxidoreductase | ||||
| UniProt ID | |||||
| Drug Binding Sites of Target | Top | |||||
|---|---|---|---|---|---|---|
| Ligand Name: Pyruvic acid | Ligand Info | |||||
| Structure Description | Crystal structure of human JMJD2A in complex with pyruvate | PDB:5FYI | ||||
| Method | X-ray diffraction | Resolution | 2.10 Å | Mutation | No | [1] |
| PDB Sequence |
ESETLNPSAR
13 IMTFYPTMEE23 FRNFSRYIAY33 IESQGAHRAG43 LAKVVPPKEW53 KPRASYDDID 63 DLVIPAPIQQ73 LVTGQSGLFT83 QYNIQKKAMT93 VREFRKIANS103 DKYCTPRYSE 113 FEELERKYWK123 NLTFNPPIYG133 ADVNGTLYEK143 HVDEWNIGRL153 RTILDLVEKE 163 SGITIEGVNT173 PYLYFGMWKT183 SFAWHTEDMD193 LYSINYLHFG203 EPKSWYSVPP 213 EHGKRLERLA223 KGFFPGSAQS233 CEAFLRHKMT243 LISPLMLKKY253 GIPFDKVTQE 263 AGEFMITFPY273 GYHAGFNHGF283 NCAESTNFAT293 RRWIEYGKQA303 VLCSCRKDMV 313 KISMDVFVRK323 FQPERYKLWK333 AGKDNTVIDH343 TLPTPEAAEF353 L |
|||||
|
|
||||||
| Ligand Name: Fumaric acid | Ligand Info | |||||
| Structure Description | Crystal structure of human JMJD2A in complex with succinate | PDB:5FYC | ||||
| Method | X-ray diffraction | Resolution | 2.26 Å | Mutation | No | [2] |
| PDB Sequence |
LNPSARIMTF
17 YPTMEEFRNF27 SRYIAYIESQ37 GAHRAGLAKV47 VPPKEWKPRA57 SYDDIDDLVI 67 PAPIQQLVTG77 QSGLFTQYNI87 QKKAMTVREF97 RKIANSDKYC107 TPRYSEFEEL 117 ERKYWKNLTF127 NPPIYGADVN137 GTLYEKHVDE147 WNIGRLRTIL157 DLVEKESGIT 167 IEGVNTPYLY177 FGMWKTSFAW187 HTEDMDLYSI197 NYLHFGEPKS207 WYSVPPEHGK 217 RLERLAKGFF227 PGSAQSCEAF237 LRHKMTLISP247 LMLKKYGIPF257 DKVTQEAGEF 267 MITFPYGYHA277 GFNHGFNCAE287 STNFATRRWI297 EYGKQAVLCS307 CRKDMVKISM 317 DVFVRKFQPE327 RYKLWKAGKD337 NTVIDHTLPT347 PEAAEF
|
|||||
|
|
||||||
| Click to View More Binding Site Information of This Target and Ligand Pair | ||||||
| Ligand Name: 2-(carboxymethylamino)-2-oxoacetic acid | Ligand Info | |||||
| Structure Description | JMJD2A COMPLEXED WITH NI(II), NOG AND HISTONE H3K27me3 PEPTIDE (16-35) | PDB:4V2W | ||||
| Method | X-ray diffraction | Resolution | 1.81 Å | Mutation | No | [3] |
| PDB Sequence |
TLNPSARIMT
16 FYPTMEEFRN26 FSRYIAYIES36 QGAHRAGLAK46 VVPPKEWKPR56 ASYDDIDDLV 66 IPAPIQQLVT76 GQSGLFTQYN86 IQKKAMTVRE96 FRKIANSDKY106 CTPRYSEFEE 116 LERKYWKNLT126 FNPPIYGADV136 NGTLYEKHVD146 EWNIGRLRTI156 LDLVEKESGI 166 TIEGVNTPYL176 YFGMWKTSFA186 WHTEDMDLYS196 INYLHFGEPK206 SWYSVPPEHG 216 KRLERLAKGF226 FPGSAQSCEA236 FLRHKMTLIS246 PLMLKKYGIP256 FDKVTQEAGE 266 FMITFPYGYH276 AGFNHGFNCA286 ESTNFATRRW296 IEYGKQAVLC306 SCRKDMVKIS 316 MDVFVRKFQP326 ERYKLWKAGK336 DNTVIDHTLP346 TPEAAEFL
|
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .OGA or .OGA2 or .OGA3 or :3OGA;style chemicals stick;color identity;select .A:132 or .A:177 or .A:185 or .A:188 or .A:190 or .A:196 or .A:197 or .A:198 or .A:206 or .A:208 or .A:270 or .A:276 or .A:280 or .A:286 or .A:288; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
||||||
| Click to View More Binding Site Information of This Target and Ligand Pair | ||||||
| Ligand Name: N-Trimethyllysine | Ligand Info | |||||
| Structure Description | JMJD2A COMPLEXED WITH NI(II), NOG AND HISTONE H3K27me3 PEPTIDE (16-35) | PDB:4V2W | ||||
| Method | X-ray diffraction | Resolution | 1.81 Å | Mutation | No | [3] |
| PDB Sequence |
TLNPSARIMT
16 FYPTMEEFRN26 FSRYIAYIES36 QGAHRAGLAK46 VVPPKEWKPR56 ASYDDIDDLV 66 IPAPIQQLVT76 GQSGLFTQYN86 IQKKAMTVRE96 FRKIANSDKY106 CTPRYSEFEE 116 LERKYWKNLT126 FNPPIYGADV136 NGTLYEKHVD146 EWNIGRLRTI156 LDLVEKESGI 166 TIEGVNTPYL176 YFGMWKTSFA186 WHTEDMDLYS196 INYLHFGEPK206 SWYSVPPEHG 216 KRLERLAKGF226 FPGSAQSCEA236 FLRHKMTLIS246 PLMLKKYGIP256 FDKVTQEAGE 266 FMITFPYGYH276 AGFNHGFNCA286 ESTNFATRRW296 IEYGKQAVLC306 SCRKDMVKIS 316 MDVFVRKFQP326 ERYKLWKAGK336 DNTVIDHTLP346 TPEAAEFL
|
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .M3L or .M3L2 or .M3L3 or :3M3L;style chemicals stick;color identity;select .A:135 or .A:168 or .A:169 or .A:170 or .A:171 or .A:173 or .A:175 or .A:177 or .A:188 or .A:190 or .A:191 or .A:196 or .A:197 or .A:198 or .A:241 or .A:288 or .A:289 or .A:290 or .A:313; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
||||||
| Click to View More Binding Site Information of This Target and Ligand Pair | ||||||
| Ligand Name: SDMA | Ligand Info | |||||
| Structure Description | JMJD2A COMPLEXED WITH NI(II), NOG AND HISTONE H4(1-15)R3me2s PEPTIDE | PDB:5FWE | ||||
| Method | X-ray diffraction | Resolution | 2.05 Å | Mutation | No | [4] |
| PDB Sequence |
TLNPSARIMT
16 FYPTMEEFRN26 FSRYIAYIES36 QGAHRAGLAK46 VVPPKEWKPR56 ASYDDIDDLV 66 IPAPIQQLVT76 GQSGLFTQYN86 IQKKAMTVRE96 FRKIANSDKY106 CTPRYSEFEE 116 LERKYWKNLT126 FNPPIYGADV136 NGTLYEKHVD146 EWNIGRLRTI156 LDLVEKESGI 166 TIEGVNTPYL176 YFGMWKTSFA186 WHTEDMDLYS196 INYLHFGEPK206 SWYSVPPEHG 216 KRLERLAKGF226 FPGSAQSCEA236 FLRHKMTLIS246 PLMLKKYGIP256 FDKVTQEAGE 266 FMITFPYGYH276 AGFNHGFNCA286 ESTNFATRRW296 IEYGKQAVLC306 SCRKDMVKIS 316 MDVFVRKFQP326 ERYKLWKAGK336 DNTVIDHTLP346 TPEAAEFL
|
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .2MR or .2MR2 or .2MR3 or :32MR;style chemicals stick;color identity;select .A:135 or .A:168 or .A:169 or .A:170 or .A:171 or .A:175 or .A:177 or .A:190 or .A:191 or .A:241 or .A:288 or .A:289 or .A:290 or .A:313; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
||||||
| Ligand Name: Daminozide | Ligand Info | |||||
| Structure Description | JMJD2A Complexed with Daminozide | PDB:4AI9 | ||||
| Method | X-ray diffraction | Resolution | 2.25 Å | Mutation | No | [5] |
| PDB Sequence |
LNPSARIMTF
17 YPTMEEFRNF27 SRYIAYIESQ37 GAHRAGLAKV47 VPPKEWKPRA57 SYDDIDDLVI 67 PAPIQQLVTG77 QSGLFTQYNI87 QKKAMTVREF97 RKIANSDKYC107 TPRYSEFEEL 117 ERKYWKNLTF127 NPPIYGADVN137 GTLYEKHVDE147 WNIGRLRTIL157 DLVEKESGIT 167 IEGVNTPYLY177 FGMWKTSFAW187 HTEDMDLYSI197 NYLHFGEPKS207 WYSVPPEHGK 217 RLERLAKGFF227 PGSAQSCEAF237 LRHKMTLISP247 LMLKKYGIPF257 DKVTQEAGEF 267 MITFPYGYHA277 GFNHGFNCAE287 STNFATRRWI297 EYGKQAVLCS307 CRKDMVKISM 317 DVFVRKFQPE327 RYKLWKAGKD337 NTVIDHTLPT347 PEAAEFLK
|
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .DZA or .DZA2 or .DZA3 or :3DZA;style chemicals stick;color identity;select .A:23 or .A:29 or .A:30 or .A:33 or .A:37 or .A:132 or .A:177 or .A:184 or .A:185 or .A:188 or .A:190 or .A:196 or .A:198 or .A:206 or .A:208 or .A:270 or .A:276 or .A:280 or .A:288 or .A:290 or .A:353; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
GLU23
2.515
ARG29
3.868
TYR30
4.296
TYR33
3.132
GLN37
4.712
TYR132
2.583
TYR177
4.053
SER184
4.897
PHE185
3.436
HIS188
3.228
GLU190
3.272
|
|||||
| Ligand Name: Pyridine-2,4-dicarboxylic acid | Ligand Info | |||||
| Structure Description | Crystal Structure of JMJD2A complexed with inhibitor Pyridine-2,4- dicarboxylic acid | PDB:2VD7 | ||||
| Method | X-ray diffraction | Resolution | 2.25 Å | Mutation | No | [6] |
| PDB Sequence |
ETLNPSARIM
15 TFYPTMEEFR25 NFSRYIAYIE35 SQGAHRAGLA45 KVVPPKEWKP55 RASYDDIDDL 65 VIPAPIQQLV75 TGQSGLFTQY85 NIQKKAMTVR95 EFRKIANSDK105 YCTPRYSEFE 115 ELERKYWKNL125 TFNPPIYGAD135 VNGTLYEKHV145 DEWNIGRLRT155 ILDLVEKESG 165 ITIEGVNTPY175 LYFGMWKTSF185 AWHTEDMDLY195 SINYLHFGEP205 KSWYSVPPEH 215 GKRLERLAKG225 FFPGSAQSCE235 AFLRHKMTLI245 SPLMLKKYGI255 PFDKVTQEAG 265 EFMITFPYGY275 HAGFNHGFNC285 AESTNFATRR295 WIEYGKQAVL305 CSCRKDMVKI 315 SMDVFVRKFQ325 PERYKLWKAG335 KDNTVIDHTL345 PTPEAAEFLK355 |
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .PD2 or .PD22 or .PD23 or :3PD2;style chemicals stick;color identity;select .A:132 or .A:177 or .A:185 or .A:188 or .A:190 or .A:198 or .A:206 or .A:208 or .A:241 or .A:276 or .A:280; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
||||||
| Ligand Name: Hydroxyqunoline analog 2 | Ligand Info | |||||
| Structure Description | JMJD2A COMPLEXED WITH 8-HYDROXYQUINOLINE-4-CARBOXYLIC ACID | PDB:4BIS | ||||
| Method | X-ray diffraction | Resolution | 2.49 Å | Mutation | No | [7] |
| PDB Sequence |
LNPSARIMTF
17 YPTMEEFRNF27 SRYIAYIESQ37 GAHRAGLAKV47 VPPKEWKPRA57 SYDDIDDLVI 67 PAPIQQLVTG77 QSGLFTQYNI87 QKKAMTVREF97 RKIANSDKYC107 TPRYSEFEEL 117 ERKYWKNLTF127 NPPIYGADVN137 GTLYEKHVDE147 WNIGRLRTIL157 DLVEKESGIT 167 IEGVNTPYLY177 FGMWKTSFAW187 HTEDMDLYSI197 NYLHFGEPKS207 WYSVPPEHGK 217 RLERLAKGFF227 PGSAQSCEAF237 LRHKMTLISP247 LMLKKYGIPF257 DKVTQEAGEF 267 MITFPYGYHA277 GFNHGFNCAE287 STNFATRRWI297 EYGKQAVLCS307 CRKDMVKISM 317 DVFVRKFQPE327 RYKLWKAGKD337 NTVIDHTLPT347 PEAAEFLK
|
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .8HQ or .8HQ2 or .8HQ3 or :38HQ;style chemicals stick;color identity;select .A:132 or .A:177 or .A:185 or .A:188 or .A:190 or .A:198 or .A:206 or .A:208 or .A:241 or .A:276 or .A:280; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
||||||
| Ligand Name: Propanoic acid | Ligand Info | |||||
| Structure Description | JMJD2A/ KDM4A COMPLEXED WITH NI(II) AND Macrocyclic PEPTIDE Inhibitor CP2 (13-mer) | PDB:5LY1 | ||||
| Method | X-ray diffraction | Resolution | 2.50 Å | Mutation | No | [8] |
| PDB Sequence |
TLNPSARIMT
16 FYPTMEEFRN26 FSRYIAYIES36 QGAHRAGLAK46 VVPPKEWKPR56 ASYDDIDDLV 66 IPAPIQQLVT76 GQSGLFTQYN86 IQKKAMTVRE96 FRKIANSDKY106 CTPRYSEFEE 116 LERKYWKNLT126 FNPPIYGADV136 NGTLYEKHVD146 EWNIGRLRTI156 LDLVEKESGI 166 TIEGVNTPYL176 YFGMWKTSFA186 WHTEDMDLYS196 INYLHFGEPK206 SWYSVPPEHG 216 KRLERLAKGF226 FPGSAQSCEA236 FLRHKMTLIS246 PLMLKKYGIP256 FDKVTQEAGE 266 FMITFPYGYH276 AGFNHGFNCA286 ESTNFATRRW296 IEYGKQAVLC306 SCRKDMVKIS 316 MDVFVRKFQP326 ERYKLWKAGK336 DNTVIDHTLP346 TPEAAEFLK
|
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .PPI or .PPI2 or .PPI3 or :3PPI;style chemicals stick;color identity;select .A:135 or .A:169 or .A:170 or .A:171 or .A:175 or .A:177 or .A:190 or .A:191 or .A:196 or .A:241 or .A:288 or .A:289 or .A:290; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
||||||
| Ligand Name: Hydroxyqunoline analog 1 | Ligand Info | |||||
| Structure Description | Crystal structure of JMJD2A complexed with 5-carboxy-8-hydroxyquinoline | PDB:3NJY | ||||
| Method | X-ray diffraction | Resolution | 2.60 Å | Mutation | No | [9] |
| PDB Sequence |
LNPSARIMTF
17 YPTMEEFRNF27 SRYIAYIESQ37 GAHRAGLAKV47 VPPKEWKPRA57 SYDDIDDLVI 67 PAPIQQLVTG77 QSGLFTQYNI87 QKKAMTVREF97 RKIANSDKYC107 TPRYSEFEEL 117 ERKYWKNLTF127 NPPIYGADVN137 GTLYEKHVDE147 WNIGRLRTIL157 DLVEKESGIT 167 IEGVNTPYLY177 FGMWKTSFAW187 HTEDMDLYSI197 NYLHFGEPKS207 WYSVPPEHGK 217 RLERLAKGFF227 PGSAQSCEAF237 LRHKMTLISP247 LMLKKYGIPF257 DKVTQEAGEF 267 MITFPYGYHA277 GFNHGFNCAE287 STNFATRRWI297 EYGKQAVLCS307 CRKDMVKISM 317 DVFVRKFQPE327 RYKLWKAGKD337 NTVIDHTLPT347 PEAAEFL
|
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .8XQ or .8XQ2 or .8XQ3 or :38XQ;style chemicals stick;color identity;select .A:132 or .A:135 or .A:177 or .A:185 or .A:188 or .A:190 or .A:196 or .A:198 or .A:206 or .A:208 or .A:241 or .A:270 or .A:276 or .A:280; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
||||||
| Ligand Name: Alpha-ketoglutaric acid | Ligand Info | |||||
| Structure Description | Crystal structure of JMJD2A in ternary complex with an histone H3K9me3 peptide and 2-oxoglutarate | PDB:2Q8C | ||||
| Method | X-ray diffraction | Resolution | 2.05 Å | Mutation | No | [10] |
| PDB Sequence |
SESETLNPSA
12 RIMTFYPTME22 EFRNFSRYIA32 YIESQGAHRA42 GLAKVVPPKE52 WKPRASYDDI 62 DDLVIPAPIQ72 QLVTGQSGLF82 TQYNIQKKAM92 TVREFRKIAN102 SDKYCTPRYS 112 EFEELERKYW122 KNLTFNPPIY132 GADVNGTLYE142 KHVDEWNIGR152 LRTILDLVEK 162 ESGITIEGVN172 TPYLYFGMWK182 TSFAWHTEDM192 DLYSINYLHF202 GEPKSWYSVP 212 PEHGKRLERL222 AKGFFPGSAQ232 SCEAFLRHKM242 TLISPLMLKK252 YGIPFDKVTQ 262 EAGEFMITFP272 YGYHAGFNHG282 FNCAESTNFA292 TRRWIEYGKQ302 AVLCSCRKDM 312 VKISMDVFVR322 KFQPERYKLW332 KAGKDNTVID342 HTLPT
|
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .AKG or .AKG2 or .AKG3 or :3AKG;style chemicals stick;color identity;select .A:132 or .A:177 or .A:185 or .A:188 or .A:190 or .A:196 or .A:198 or .A:206 or .A:208 or .A:270 or .A:276 or .A:286 or .A:288; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
||||||
| Click to View More Binding Site Information of This Target and Ligand Pair | ||||||
| Ligand Name: N(6),N(6)-Dimethyl-L-lysine | Ligand Info | |||||
| Structure Description | Crystal structure of JMJD2A complexed with histone H3 peptide dimethylated at Lys9 | PDB:2OX0 | ||||
| Method | X-ray diffraction | Resolution | 1.95 Å | Mutation | No | [11] |
| PDB Sequence |
TLNPSARIMT
16 FYPTMEEFRN26 FSRYIAYIES36 QGAHRAGLAK46 VVPPKEWKPR56 ASYDDIDDLV 66 IPAPIQQLVT76 GQSGLFTQYN86 IQKKAMTVRE96 FRKIANSDKY106 CTPRYSEFEE 116 LERKYWKNLT126 FNPPIYGADV136 NGTLYEKHVD146 EWNIGRLRTI156 LDLVEKESGI 166 TIEGVNTPYL176 YFGMWKTSFA186 WHTEDMDLYS196 INYLHFGEPK206 SWYSVPPEHG 216 KRLERLAKGF226 FPGSAQSCEA236 FLRHKMTLIS246 PLMLKKYGIP256 FDKVTQEAGE 266 FMITFPYGYH276 AGFNHGFNCA286 ESTNFATRRW296 IEYGKQAVLC306 SCRKDMVKIS 316 MDVFVRKFQP326 ERYKLWKAGK336 DNTVIDHTLP346 TPEAAEFLK
|
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .MLY or .MLY2 or .MLY3 or :3MLY;style chemicals stick;color identity;select .A:135 or .A:168 or .A:169 or .A:170 or .A:171 or .A:175 or .A:177 or .A:190 or .A:191 or .A:196 or .A:241 or .A:288 or .A:289 or .A:290 or .A:313; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
||||||
| Ligand Name: N6-Acetyl-L-lysine | Ligand Info | |||||
| Structure Description | Crystal structure of JMJD2A complexed with histone H3 peptide dimethylated at Lys9 | PDB:2OX0 | ||||
| Method | X-ray diffraction | Resolution | 1.95 Å | Mutation | No | [11] |
| PDB Sequence |
TLNPSARIMT
16 FYPTMEEFRN26 FSRYIAYIES36 QGAHRAGLAK46 VVPPKEWKPR56 ASYDDIDDLV 66 IPAPIQQLVT76 GQSGLFTQYN86 IQKKAMTVRE96 FRKIANSDKY106 CTPRYSEFEE 116 LERKYWKNLT126 FNPPIYGADV136 NGTLYEKHVD146 EWNIGRLRTI156 LDLVEKESGI 166 TIEGVNTPYL176 YFGMWKTSFA186 WHTEDMDLYS196 INYLHFGEPK206 SWYSVPPEHG 216 KRLERLAKGF226 FPGSAQSCEA236 FLRHKMTLIS246 PLMLKKYGIP256 FDKVTQEAGE 266 FMITFPYGYH276 AGFNHGFNCA286 ESTNFATRRW296 IEYGKQAVLC306 SCRKDMVKIS 316 MDVFVRKFQP326 ERYKLWKAGK336 DNTVIDHTLP346 TPEAAEFLK
|
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .ALY or .ALY2 or .ALY3 or :3ALY;style chemicals stick;color identity;select .A:85 or .A:86 or .A:87 or .A:88 or .A:242 or .A:309; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
||||||
| Click to View More Binding Site Information of This Target and Ligand Pair | ||||||
| Ligand Name: 4'-[(2-Aminoethyl)carbamoyl]-2,2'-Bipyridine-4-Carboxylic Acid | Ligand Info | |||||
| Structure Description | Crystal structure of JMJD2A complexed with bipyridyl inhibitor | PDB:3PDQ | ||||
| Method | X-ray diffraction | Resolution | 1.99 Å | Mutation | No | [12] |
| PDB Sequence |
SESETLNPSA
12 RIMTFYPTME22 EFRNFSRYIA32 YIESQGAHRA42 GLAKVVPPKE52 WKPRASYDDI 62 DDLVIPAPIQ72 QLVTGQSGLF82 TQYNIQKKAM92 TVREFRKIAN102 SDKYCTPRYS 112 EFEELERKYW122 KNLTFNPPIY132 GADVNGTLYE142 KHVDEWNIGR152 LRTILDLVEK 162 ESGITIEGVN172 TPYLYFGMWK182 TSFAWHTEDM192 DLYSINYLHF202 GEPKSWYSVP 212 PEHGKRLERL222 AKGFFPGSAQ232 SCEAFLRHKM242 TLISPLMLKK252 YGIPFDKVTQ 262 EAGEFMITFP272 YGYHAGFNHG282 FNCAESTNFA292 TRRWIEYGKQ302 AVLCSCRKDM 312 VKISMDVFVR322 KFQPERYKLW332 KAGKDNTVID342 HTLPTPEAAE352 FLK |
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .KC6 or .KC62 or .KC63 or :3KC6;style chemicals stick;color identity;select .A:132 or .A:135 or .A:175 or .A:177 or .A:185 or .A:188 or .A:190 or .A:191 or .A:198 or .A:206 or .A:208 or .A:241 or .A:276; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
||||||
| Ligand Name: 2-(5-Azanyl-2-Oxidanyl-Phenyl)pyridine-4-Carboxylic Acid | Ligand Info | |||||
| Structure Description | Crystal structure of human JMJD2A in complex with compound 30 | PDB:5A7Q | ||||
| Method | X-ray diffraction | Resolution | 2.00 Å | Mutation | No | [13] |
| PDB Sequence |
SESETLNPSA
12 RIMTFYPTME22 EFRNFSRYIA32 YIESQGAHRA42 GLAKVVPPKE52 WKPRASYDDI 62 DDLVIPAPIQ72 QLVTGQSGLF82 TQYNIQKKAM92 TVREFRKIAN102 SDKYCTPRYS 112 EFEELERKYW122 KNLTFNPPIY132 GADVNGTLYE142 KHVDEWNIGR152 LRTILDLVEK 162 ESGITIEGVN172 TPYLYFGMWK182 TSFAWHTEDM192 DLYSINYLHF202 GEPKSWYSVP 212 PEHGKRLERL222 AKGFFPGSAQ232 SCEAFLRHKM242 TLISPLMLKK252 YGIPFDKVTQ 262 EAGEFMITFP272 YGYHAGFNHG282 FNCAESTNFA292 TRRWIEYGKQ302 AVLCSCRKDM 312 VKISMDVFVR322 KFQPERYKLW332 KAGKDNTVID342 HTLPTPEAAE352 F |
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .KCH or .KCH2 or .KCH3 or :3KCH;style chemicals stick;color identity;select .A:132 or .A:135 or .A:177 or .A:185 or .A:188 or .A:190 or .A:196 or .A:198 or .A:206 or .A:208 or .A:241 or .A:276 or .A:286; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
||||||
| Ligand Name: (2R)-2-hydroxypentanedioic acid | Ligand Info | |||||
| Structure Description | JMJD2A COMPLEXED WITH R-2-HYDROXYGLUTARATE AND HISTONE H3K36me3 PEPTIDE (30-41) | PDB:2YBP | ||||
| Method | X-ray diffraction | Resolution | 2.02 Å | Mutation | No | [14] |
| PDB Sequence |
TLNPSARIMT
16 FYPTMEEFRN26 FSRYIAYIES36 QGAHRAGLAK46 VVPPKEWKPR56 ASYDDIDDLV 66 IPAPIQQLVT76 GQSGLFTQYN86 IQKKAMTVRE96 FRKIANSDKY106 CTPRYSEFEE 116 LERKYWKNLT126 FNPPIYGADV136 NGTLYEKHVD146 EWNIGRLRTI156 LDLVEKESGI 166 TIEGVNTPYL176 YFGMWKTSFA186 WHTEDMDLYS196 INYLHFGEPK206 SWYSVPPEHG 216 KRLERLAKGF226 FPGSAQSCEA236 FLRHKMTLIS246 PLMLKKYGIP256 FDKVTQEAGE 266 FMITFPYGYH276 AGFNHGFNCA286 ESTNFATRRW296 IEYGKQAVLC306 SCRKDMVKIS 316 MDVFVRKFQP326 ERYKLWKAGK336 DNTVIDHTLP346 TPEAAEFLK
|
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .2HG or .2HG2 or .2HG3 or :32HG;style chemicals stick;color identity;select .A:132 or .A:177 or .A:185 or .A:188 or .A:190 or .A:196 or .A:197 or .A:198 or .A:206 or .A:208 or .A:270 or .A:276 or .A:286 or .A:288; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
||||||
| Click to View More Binding Site Information of This Target and Ligand Pair | ||||||
| Ligand Name: 2-[5-(2-Methoxyethanoylamino)-2-Oxidanyl-Phenyl]pyridine-4-Carboxylic Acid | Ligand Info | |||||
| Structure Description | Crystal structure of human JMJD2A in complex with compound 42 | PDB:5A7O | ||||
| Method | X-ray diffraction | Resolution | 2.15 Å | Mutation | No | [13] |
| PDB Sequence |
ESETLNPSAR
13 IMTFYPTMEE23 FRNFSRYIAY33 IESQGAHRAG43 LAKVVPPKEW53 KPRASYDDID 63 DLVIPAPIQQ73 LVTGQSGLFT83 QYNIQKKAMT93 VREFRKIANS103 DKYCTPRYSE 113 FEELERKYWK123 NLTFNPPIYG133 ADVNGTLYEK143 HVDEWNIGRL153 RTILDLVEKE 163 SGITIEGVNT173 PYLYFGMWKT183 SFAWHTEDMD193 LYSINYLHFG203 EPKSWYSVPP 213 EHGKRLERLA223 KGFFPGSAQS233 CEAFLRHKMT243 LISPLMLKKY253 GIPFDKVTQE 263 AGEFMITFPY273 GYHAGFNHGF283 NCAESTNFAT293 RRWIEYGKQA303 VLCSCRKDMV 313 KISMDVFVRK323 FQPERYKLWK333 AGKDNTVIDH343 TLPTPEAAEF353 E |
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .7WH or .7WH2 or .7WH3 or :37WH;style chemicals stick;color identity;select .A:86 or .A:132 or .A:135 or .A:177 or .A:185 or .A:186 or .A:188 or .A:190 or .A:196 or .A:198 or .A:206 or .A:208 or .A:240 or .A:241 or .A:276 or .A:286; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
||||||
| Ligand Name: N-(Carboxycarbonyl)-D-Cysteine | Ligand Info | |||||
| Structure Description | Histone Lysine demethylase JMJD2A in complex with T11C peptide substrate crosslinked to N-oxalyl-D-cysteine | PDB:3U4S | ||||
| Method | X-ray diffraction | Resolution | 2.15 Å | Mutation | Yes | [15] |
| PDB Sequence |
LNPSARIMTF
17 YPTMEEFRNF27 SRYIAYIESQ37 GAHRAGLAKV47 VPPKEWKPRA57 SYDDIDDLVI 67 PAPIQQLVTG77 QSGLFTQYNI87 QKKAMTVREF97 RKIANSDKYC107 TPRYSEFEEL 117 ERKYWKNLTF127 NPPIYGADVN137 GTLYEKHVDE147 WNIGRLRTIL157 DLVEKESGIT 167 IEGVNTPYLY177 FGMWKTSFAW187 HTEDMDLYSI197 NYLHFGEPKS207 WYSVPPEHGK 217 RLERLAKGFF227 PGSAQSCEAF237 LRHKMTLISP247 LMLKKYGIPF257 DKVTQEAGEF 267 MITFPYGYHA277 GFNHGFNCAE287 STNFATRRWI297 EYGKQAVLCS307 CRKDMVKISM 317 DVFVRKFQPE327 RYKLWKAGKD337 NTVIDHTLPT347 PEAAE
|
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .08P or .08P2 or .08P3 or :308P;style chemicals stick;color identity;select .A:132 or .A:177 or .A:185 or .A:188 or .A:190 or .A:196 or .A:197 or .A:198 or .A:206 or .A:208 or .A:241 or .A:270 or .A:276 or .A:280 or .A:288; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
||||||
| Ligand Name: 2-(5-Acetamido-2-Oxidanyl-Phenyl)pyridine-4-Carboxylic Acid | Ligand Info | |||||
| Structure Description | Crystal structure of human JMJD2A in complex with compound 44 | PDB:5A7S | ||||
| Method | X-ray diffraction | Resolution | 2.20 Å | Mutation | No | [13] |
| PDB Sequence |
PSARIMTFYP
19 TMEEFRNFSR29 YIAYIESQGA39 HRAGLAKVVP49 PKEWKPRASY59 DDIDDLVIPA 69 PIQQLVTGQS79 GLFTQYNIQK89 KAMTVREFRK99 IANSDKYCTP109 RYSEFEELER 119 KYWKNLTFNP129 PIYGADVNGT139 LYEKHVDEWN149 IGRLRTILDL159 VEKESGITIE 169 GVNTPYLYFG179 MWKTSFAWHT189 EDMDLYSINY199 LHFGEPKSWY209 SVPPEHGKRL 219 ERLAKGFFPG229 SAQSCEAFLR239 HKMTLISPLM249 LKKYGIPFDK259 VTQEAGEFMI 269 TFPYGYHAGF279 NHGFNCAEST289 NFATRRWIEY299 GKQAVLCSCR309 KDMVKISMDV 319 FVRKFQPERY329 KLWKAGKDNT339 VIDHTLPTPE349 AAEFL
|
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .S2X or .S2X2 or .S2X3 or :3S2X;style chemicals stick;color identity;select .A:86 or .A:132 or .A:135 or .A:177 or .A:185 or .A:188 or .A:190 or .A:196 or .A:198 or .A:206 or .A:208 or .A:241 or .A:276 or .A:280 or .A:286; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
||||||
| Ligand Name: 8-Hydroxy-3-(Piperazin-1-Yl)quinoline-5-Carboxylic Acid | Ligand Info | |||||
| Structure Description | Crystal Structure of JMJD2A Complexed with Inhibitor | PDB:3RVH | ||||
| Method | X-ray diffraction | Resolution | 2.25 Å | Mutation | No | [16] |
| PDB Sequence |
SESETLNPSA
12 RIMTFYPTME22 EFRNFSRYIA32 YIESQGAHRA42 GLAKVVPPKE52 WKPRASYDDI 62 DDLVIPAPIQ72 QLVTGQSGLF82 TQYNIQKKAM92 TVREFRKIAN102 SDKYCTPRYS 112 EFEELERKYW122 KNLTFNPPIY132 GADVNGTLYE142 KHVDEWNIGR152 LRTILDLVEK 162 ESGITIEGVN172 TPYLYFGMWK182 TSFAWHTEDM192 DLYSINYLHF202 GEPKSWYSVP 212 PEHGKRLERL222 AKGFFPGSAQ232 SCEAFLRHKM242 TLISPLMLKK252 YGIPFDKVTQ 262 EAGEFMITFP272 YGYHAGFNHG282 FNCAESTNFA292 TRRWIEYGKQ302 AVLCSCRKDM 312 VKISMDVFVR322 KFQPERYKLW332 KAGKDNTVID342 HTLPTPEAAE352 F |
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .HQ2 or .HQ22 or .HQ23 or :3HQ2;style chemicals stick;color identity;select .A:71 or .A:132 or .A:134 or .A:135 or .A:177 or .A:184 or .A:185 or .A:188 or .A:190 or .A:196 or .A:198 or .A:206 or .A:208 or .A:241 or .A:276 or .A:280; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
||||||
| Ligand Name: 2-[5-[(4-Hydroxyphenyl)carbonylamino]-2-Oxidanyl-Phenyl]pyridine-4-Carboxylic Acid | Ligand Info | |||||
| Structure Description | Crystal structure of human JMJD2A in complex with compound 35 | PDB:5A7W | ||||
| Method | X-ray diffraction | Resolution | 2.27 Å | Mutation | No | [13] |
| PDB Sequence |
> Chain A
LNPSARIMTF 17 YPTMEEFRNF27 SRYIAYIESQ37 GAHRAGLAKV47 VPPKEWKPRA57 SYDDIDDLVI 67 PAPIQQLVTG77 QSGLFTQYNI87 QKKAMTVREF97 RKIANSDKYC107 TPRYSEFEEL 117 ERKYWKNLTF127 NPPIYGADVN137 GTLYEKHVDE147 WNIGRLRTIL157 DLVEKESGIT 167 IEGVNTPYLY177 FGMWKTSFAW187 HTEDMDLYSI197 NYLHFGEPKS207 WYSVPPEHGK 217 RLERLAKGFF227 PGSAQSCEAF237 LRHKMTLISP247 LMLKKYGIPF257 DKVTQEAGEF 267 MITFPYGYHA277 GFNHGFNCAE287 STNFATRRWI297 EYGKQAVLCS307 CRKDMVKISM 317 DVFVRKFQPE327 RYKLWKAGKD337 NTVIDHTLPT347 PEAAEF> Chain B LNPSARIMTF 17 YPTMEEFRNF27 SRYIAYIESQ37 GAHRAGLAKV47 VPPKEWKPRA57 SYDDIDDLVI 67 PAPIQQLVTG77 QSGLFTQYNI87 QKKAMTVREF97 RKIANSDKYC107 TPRYSEFEEL 117 ERKYWKNLTF127 NPPIYGADVN137 GTLYEKHVDE147 WNIGRLRTIL157 DLVEKESGIT 167 IEGVNTPYLY177 FGMWKTSFAW187 HTEDMDLYSI197 NYLHFGEPKS207 WYSVPPEHGK 217 RLERLAKGFF227 PGSAESCEAF237 LRHKMTLISP247 LMLKKYGIPF257 DKVTQEAGEF 267 MITFPYGYHA277 GFNHGFNCAE287 STNFATRRWI297 EYGKQAVLCS307 CRKDMVKISM 317 DVFVRKFQPE327 RYKLWKAGKD337 NTVIDHTLPT347 PEAAEF
|
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .35M or .35M2 or .35M3 or :335M;style chemicals stick;color identity;select .A:86 or .A:132 or .A:135 or .A:177 or .A:184 or .A:185 or .A:186 or .A:188 or .A:190 or .A:196 or .A:198 or .A:206 or .A:208 or .A:240 or .A:241 or .A:276 or .B:71 or .B:86 or .B:132 or .B:134 or .B:135 or .B:177 or .B:185 or .B:188 or .B:190 or .B:198 or .B:206 or .B:208 or .B:240 or .B:241 or .B:276 or .B:280 or .B:286; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
ASN86[A]
3.139
TYR132[A]
2.313
ASP135[A]
4.607
TYR177[A]
3.855
SER184[A]
4.946
PHE185[A]
3.125
ALA186[A]
4.828
HIS188[A]
3.123
GLU190[A]
2.492
SER196[A]
4.931
ASN198[A]
3.562
LYS206[A]
2.962
TRP208[A]
3.697
HIS240[A]
4.192
LYS241[A]
3.439
HIS276[A]
3.708
ILE71[B]
3.840
|
|||||
| Ligand Name: 2-[5-[(5-Methyl-1,2-oxazol-3-yl)carbonylamino]-2-oxidanyl-phenyl]pyridine-4-carboxylic acid | Ligand Info | |||||
| Structure Description | Crystal structure of human JMJD2A in complex with compound 36 | PDB:5A7P | ||||
| Method | X-ray diffraction | Resolution | 2.28 Å | Mutation | No | [13] |
| PDB Sequence |
ESETLNPSAR
13 IMTFYPTMEE23 FRNFSRYIAY33 IESQGAHRAG43 LAKVVPPKEW53 KPRASYDDID 63 DLVIPAPIQQ73 LVTGQSGLFT83 QYNIQKKAMT93 VREFRKIANS103 DKYCTPRYSE 113 FEELERKYWK123 NLTFNPPIYG133 ADVNGTLYEK143 HVDEWNIGRL153 RTILDLVEKE 163 SGITIEGVNT173 PYLYFGMWKT183 SFAWHTEDMD193 LYSINYLHFG203 EPKSWYSVPP 213 EHGKRLERLA223 KGFFPGSAQS233 CEAFLRHKMT243 LISPLMLKKY253 GIPFDKVTQE 263 AGEFMITFPY273 GYHAGFNHGF283 NCAESTNFAT293 RRWIEYGKQA303 VLCSCRKDMV 313 KISMDVFVRK323 FQPERYKLWK333 AGKDNTVIDH343 TLPTPEAAEF353 |
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .6Z1 or .6Z12 or .6Z13 or :36Z1;style chemicals stick;color identity;select .A:86 or .A:132 or .A:135 or .A:177 or .A:185 or .A:188 or .A:190 or .A:198 or .A:206 or .A:208 or .A:240 or .A:241 or .A:276 or .A:280; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
||||||
| Ligand Name: 2-[5-[2-(3-Methoxyphenyl)ethanoylamino]-2-Oxidanyl-Phenyl]pyridine-4-Carboxylic Acid | Ligand Info | |||||
| Structure Description | Crystal structure of human JMJD2A in complex with compound 40 | PDB:5A80 | ||||
| Method | X-ray diffraction | Resolution | 2.28 Å | Mutation | No | [13] |
| PDB Sequence |
ESETLNPSAR
13 IMTFYPTMEE23 FRNFSRYIAY33 IESQGAHRAG43 LAKVVPPKEW53 KPRASYDDID 63 DLVIPAPIQQ73 LVTGQSGLFT83 QYNIQKKAMT93 VREFRKIANS103 DKYCTPRYSE 113 FEELERKYWK123 NLTFNPPIYG133 ADVNGTLYEK143 HVDEWNIGRL153 RTILDLVEKE 163 SGITIEGVNT173 PYLYFGMWKT183 SFAWHTEDMD193 LYSINYLHFG203 EPKSWYSVPP 213 EHGKRLERLA223 KGFFPGSAQS233 CEAFLRHKMT243 LISPLMLKKY253 GIPFDKVTQE 263 AGEFMITFPY273 GYHAGFNHGF283 NCAESTNFAT293 RRWIEYGKQA303 VLCSCRKDMV 313 KISMDVFVRK323 FQPERYKLWK333 AGKDNTVIDH343 TLPTPEAAEF353 L |
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .9CJ or .9CJ2 or .9CJ3 or :39CJ;style chemicals stick;color identity;select .A:86 or .A:132 or .A:135 or .A:177 or .A:185 or .A:188 or .A:190 or .A:196 or .A:198 or .A:206 or .A:208 or .A:240 or .A:241 or .A:242 or .A:276 or .A:309; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
||||||
| Ligand Name: (2S)-2-hydroxypentanedioic acid | Ligand Info | |||||
| Structure Description | JMJD2A COMPLEXED WITH S-2-HYDROXYGLUTARATE AND HISTONE H3K36me3 PEPTIDE (30-41) | PDB:2YBS | ||||
| Method | X-ray diffraction | Resolution | 2.32 Å | Mutation | No | [14] |
| PDB Sequence |
LNPSARIMTF
17 YPTMEEFRNF27 SRYIAYIESQ37 GAHRAGLAKV47 VPPKEWKPRA57 SYDDIDDLVI 67 PAPIQQLVTG77 QSGLFTQYNI87 QKKAMTVREF97 RKIANSDKYC107 TPRYSEFEEL 117 ERKYWKNLTF127 NPPIYGADVN137 GTLYEKHVDE147 WNIGRLRTIL157 DLVEKESGIT 167 IEGVNTPYLY177 FGMWKTSFAW187 HTEDMDLYSI197 NYLHFGEPKS207 WYSVPPEHGK 217 RLERLAKGFF227 PGSAQSCEAF237 LRHKMTLISP247 LMLKKYGIPF257 DKVTQEAGEF 267 MITFPYGYHA277 GFNHGFNCAE287 STNFATRRWI297 EYGKQAVLCS307 CRKDMVKISM 317 DVFVRKFQPE327 RYKLWKAGKD337 NTVIDHTLPT347 PEAAEFLK
|
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .S2G or .S2G2 or .S2G3 or :3S2G;style chemicals stick;color identity;select .A:132 or .A:177 or .A:185 or .A:188 or .A:190 or .A:196 or .A:197 or .A:198 or .A:206 or .A:208 or .A:270 or .A:276 or .A:288; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
||||||
| Ligand Name: 2-(1h-Pyrazol-3-Yl)pyridine-4-Carboxylic Acid | Ligand Info | |||||
| Structure Description | Crystal Structure of JMJD2A Complexed with Inhibitor | PDB:4GD4 | ||||
| Method | X-ray diffraction | Resolution | 2.33 Å | Mutation | No | [17] |
| PDB Sequence |
SETLNPSARI
14 MTFYPTMEEF24 RNFSRYIAYI34 ESQGAHRAGL44 AKVVPPKEWK54 PRASYDDIDD 64 LVIPAPIQQL74 VTGQSGLFTQ84 YNIQKKAMTV94 REFRKIANSD104 KYCTPRYSEF 114 EELERKYWKN124 LTFNPPIYGA134 DVNGTLYEKH144 VDEWNIGRLR154 TILDLVEKES 164 GITIEGVNTP174 YLYFGMWKTS184 FAWHTEDMDL194 YSINYLHFGE204 PKSWYSVPPE 214 HGKRLERLAK224 GFFPGSAQSC234 EAFLRHKMTL244 ISPLMLKKYG254 IPFDKVTQEA 264 GEFMITFPYG274 YHAGFNHGFN284 CAESTNFATR294 RWIEYGKQAV304 LCSCRKDMVK 314 ISMDVFVRKF324 QPERYKLWKA334 GKDNTVIDHT344 LPTPEAAEFL354 |
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .0WS or .0WS2 or .0WS3 or :30WS;style chemicals stick;color identity;select .A:132 or .A:135 or .A:177 or .A:185 or .A:188 or .A:190 or .A:191 or .A:198 or .A:206 or .A:208 or .A:241 or .A:270 or .A:276 or .A:280 or .A:290; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
||||||
| Ligand Name: D-erythro-Isocitric acid | Ligand Info | |||||
| Structure Description | Crystal structure of human JMJD2A in complex with D-threo-isocitrate | PDB:5FY8 | ||||
| Method | X-ray diffraction | Resolution | 2.34 Å | Mutation | No | [18] |
| PDB Sequence |
ESETLNPSAR
13 IMTFYPTMEE23 FRNFSRYIAY33 IESQGAHRAG43 LAKVVPPKEW53 KPRASYDDID 63 DLVIPAPIQQ73 LVTGQSGLFT83 QYNIQKKAMT93 VREFRKIANS103 DKYCTPRYSE 113 FEELERKYWK123 NLTFNPPIYG133 ADVNGTLYEK143 HVDEWNIGRL153 RTILDLVEKE 163 SGITIEGVNT173 PYLYFGMWKT183 SFAWHTEDMD193 LYSINYLHFG203 EPKSWYSVPP 213 EHGKRLERLA223 KGFFPGSAQS233 CEAFLRHKMT243 LISPLMLKKY253 GIPFDKVTQE 263 AGEFMITFPY273 GYHAGFNHGF283 NCAESTNFAT293 RRWIEYGKQA303 VLCSCRKDMV 313 KISMDVFVRK323 FQPERYKLWK333 AGKDNTVIDH343 TLPTPEAAEF353 |
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .N81 or .N812 or .N813 or :3N81;style chemicals stick;color identity;select .A:132 or .A:177 or .A:185 or .A:188 or .A:190 or .A:196 or .A:198 or .A:206 or .A:208 or .A:241 or .A:270 or .A:276 or .A:288; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
||||||
| Ligand Name: 2-(5-Cyano-2-Oxidanyl-Phenyl)pyridine-4-Carboxylic Acid | Ligand Info | |||||
| Structure Description | Crystal structure of human JMJD2A in complex with compound 43 | PDB:5A7N | ||||
| Method | X-ray diffraction | Resolution | 2.39 Å | Mutation | No | [13] |
| PDB Sequence |
ESETLNPSAR
13 IMTFYPTMEE23 FRNFSRYIAY33 IESQGAHRAG43 LAKVVPPKEW53 KPRASYDDID 63 DLVIPAPIQQ73 LVTGQSGLFT83 QYNIQKKAMT93 VREFRKIANS103 DKYCTPRYSE 113 FEELERKYWK123 NLTFNPPIYG133 ADVNGTLYEK143 HVDEWNIGRL153 RTILDLVEKE 163 SGITIEGVNT173 PYLYFGMWKT183 SFAWHTEDMD193 LYSINYLHFG203 EPKSWYSVPP 213 EHGKRLERLA223 KGFFPGSAQS233 CEAFLRHKMT243 LISPLMLKKY253 GIPFDKVTQE 263 AGEFMITFPY273 GYHAGFNHGF283 NCAESTNFAT293 RRWIEYGKQA303 VLCSCRKDMV 313 KISMDVFVRK323 FQPERYKLWK333 AGKDNTVIDH343 TLPTPEAAEF353 L |
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .VAO or .VAO2 or .VAO3 or :3VAO;style chemicals stick;color identity;select .A:132 or .A:177 or .A:185 or .A:188 or .A:190 or .A:196 or .A:198 or .A:206 or .A:208 or .A:241 or .A:276 or .A:280 or .A:286; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
||||||
| Ligand Name: D-tyrosine | Ligand Info | |||||
| Structure Description | JMJD2A/ KDM4A COMPLEXED WITH NI(II), NOG AND Macrocyclic PEPTIDE Inhibitor CP2_R6Kme3 (13-mer) | PDB:5LY2 | ||||
| Method | X-ray diffraction | Resolution | 2.43 Å | Mutation | No | [8] |
| PDB Sequence |
TLNPSARIMT
16 FYPTMEEFRN26 FSRYIAYIES36 QGAHRAGLAK46 VVPPKEWKPR56 ASYDDIDDLV 66 IPAPIQQLVT76 GQSGLFTQYN86 IQKKAMTVRE96 FRKIANSDKY106 CTPRYSEFEE 116 LERKYWKNLT126 FNPPIYGADV136 NGTLYEKHVD146 EWNIGRLRTI156 LDLVEKESGI 166 TIEGVNTPYL176 YFGMWKTSFA186 WHTEDMDLYS196 INYLHFGEPK206 SWYSVPPEHG 216 KRLERLAKGF226 FPGSAQSCEA236 FLRHKMTLIS246 PLMLKKYGIP256 FDKVTQEAGE 266 FMITFPYGYH276 AGFNHGFNCA286 ESTNFATRRW296 IEYGKQAVLC306 SCRKDMVKIS 316 MDVFVRKFQP326 ERYKLWKAGK336 DNTVIDHTLP346 TPEAAEFL
|
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .DTY or .DTY2 or .DTY3 or :3DTY;style chemicals stick;color identity;select .A:309; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
||||||
| Ligand Name: 3-[({(1r)-6-[methyl(Phenyl)amino]-1,2,3,4-Tetrahydronaphthalen-1-Yl}methyl)amino]pyridine-4-Carboxylic Acid | Ligand Info | |||||
| Structure Description | Crystal Structure of KDM4 with the Small Molecule Inhibitor QC6352 | PDB:5VGI | ||||
| Method | X-ray diffraction | Resolution | 2.07 Å | Mutation | No | [19] |
| PDB Sequence |
NPSARIMTFY
18 PTMEEFRNFS28 RYIAYIESQG38 AHRAGLAKVV48 PPKEWKPRAS58 YDDIDDLVIP 68 APIQQLVTGQ78 SGLFTQYNIQ88 KKAMTVREFR98 KIANSDKYCT108 PRYSEFEELE 118 RKYWKNLTFN128 PPIYGADVNG138 TLYEKHVDEW148 NIGRLRTILD158 LVEKESGITI 168 EGVNTPYLYF178 GMWKTSFAWH188 TEDMDLYSIN198 YLHFGEPKSW208 YSVPPEHGKR 218 LERLAKGFFP228 GSAQSCEAFL238 RHKMTLISPL248 MLKKYGIPFD258 KVTQEAGEFM 268 ITFPYGYHAG278 FNHGFNCAES288 TNFATRRWIE298 YGKQAVLCSC308 RKDMVKISMD 318 VFVRKFQPER328 YKLWKAGKDN338 TVIDHTLPTP348 EAAEF
|
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .9DJ or .9DJ2 or .9DJ3 or :39DJ;style chemicals stick;color identity;select .A:71 or .A:73 or .A:84 or .A:86 or .A:132 or .A:134 or .A:135 or .A:177 or .A:184 or .A:185 or .A:188 or .A:190 or .A:198 or .A:206 or .A:208 or .A:239 or .A:240 or .A:241 or .A:242 or .A:276 or .A:309 or .A:312; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
ILE71
4.141
GLN73
3.543
GLN84
3.990
ASN86
3.260
TYR132
2.449
ALA134
4.324
ASP135
4.090
TYR177
3.747
SER184
3.600
PHE185
3.422
HIS188
3.171
|
|||||
| Ligand Name: 3-({[(1r)-6-Methoxy-1,2,3,4-Tetrahydronaphthalen-1-Yl]methyl}amino)pyridine-4-Carboxylic Acid | Ligand Info | |||||
| Structure Description | Crystal Structure of Human KDM4 with Small Molecule Inhibitor QC5714 | PDB:5VMP | ||||
| Method | X-ray diffraction | Resolution | 2.48 Å | Mutation | No | [19] |
| PDB Sequence |
SETLNPSARI
14 MTFYPTMEEF24 RNFSRYIAYI34 ESQGAHRAGL44 AKVVPPKEWK54 PRASYDDIDD 64 LVIPAPIQQL74 VTGQSGLFTQ84 YNIQKKAMTV94 REFRKIANSD104 KYCTPRYSEF 114 EELERKYWKN124 LTFNPPIYGA134 DVNGTLYEKH144 VDEWNIGRLR154 TILDLVEKES 164 GITIEGVNTP174 YLYFGMWKTS184 FAWHTEDMDL194 YSINYLHFGE204 PKSWYSVPPE 214 HGKRLERLAK224 GFFPGSAQSC234 EAFLRHKMTL244 ISPLMLKKYG254 IPFDKVTQEA 264 GEFMITFPYG274 YHAGFNHGFN284 CAESTNFATR294 RWIEYGKQAV304 LCSCRVKISM 317 DVFVRKFQPE327 RYKLWKAGKD337 NTVIDHTLPT347 PEAAEFL
|
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .9FJ or .9FJ2 or .9FJ3 or :39FJ;style chemicals stick;color identity;select .A:71 or .A:73 or .A:84 or .A:86 or .A:132 or .A:134 or .A:135 or .A:177 or .A:184 or .A:185 or .A:188 or .A:190 or .A:198 or .A:206 or .A:208 or .A:240 or .A:241 or .A:276; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
||||||
| Ligand Name: 2-[[(Phenylmethyl)amino]methyl]pyridine-4-Carboxylic Acid | Ligand Info | |||||
| Structure Description | Crystal Structure of human JMJD2A complexed with KDOOA011340 | PDB:5F5I | ||||
| Method | X-ray diffraction | Resolution | 2.63 Å | Mutation | No | [20] |
| PDB Sequence |
ESETLNPSAR
13 IMTFYPTMEE23 FRNFSRYIAY33 IESQGAHRAG43 LAKVVPPKEW53 KPRASYDDID 63 DLVIPAPIQQ73 LVTGQSGLFT83 QYNIQKKAMT93 VREFRKIANS103 DKYCTPRYSE 113 FEELERKYWK123 NLTFNPPIYG133 ADVNGTLYEK143 HVDEWNIGRL153 RTILDLVEKE 163 SGITIEGVNT173 PYLYFGMWKT183 SFAWHTEDMD193 LYSINYLHFG203 EPKSWYSVPP 213 EHGKRLERLA223 KGFFPGSAQS233 CEAFLRHKMT243 LISPLMLKKY253 GIPFDKVTQE 263 AGEFMITFPY273 GYHAGFNHGF283 NCAESTNFAT293 RRWIEYGKQA303 VLCSCRKDMV 313 KISMDVFVRK323 FQPERYKLWK333 AGKDNTVIDH343 TLPTPEAAE
|
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .5V1 or .5V12 or .5V13 or :35V1;style chemicals stick;color identity;select .A:132 or .A:170 or .A:171 or .A:175 or .A:177 or .A:185 or .A:188 or .A:190 or .A:196 or .A:198 or .A:206 or .A:208 or .A:241 or .A:276 or .A:286 or .A:288 or .A:289 or .A:290; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
||||||
| Ligand Name: 8-(2-Azanyl-1,3-Thiazol-4-Yl)-3~{h}-Pyrido[3,4-D]pyrimidin-4-One | Ligand Info | |||||
| Structure Description | Crystal structure of human KDM4A in complex with compound 40 | PDB:5F32 | ||||
| Method | X-ray diffraction | Resolution | 2.05 Å | Mutation | No | [20] |
| PDB Sequence |
SARIMTFYPT
20 MEEFRNFSRY30 IAYIESQGAH40 RAGLAKVVPP50 KEWKPRASYD60 DIDDLVIPAP 70 IQQLVTGQSG80 LFTQYNIQKK90 AMTVREFRKI100 ANSDKYCTPR110 YSEFEELERK 120 YWKNLTFNPP130 IYGADVNGTL140 YEKHVDEWNI150 GRLRTILDLV160 EKESGITIEG 170 VNTPYLYFGM180 WKTSFAWHTE190 DMDLYSINYL200 HFGEPKSWYS210 VPPEHGKRLE 220 RLAKGFFPGS230 AQSCEAFLRH240 KMTLISPLML250 KKYGIPFDKV260 TQEAGEFMIT 270 FPYGYHAGFN280 HGFNCAESTN290 FATRRWIEYG300 KQAVLCSCRM312 VKISMDVFVR 322 KFQPERYKLW332 KAGKDNTVID342 HTLPTPEAAE352 FL
|
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .5V7 or .5V72 or .5V73 or :35V7;style chemicals stick;color identity;select .A:132 or .A:177 or .A:185 or .A:188 or .A:189 or .A:190 or .A:191 or .A:198 or .A:206 or .A:208 or .A:241 or .A:276 or .A:280; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
||||||
| Ligand Name: 8-[4-[2-[(4-Fluorophenyl)methyl-Methyl-Amino]ethyl]pyrazol-1-Yl]-3~{h}-Pyrido[3,4-D]pyrimidin-4-One | Ligand Info | |||||
| Structure Description | Crystal structure of human KDM4A in complex with compound 52d | PDB:5F3C | ||||
| Method | X-ray diffraction | Resolution | 2.06 Å | Mutation | No | [20] |
| PDB Sequence |
PSARIMTFYP
19 TMEEFRNFSR29 YIAYIESQGA39 HRAGLAKVVP49 PKEWKPRASY59 DDIDDLVIPA 69 PIQQLVTGQS79 GLFTQYNIQK89 KAMTVREFRK99 IANSDKYCTP109 RYSEFEELER 119 KYWKNLTFNP129 PIYGADVNGT139 LYEKHVDEWN149 IGRLRTILDL159 VEKESGITIE 169 GVNTPYLYFG179 MWKTSFAWHT189 EDMDLYSINY199 LHFGEPKSWY209 SVPPEHGKRL 219 ERLAKGFFPG229 SAQSCEAFLR239 HKMTLISPLM249 LKKYGIPFDK259 VTQEAGEFMI 269 TFPYGYHAGF279 NHGFNCAEST289 NFATRRWIEY299 GKQAVLCSCR309 MVKISMDVFV 321 RKFQPERYKL331 WKAGKDNTVI341 DHTLPTPEAA351 EFL
|
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .5U8 or .5U82 or .5U83 or :35U8;style chemicals stick;color identity;select .A:73 or .A:84 or .A:86 or .A:132 or .A:134 or .A:135 or .A:177 or .A:184 or .A:185 or .A:188 or .A:190 or .A:198 or .A:206 or .A:208 or .A:241 or .A:276 or .A:280; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
||||||
| Ligand Name: 2-(2-Azanyl-1,3-Thiazol-4-Yl)pyridine-4-Carboxylic Acid | Ligand Info | |||||
| Structure Description | Crystal structure of human KDM4A in complex with compound 15 | PDB:5F2S | ||||
| Method | X-ray diffraction | Resolution | 2.08 Å | Mutation | No | [20] |
| PDB Sequence |
NPSARIMTFY
18 PTMEEFRNFS28 RYIAYIESQG38 AHRAGLAKVV48 PPKEWKPRAS58 YDDIDDLVIP 68 APIQQLVTGQ78 SGLFTQYNIQ88 KKAMTVREFR98 KIANSDKYCT108 PRYSEFEELE 118 RKYWKNLTFN128 PPIYGADVNG138 TLYEKHVDEW148 NIGRLRTILD158 LVEKESGITI 168 EGVNTPYLYF178 GMWKTSFAWH188 TEDMDLYSIN198 YLHFGEPKSW208 YSVPPEHGKR 218 LERLAKGFFP228 GSAQSCEAFL238 RHKMTLISPL248 MLKKYGIPFD258 KVTQEAGEFM 268 ITFPYGYHAG278 FNHGFNCAES288 TNFATRRWIE298 YGKQAVLCSC308 VKISMDVFVR 322 KFQPERYKLW332 KAGKDNTVID342 HTLPTPEAAE352 FL
|
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .5TZ or .5TZ2 or .5TZ3 or :35TZ;style chemicals stick;color identity;select .A:132 or .A:177 or .A:185 or .A:188 or .A:189 or .A:190 or .A:191 or .A:198 or .A:206 or .A:208 or .A:241 or .A:276 or .A:290; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
||||||
| Ligand Name: 8-[4-[2-[4-[4-[2-(dimethylamino)ethyl]phenyl]piperidin-1-yl]ethyl]pyrazol-1-yl]-3~{H}-pyrido[3,4-d]pyrimidin-4-one | Ligand Info | |||||
| Structure Description | Crystal structure of human KDM4A in complex with compound 17f | PDB:6H4R | ||||
| Method | X-ray diffraction | Resolution | 2.14 Å | Mutation | No | [21] |
| PDB Sequence |
ETLNPSARIM
15 TFYPTMEEFR25 NFSRYIAYIE35 SQGAHRAGLA45 KVVPPKEWKP55 RASYDDIDDL 65 VIPAPIQQLV75 TGQSGLFTQY85 NIQKKAMTVR95 EFRKIANSDK105 YCTPRYSEFE 115 ELERKYWKNL125 TFNPPIYGAD135 VNGTLYEKHV145 DEWNIGRLRT155 ILDLVEGVNT 173 PYLYFGMWKT183 SFAWHTEDMD193 LYSINYLHFG203 EPKSWYSVPP213 EHGKRLERLA 223 KGFFPGSAQS233 CEAFLRHKMT243 LISPLMLKKY253 GIPFDKVTQE263 AGEFMITFPY 273 GYHAGFNHGF283 NCAESTNFAT293 RRWIEYGKQA303 VLCSCRKDMV313 KISMDVFVRK 323 FQPERYKLWK333 AGKDNTVIDH343 TLPTPEAAEF353 L
|
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .FQB or .FQB2 or .FQB3 or :3FQB;style chemicals stick;color identity;select .A:132 or .A:135 or .A:170 or .A:175 or .A:177 or .A:185 or .A:188 or .A:190 or .A:191 or .A:198 or .A:206 or .A:208 or .A:241 or .A:276 or .A:280 or .A:313; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
||||||
| Ligand Name: 8-[4-(1-cyclopentylpiperidin-4-yl)pyrazol-1-yl]-3H-pyrido[3,4-d]pyrimidin-4-one | Ligand Info | |||||
| Structure Description | Crystal structure of human KDM4A in complex with compound 34g | PDB:6H4V | ||||
| Method | X-ray diffraction | Resolution | 2.15 Å | Mutation | No | [21] |
| PDB Sequence |
ETLNPSARIM
15 TFYPTMEEFR25 NFSRYIAYIE35 SQGAHRAGLA45 KVVPPKEWKP55 RASYDDIDDL 65 VIPAPIQQLV75 TGQSGLFTQY85 NIQKKAMTVR95 EFRKIANSDK105 YCTPRYSEFE 115 ELERKYWKNL125 TFNPPIYGAD135 VNGTLYEKHV145 DEWNIGRLRT155 ILDLVEGVNT 173 PYLYFGMWKT183 SFAWHTEDMD193 LYSINYLHFG203 EPKSWYSVPP213 EHGKRLERLA 223 KGFFPGSAQS233 CEAFLRHKMT243 LISPLMLKKY253 GIPFDKVTQE263 AGEFMITFPY 273 GYHAGFNHGF283 NCAESTNFAT293 RRWIEYGKQA303 VLCSCRKDMV313 KISMDVFVRK 323 FQPERYKLWK333 AGKDNTVIDH343 TLPTPEAAEF353 L
|
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .FQN or .FQN2 or .FQN3 or :3FQN;style chemicals stick;color identity;select .A:132 or .A:135 or .A:175 or .A:177 or .A:185 or .A:188 or .A:190 or .A:191 or .A:198 or .A:206 or .A:208 or .A:241 or .A:276; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
||||||
| Ligand Name: 8-[4-[2-[4-(4-Chlorophenyl)piperidin-1-Yl]ethyl]pyrazol-1-Yl]-3~{h}-Pyrido[3,4-D]pyrimidin-4-One | Ligand Info | |||||
| Structure Description | Crystal structure of human KDM4A in complex with compound 54a | PDB:5F3E | ||||
| Method | X-ray diffraction | Resolution | 2.16 Å | Mutation | No | [20] |
| PDB Sequence |
ETLNPSARIM
15 TFYPTMEEFR25 NFSRYIAYIE35 SQGAHRAGLA45 KVVPPKEWKP55 RASYDDIDDL 65 VIPAPIQQLV75 TGQSGLFTQY85 NIQKKAMTVR95 EFRKIANSDK105 YCTPRYSEFE 115 ELERKYWKNL125 TFNPPIYGAD135 VNGTLYEKHV145 DEWNIGRLRT155 ILDLVVNTPY 175 LYFGMWKTSF185 AWHTEDMDLY195 SINYLHFGEP205 KSWYSVPPEH215 GKRLERLAKG 225 FFPGSAQSCE235 AFLRHKMTLI245 SPLMLKKYGI255 PFDKVTQEAG265 EFMITFPYGY 275 HAGFNHGFNC285 AESTNFATRR295 WIEYGKQAVL305 CSCRMVKISM317 DVFVRKFQPE 327 RYKLWKAGKD337 NTVIDHTLPT347 PEAAEFL
|
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .5UO or .5UO2 or .5UO3 or :35UO;style chemicals stick;color identity;select .A:132 or .A:135 or .A:175 or .A:177 or .A:185 or .A:188 or .A:190 or .A:191 or .A:198 or .A:206 or .A:208 or .A:241 or .A:276 or .A:280; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
||||||
| Ligand Name: 8-[4-[2-[4-(3-chlorophenyl)piperidin-1-yl]ethyl]pyrazol-1-yl]-3~{H}-pyrido[3,4-d]pyrimidin-4-one | Ligand Info | |||||
| Structure Description | Crystal structure of human KDM4A in complex with compound 16a | PDB:6H4P | ||||
| Method | X-ray diffraction | Resolution | 2.19 Å | Mutation | No | [21] |
| PDB Sequence |
ETLNPSARIM
15 TFYPTMEEFR25 NFSRYIAYIE35 SQGAHRAGLA45 KVVPPKEWKP55 RASYDDIDDL 65 VIPAPIQQLV75 TGQSGLFTQY85 NIQKKAMTVR95 EFRKIANSDK105 YCTPRYSEFE 115 ELERKYWKNL125 TFNPPIYGAD135 VNGTLYEKHV145 DEWNIGRLRT155 ILDLVEKESG 165 ITIEGVNTPY175 LYFGMWKTSF185 AWHTEDMDLY195 SINYLHFGEP205 KSWYSVPPEH 215 GKRLERLAKG225 FFPGSAQSCE235 AFLRHKMTLI245 SPLMLKKYGI255 PFDKVTQEAG 265 EFMITFPYGY275 HAGFNHGFNC285 AESTNFATRR295 WIEYGKQAVL305 CSCRKDMVKI 315 SMDVFVRKFQ325 PERYKLWKAG335 KDNTVIDHTL345 PTPEAAEFL
|
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .FQ5 or .FQ52 or .FQ53 or :3FQ5;style chemicals stick;color identity;select .A:132 or .A:135 or .A:177 or .A:185 or .A:188 or .A:190 or .A:198 or .A:206 or .A:208 or .A:241 or .A:276 or .A:280; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
||||||
| Ligand Name: 8-[4-(1-methylpiperidin-4-yl)pyrazol-1-yl]-3~{H}-pyrido[3,4-d]pyrimidin-4-one | Ligand Info | |||||
| Structure Description | Crystal structure of human KDM4A in complex with compound 34b | PDB:6H4U | ||||
| Method | X-ray diffraction | Resolution | 2.21 Å | Mutation | No | [21] |
| PDB Sequence |
LNPSARIMTF
17 YPTMEEFRNF27 SRYIAYIESQ37 GAHRAGLAKV47 VPPKEWKPRA57 SYDDIDDLVI 67 PAPIQQLVTG77 QSGLFTQYNI87 QKKAMTVREF97 RKIANSDKYC107 TPRYSEFEEL 117 ERKYWKNLTF127 NPPIYGADVN137 GTLYEKHVDE147 WNIGRLRTIL157 DLVEKESEGV 171 NTPYLYFGMW181 KTSFAWHTED191 MDLYSINYLH201 FGEPKSWYSV211 PPEHGKRLER 221 LAKGFFPGSA231 QSCEAFLRHK241 MTLISPLMLK251 KYGIPFDKVT261 QEAGEFMITF 271 PYGYHAGFNH281 GFNCAESTNF291 ATRRWIEYGK301 QAVLCSCRDM312 VKISMDVFVR 322 KFQPERYKLW332 KAGKDNTVID342 HTLPTPEAAE352 F
|
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .FO2 or .FO22 or .FO23 or :3FO2;style chemicals stick;color identity;select .A:132 or .A:135 or .A:175 or .A:177 or .A:185 or .A:188 or .A:190 or .A:191 or .A:198 or .A:206 or .A:208 or .A:241 or .A:276; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
||||||
| Click to View More Binding Site Information of This Target and Ligand Pair | ||||||
| Ligand Name: Pyrido[3,4-d]pyrimidin-4(3H)-one | Ligand Info | |||||
| Structure Description | Crystal structure of human KDM4A in complex with compound 58 | PDB:5F37 | ||||
| Method | X-ray diffraction | Resolution | 2.22 Å | Mutation | No | [20] |
| PDB Sequence |
SETLNPSARI
14 MTFYPTMEEF24 RNFSRYIAYI34 ESQGAHRAGL44 AKVVPPKEWK54 PRASYDDIDD 64 LVIPAPIQQL74 VTGQSGLFTQ84 YNIQKKAMTV94 REFRKIANSD104 KYCTPRYSEF 114 EELERKYWKN124 LTFNPPIYGA134 DVNGTLYEKH144 VDEWNIGRLR154 TILDLVEKES 164 GITIEGVNTP174 YLYFGMWKTS184 FAWHTEDMDL194 YSINYLHFGE204 PKSWYSVPPE 214 HGKRLERLAK224 GFFPGSAQSC234 EAFLRHKMTL244 ISPLMLKKYG254 IPFDKVTQEA 264 GEFMITFPYG274 YHAGFNHGFN284 CAESTNFATR294 RWIEYGKQAV304 LCSCRKDMVK 314 ISMDVFVRKF324 QPERYKLWKA334 GKDNTVIDHT344 LPTPEAAEFL354 |
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .N5J or .N5J2 or .N5J3 or :3N5J;style chemicals stick;color identity;select .A:132 or .A:177 or .A:185 or .A:188 or .A:190 or .A:198 or .A:206 or .A:208 or .A:241 or .A:276 or .A:286; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
||||||
| Ligand Name: 2-(2h-1,2,3-Triazol-4-Yl)pyridine-4-Carboxylic Acid | Ligand Info | |||||
| Structure Description | Crystal structure of human JMJD2A in complex with compound 14a | PDB:4URA | ||||
| Method | X-ray diffraction | Resolution | 2.23 Å | Mutation | No | [22] |
| PDB Sequence |
ESETLNPSAR
13 IMTFYPTMEE23 FRNFSRYIAY33 IESQGAHRAG43 LAKVVPPKEW53 KPRASYDDID 63 DLVIPAPIQQ73 LVTGQSGLFT83 QYNIQKKAMT93 VREFRKIANS103 DKYCTPRYSE 113 FEELERKYWK123 NLTFNPPIYG133 ADVNGTLYEK143 HVDEWNIGRL153 RTILDLVEKE 163 SGITIEGVNT173 PYLYFGMWKT183 SFAWHTEDMD193 LYSINYLHFG203 EPKSWYSVPP 213 EHGKRLERLA223 KGFFPGSAQS233 CEAFLRHKMT243 LISPLMLKKY253 GIPFDKVTQE 263 AGEFMITFPY273 GYHAGFNHGF283 NCAESTNFAT293 RRWIEYGKQA303 VLCSCRKDMV 313 KISMDVFVRK323 FQPERYKLWK333 AGKDNTVIDH343 TLPTPEAAE
|
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .LEL or .LEL2 or .LEL3 or :3LEL;style chemicals stick;color identity;select .A:132 or .A:177 or .A:184 or .A:185 or .A:188 or .A:190 or .A:198 or .A:206 or .A:208 or .A:241 or .A:276 or .A:286; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
||||||
| Ligand Name: 8-[4-[2-[4-[3,5-Bis(Chloranyl)phenyl]piperidin-1-Yl]ethyl]pyrazol-1-Yl]-3~{h}-Pyrido[3,4-D]pyrimidin-4-One | Ligand Info | |||||
| Structure Description | Crystal structure of human KDM4A in complex with compound 54j | PDB:5F3I | ||||
| Method | X-ray diffraction | Resolution | 2.24 Å | Mutation | No | [20] |
| PDB Sequence |
ETLNPSARIM
15 TFYPTMEEFR25 NFSRYIAYIE35 SQGAHRAGLA45 KVVPPKEWKP55 RASYDDIDDL 65 VIPAPIQQLV75 TGQSGLFTQY85 NIQKKAMTVR95 EFRKIANSDK105 YCTPRYSEFE 115 ELERKYWKNL125 TFNPPIYGAD135 VNGTLYEKHV145 DEWNIGRLRT155 ILDLVEKGVN 172 TPYLYFGMWK182 TSFAWHTEDM192 DLYSINYLHF202 GEPKSWYSVP212 PEHGKRLERL 222 AKGFFPGSAQ232 SCEAFLRHKM242 TLISPLMLKK252 YGIPFDKVTQ262 EAGEFMITFP 272 YGYHAGFNHG282 FNCAESTNFA292 TRRWIEYGKQ302 AVLCSCRKMV313 KISMDVFVRK 323 FQPERYKLWK333 AGKDNTVIDH343 TLPTPEAAEF353 LK
|
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .5UJ or .5UJ2 or .5UJ3 or :35UJ;style chemicals stick;color identity;select .A:132 or .A:135 or .A:170 or .A:175 or .A:177 or .A:185 or .A:188 or .A:190 or .A:191 or .A:198 or .A:206 or .A:208 or .A:241 or .A:276 or .A:280; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
||||||
| Ligand Name: 8-[4-[2-[4-[3-(trifluoromethyl)phenyl]piperidin-1-yl]ethyl]pyrazol-1-yl]-3~{H}-pyrido[3,4-d]pyrimidin-4-one | Ligand Info | |||||
| Structure Description | Crystal structure of human KDM4A in complex with compound 18a | PDB:6H4O | ||||
| Method | X-ray diffraction | Resolution | 2.25 Å | Mutation | No | [21] |
| PDB Sequence |
LNPSARIMTF
17 YPTMEEFRNF27 SRYIAYIESQ37 GAHRAGLAKV47 VPPKEWKPRA57 SYDDIDDLVI 67 PAPIQQLVTG77 QSGLFTQYNI87 QKKAMTVREF97 RKIANSDKYC107 TPRYSEFEEL 117 ERKYWKNLTF127 NPPIYGADVN137 GTLYEKHVDE147 WNIGRLRTIL157 DLVEGVNTPY 175 LYFGMWKTSF185 AWHTEDMDLY195 SINYLHFGEP205 KSWYSVPPEH215 GKRLERLAKG 225 FFPGSAQSCE235 AFLRHKMTLI245 SPLMLKKYGI255 PFDKVTQEAG265 EFMITFPYGY 275 HAGFNHGFNC285 AESTNFATRR295 WIEYGKQAVL305 CSCRKMVKIS316 MDVFVRKFQP 326 ERYKLWKAGK336 DNTVIDHTLP346 TPEAAEFL
|
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .FQH or .FQH2 or .FQH3 or :3FQH;style chemicals stick;color identity;select .A:132 or .A:135 or .A:177 or .A:185 or .A:188 or .A:190 or .A:191 or .A:198 or .A:206 or .A:208 or .A:241 or .A:276 or .A:313; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
||||||
| Ligand Name: 8-[4-[2-[4-(4-pyridin-3-ylphenyl)piperidin-1-yl]ethyl]pyrazol-1-yl]-3H-pyrido[3,4-d]pyrimidin-4-one | Ligand Info | |||||
| Structure Description | Crystal structure of human KDM4A in complex with compound 17b | PDB:6H4X | ||||
| Method | X-ray diffraction | Resolution | 2.34 Å | Mutation | No | [21] |
| PDB Sequence |
ETLNPSARIM
15 TFYPTMEEFR25 NFSRYIAYIE35 SQGAHRAGLA45 KVVPPKEWKP55 RASYDDIDDL 65 VIPAPIQQLV75 TGQSGLFTQY85 NIQKKAMTVR95 EFRKIANSDK105 YCTPRYSEFE 115 ELERKYWKNL125 TFNPPIYGAD135 VNGTLYEKHV145 DEWNIGRLRT155 ILDLVEEGVN 172 TPYLYFGMWK182 TSFAWHTEDM192 DLYSINYLHF202 GEPKSWYSVP212 PEHGKRLERL 222 AKGFFPGSAQ232 SCEAFLRHKM242 TLISPLMLKK252 YGIPFDKVTQ262 EAGEFMITFP 272 YGYHAGFNHG282 FNCAESTNFA292 TRRWIEYGKQ302 AVLCSCRMVK314 ISMDVFVRKF 324 QPERYKLWKA334 GKDNTVIDHT344 LPTPEAAEFL354
|
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .FNQ or .FNQ2 or .FNQ3 or :3FNQ;style chemicals stick;color identity;select .A:132 or .A:135 or .A:177 or .A:185 or .A:188 or .A:190 or .A:191 or .A:198 or .A:206 or .A:208 or .A:241 or .A:276 or .A:280 or .A:288; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
||||||
| Ligand Name: 8-[4-(2-spiro[1,2-dihydroindene-3,4'-piperidine]-1'-ylethyl)pyrazol-1-yl]-3~{H}-pyrido[3,4-d]pyrimidin-4-one | Ligand Info | |||||
| Structure Description | Crystal structure of human KDM4A in complex with compound 19a | PDB:6H4T | ||||
| Method | X-ray diffraction | Resolution | 2.38 Å | Mutation | No | [21] |
| PDB Sequence |
TLNPSARIMT
16 FYPTMEEFRN26 FSRYIAYIES36 QGAHRAGLAK46 VVPPKEWKPR56 ASYDDIDDLV 66 IPAPIQQLVT76 GQSGLFTQYN86 IQKKAMTVRE96 FRKIANSDKY106 CTPRYSEFEE 116 LERKYWKNLT126 FNPPIYGADV136 NGTLYEKHVD146 EWNIGRLRTI156 LDLVEGVNTP 174 YLYFGMWKTS184 FAWHTEDMDL194 YSINYLHFGE204 PKSWYSVPPE214 HGKRLERLAK 224 GFFPGSAQSC234 EAFLRHKMTL244 ISPLMLKKYG254 IPFDKVTQEA264 GEFMITFPYG 274 YHAGFNHGFN284 CAESTNFATR294 RWIEYGKQAV304 LCSCRKDMVK314 ISMDVFVRKF 324 QPERYKLWKA334 GKDNTVIDHT344 LPTPEAAEFL354
|
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .FOW or .FOW2 or .FOW3 or :3FOW;style chemicals stick;color identity;select .A:132 or .A:135 or .A:170 or .A:175 or .A:177 or .A:185 or .A:188 or .A:190 or .A:191 or .A:198 or .A:206 or .A:208 or .A:241 or .A:276 or .A:280 or .A:311 or .A:313; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
||||||
| Ligand Name: 8-[4-[2-[4-[4-(2-morpholin-4-ylethyl)phenyl]piperidin-1-yl]ethyl]pyrazol-1-yl]-3H-pyrido[3,4-d]pyrimidin-4-one | Ligand Info | |||||
| Structure Description | Crystal structure of human KDM4A in complex with compound 17e | PDB:6H4Y | ||||
| Method | X-ray diffraction | Resolution | 2.38 Å | Mutation | No | [21] |
| PDB Sequence |
LNPSARIMTF
17 YPTMEEFRNF27 SRYIAYIESQ37 GAHRAGLAKV47 VPPKEWKPRA57 SYDDIDDLVI 67 PAPIQQLVTG77 QSGLFTQYNI87 QKKAMTVREF97 RKIANSDKYC107 TPRYSEFEEL 117 ERKYWKNLTF127 NPPIYGADVN137 GTLYEKHVDE147 WNIGRLRTIL157 DLVEGVNTPY 175 LYFGMWKTSF185 AWHTEDMDLY195 SINYLHFGEP205 KSWYSVPPEH215 GKRLERLAKG 225 FFPGSAQSCE235 AFLRHKMTLI245 SPLMLKKYGI255 PFDKVTQEAG265 EFMITFPYGY 275 HAGFNHGFNC285 AESTNFATRR295 WIEYGKQAVL305 CSCRKMVKIS316 MDVFVRKFQP 326 ERYKLWKAGK336 DNTVIDHTLP346 TPEAAEF
|
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .FO8 or .FO82 or .FO83 or :3FO8;style chemicals stick;color identity;select .A:132 or .A:135 or .A:177 or .A:185 or .A:188 or .A:190 or .A:191 or .A:198 or .A:206 or .A:208 or .A:241 or .A:276 or .A:280; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
||||||
| Ligand Name: 2-{[(2-{[(E)-2-(Dimethylamino)ethenyl](Ethyl)amino}-2-Oxoethyl)amino]methyl}pyridine-4-Carboxylic Acid | Ligand Info | |||||
| Structure Description | Crystal structure of human JMJD2A in complex with compound KDOAM20A | PDB:5FPV | ||||
| Method | X-ray diffraction | Resolution | 2.44 Å | Mutation | No | [23] |
| PDB Sequence |
SARIMTFYPT
21 MEEFRNFSRY31 IAYIESQGAH41 RAGLAKVVPP51 KEWKPRASYD61 DIDDLVIPAP 71 IQQLVTGQSG81 LFTQYNIQKK91 AMTVREFRKI101 ANSDKYCTPR111 YSEFEELERK 121 YWKNLTFNPP131 IYGADVNGTL141 YEKHVDEWNI151 GRLRTILDLV161 EGVNTPYLYF 179 GMWKTSFAWH189 TEDMDLYSIN199 YLHFGEPKSW209 YSVPPEHGKR219 LERLAKGFFP 229 GSAQSCEAFL239 RHKMTLISPL249 MLKKYGIPFD259 KVTQEAGEFM269 ITFPYGYHAG 279 FNHGFNCAES289 TNFATRRWIE299 YGKQAVLCSC309 RKDMVKISMD319 VFVRKFQPER 329 YKLWKAGKDN339 TVIDHTLPTP349 EAAEFLK
|
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .MMK or .MMK2 or .MMK3 or :3MMK;style chemicals stick;color identity;select .A:133 or .A:136 or .A:176 or .A:178 or .A:186 or .A:189 or .A:191 or .A:192 or .A:197 or .A:199 or .A:207 or .A:209 or .A:242 or .A:277 or .A:289 or .A:290 or .A:291; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
||||||
| Ligand Name: 8-[4-[2-[4-[3-[2-(dimethylamino)ethyl]phenyl]piperidin-1-yl]ethyl]pyrazol-1-yl]-3H-pyrido[3,4-d]pyrimidin-4-one | Ligand Info | |||||
| Structure Description | Crystal structure of human KDM4A in complex with compound 16m | PDB:6H4S | ||||
| Method | X-ray diffraction | Resolution | 2.45 Å | Mutation | No | [21] |
| PDB Sequence |
LNPSARIMTF
17 YPTMEEFRNF27 SRYIAYIESQ37 GAHRAGLAKV47 VPPKEWKPRA57 SYDDIDDLVI 67 PAPIQQLVTG77 QSGLFTQYNI87 QKKAMTVREF97 RKIANSDKYC107 TPRYSEFEEL 117 ERKYWKNLTF127 NPPIYGADVN137 GTLYEKHVDE147 WNIGRLRTIL157 DLVGVNTPYL 176 YFGMWKTSFA186 WHTEDMDLYS196 INYLHFGEPK206 SWYSVPPEHG216 KRLERLAKGF 226 FPGSAQSCEA236 FLRHKMTLIS246 PLMLKKYGIP256 FDKVTQEAGE266 FMITFPYGYH 276 AGFNHGFNCA286 ESTNFATRRW296 IEYGKQAVLC306 SCMVKISMDV319 FVRKFQPERY 329 KLWKAGKDNT339 VIDHTLPTPE349 AAEFL
|
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .FQE or .FQE2 or .FQE3 or :3FQE;style chemicals stick;color identity;select .A:132 or .A:135 or .A:170 or .A:175 or .A:177 or .A:185 or .A:188 or .A:190 or .A:191 or .A:198 or .A:206 or .A:208 or .A:241 or .A:276 or .A:313; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
||||||
| Ligand Name: 8-[4-[2-[4-[(4-Chlorophenyl)methyl]piperidin-1-Yl]ethyl]pyrazol-1-Yl]-3~{h}-Pyrido[3,4-D]pyrimidin-4-One | Ligand Info | |||||
| Structure Description | Crystal structure of human KDM4A in complex with compound 53a | PDB:5F3G | ||||
| Method | X-ray diffraction | Resolution | 2.50 Å | Mutation | No | [20] |
| PDB Sequence |
LNPSARIMTF
17 YPTMEEFRNF27 SRYIAYIESQ37 GAHRAGLAKV47 VPPKEWKPRA57 SYDDIDDLVI 67 PAPIQQLVTG77 QSGLFTQYNI87 QKKAMTVREF97 RKIANSDKYC107 TPRYSEFEEL 117 ERKYWKNLTF127 NPPIYGADVN137 GTLYEKHVDE147 WNIGRLRTIL157 DLVEKESGVN 172 TPYLYFGMWK182 TSFAWHTEDM192 DLYSINYLHF202 GEPKSWYSVP212 PEHGKRLERL 222 AKGFFPGSAQ232 SCEAFLRHKM242 TLISPLMLKK252 YGIPFDKVTQ262 EAGEFMITFP 272 YGYHAGFNHG282 FNCAESTNFA292 TRRWIEYGKQ302 AVLCSCMVKI315 SMDVFVRKFQ 325 PERYKLWKAG335 KDNTVIDHTL345 PTPEAAEFL
|
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .5UL or .5UL2 or .5UL3 or :35UL;style chemicals stick;color identity;select .A:132 or .A:135 or .A:170 or .A:175 or .A:177 or .A:185 or .A:188 or .A:190 or .A:191 or .A:198 or .A:206 or .A:208 or .A:241 or .A:276 or .A:312 or .A:313; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
||||||
| Ligand Name: 2-(2-Azanyl-1,3-Thiazol-4-Yl)pyridine-4-Carboxamide | Ligand Info | |||||
| Structure Description | Crystal structure of human KDM4A in complex with compound 16 | PDB:5F2W | ||||
| Method | X-ray diffraction | Resolution | 2.60 Å | Mutation | No | [20] |
| PDB Sequence |
NPSARIMTFY
18 PTMEEFRNFS28 RYIAYIESQG38 AHRAGLAKVV48 PPKEWKPRAS58 YDDIDDLVIP 68 APIQQLVTGQ78 SGLFTQYNIQ88 KKAMTVREFR98 KIANSDKYCT108 PRYSEFEELE 118 RKYWKNLTFN128 PPIYGADVNG138 TLYEKHVDEW148 NIGRLRTILD158 LVEKESGITI 168 EGVNTPYLYF178 GMWKTSFAWH188 TEDMDLYSIN198 YLHFGEPKSW208 YSVPPEHGKR 218 LERLAKGFFP228 GSAQSCEAFL238 RHKMTLISPL248 MLKKYGIPFD258 KVTQEAGEFM 268 ITFPYGYHAG278 FNHGFNCAES288 TNFATRRWIE298 YGKQAVLCSV313 KISMDVFVRK 323 FQPERYKLWK333 AGKDNTVIDH343 TLPTPEAAEF353 L
|
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .5UP or .5UP2 or .5UP3 or :35UP;style chemicals stick;color identity;select .A:132 or .A:177 or .A:185 or .A:188 or .A:189 or .A:190 or .A:191 or .A:198 or .A:206 or .A:208 or .A:241 or .A:276 or .A:286; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
||||||
| Ligand Name: 8-(1,3-Thiazol-4-Yl)-3~{h}-Pyrido[3,4-D]pyrimidin-4-One | Ligand Info | |||||
| Structure Description | Crystal structure of human KDM4A in complex with compound 37 | PDB:5F39 | ||||
| Method | X-ray diffraction | Resolution | 2.65 Å | Mutation | No | [20] |
| PDB Sequence |
NPSARIMTFY
18 PTMEEFRNFS28 RYIAYIESQG38 AHRAGLAKVV48 PPKEWKPRAS58 YDDIDDLVIP 68 APIQQLVTGQ78 SGLFTQYNIQ88 KKAMTVREFR98 KIANSDKYCT108 PRYSEFEELE 118 RKYWKNLTFN128 PPIYGADVNG138 TLYEKHVDEW148 NIGRLRTILD158 LVEKESGITI 168 EGVNTPYLYF178 GMWKTSFAWH188 TEDMDLYSIN198 YLHFGEPKSW208 YSVPPEHGKR 218 LERLAKGFFP228 GSAQSCEAFL238 RHKMTLISPL248 MLKKYGIPFD258 KVTQEAGEFM 268 ITFPYGYHAG278 FNHGFNCAES288 TNFATRRWIE298 YGKQAVLCSC308 MVKISMDVFV 321 RKFQPERYKL331 WKAGKDNTVI341 DHTLPTPEAA351 EFL
|
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .5UB or .5UB2 or .5UB3 or :35UB;style chemicals stick;color identity;select .A:132 or .A:177 or .A:185 or .A:188 or .A:190 or .A:198 or .A:206 or .A:208 or .A:241 or .A:276 or .A:280; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
||||||
| Ligand Name: 8-[4-[2-[4-(3-chlorophenyl)-4-methylpiperidin-1-yl]ethyl]pyrazol-1-yl]-3H-pyrido[3,4-d]pyrimidin-4-one | Ligand Info | |||||
| Structure Description | Crystal structure of human KDM4A in complex with compound 19d | PDB:6H4W | ||||
| Method | X-ray diffraction | Resolution | 2.81 Å | Mutation | No | [21] |
| PDB Sequence |
NPSARIMTFY
18 PTMEEFRNFS28 RYIAYIESQG38 AHRAGLAKVV48 PPKEWKPRAS58 YDDIDDLVIP 68 APIQQLVTGQ78 SGLFTQYNIQ88 KKAMTVREFR98 KIANSDKYCT108 PRYSEFEELE 118 RKYWKNLTFN128 PPIYGADVNG138 TLYEKHVDEW148 NIGRLRTILD158 LVEKGVNTPY 175 LYFGMWKTSF185 AWHTEDMDLY195 SINYLHFGEP205 KSWYSVPPEH215 GKRLERLAKG 225 FFPGSAQSCE235 AFLRHKMTLI245 SPLMLKKYGI255 PFDKVTQEAG265 EFMITFPYGY 275 HAGFNHGFNC285 AESTNFATRR295 WIEYGKQAVL305 CSCRVKISMD318 VFVRKFQPER 328 YKLWKAGKDN338 TVIDHTLPTP348 EAAEFLK
|
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .FQQ or .FQQ2 or .FQQ3 or :3FQQ;style chemicals stick;color identity;select .A:132 or .A:135 or .A:175 or .A:177 or .A:185 or .A:188 or .A:190 or .A:191 or .A:198 or .A:206 or .A:208 or .A:241 or .A:276 or .A:313; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
||||||
| Ligand Name: 2-{2-[(Pyridin-3-Ylmethyl)amino]pyrimidin-4-Yl}pyridine-4-Carboxylic Acid | Ligand Info | |||||
| Structure Description | inhibitors of JumonjiC domain-containing histone demethylases | PDB:5ANQ | ||||
| Method | X-ray diffraction | Resolution | 2.00 Å | Mutation | No | [24] |
| PDB Sequence |
SESETLNPSA
12 RIMTFYPTME22 EFRNFSRYIA32 YIESQGAHRA42 GLAKVVPPKE52 WKPRASYDDI 62 DDLVIPAPIQ72 QLVTGQSGLF82 TQYNIQKKAM92 TVREFRKIAN102 SDKYCTPRYS 112 EFEELERKYW122 KNLTFNPPIY132 GADVNGTLYE142 KHVDEWNIGR152 LRTILDLVEK 162 ESGITIEGVN172 TPYLYFGMWK182 TSFAWHTEDM192 DLYSINYLHF202 GEPKSWYSVP 212 PEHGKRLERL222 AKGFFPGSAQ232 SCEAFLRHKM242 TLISPLMLKK252 YGIPFDKVTQ 262 EAGEFMITFP272 YGYHAGFNHG282 FNCAESTNFA292 TRRWIEYGKQ302 AVLCSCRKDM 312 VKISMDVFVR322 KFQPERYKLW332 KAGKDNTVID342 HTLPTPEAAE352 |
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .5YQ or .5YQ2 or .5YQ3 or :35YQ;style chemicals stick;color identity;select .A:132 or .A:169 or .A:170 or .A:171 or .A:175 or .A:177 or .A:185 or .A:188 or .A:190 or .A:191 or .A:198 or .A:206 or .A:208 or .A:241 or .A:276 or .A:290 or .A:313; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
||||||
| Ligand Name: 3-[(4-Fluorobenzyl)amino]pyridine-4-carboxylic acid | Ligand Info | |||||
| Structure Description | Crystal Structure of KDM4A with Compound 14 | PDB:6CG1 | ||||
| Method | X-ray diffraction | Resolution | 2.16 Å | Mutation | No | [25] |
| PDB Sequence |
SETLNPSARI
14 MTFYPTMEEF24 RNFSRYIAYI34 ESQGAHRAGL44 AKVVPPKEWK54 PRASYDDIDD 64 LVIPAPIQQL74 VTGQSGLFTQ84 YNIQKKAMTV94 REFRKIANSD104 KYCTPRYSEF 114 EELERKYWKN124 LTFNPPIYGA134 DVNGTLYEKH144 VDEWNIGRLR154 TILDLVEKES 164 GITIEGVNTP174 YLYFGMWKTS184 FAWHTEDMDL194 YSINYLHFGE204 PKSWYSVPPE 214 HGKRLERLAK224 GFFPGSAQSC234 EAFLRHKMTL244 ISPLMLKKYG254 IPFDKVTQEA 264 GEFMITFPYG274 YHAGFNHGFN284 CAESTNFATR294 RWIEYGKQAV304 LCSCRVKISM 317 DVFVRKFQPE327 RYKLWKAGKD337 NTVIDHTLPT347 PEAAEFL
|
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .QC1 or .QC12 or .QC13 or :3QC1;style chemicals stick;color identity;select .A:71 or .A:73 or .A:84 or .A:86 or .A:132 or .A:134 or .A:135 or .A:177 or .A:184 or .A:185 or .A:188 or .A:190 or .A:198 or .A:206 or .A:208 or .A:241 or .A:276; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
||||||
| Ligand Name: 2-[5-(3-hydroxyphenyl)-1H-pyrazol-1-yl]pyridine-4-carboxylic acid | Ligand Info | |||||
| Structure Description | Crystal Structure of KDM4A with Compound 8 | PDB:6CG2 | ||||
| Method | X-ray diffraction | Resolution | 2.34 Å | Mutation | No | [25] |
| PDB Sequence |
TLNPSARIMT
16 FYPTMEEFRN26 FSRYIAYIES36 QGAHRAGLAK46 VVPPKEWKPR56 ASYDDIDDLV 66 IPAPIQQLVT76 GQSGLFTQYN86 IQKKAMTVRE96 FRKIANSDKY106 CTPRYSEFEE 116 LERKYWKNLT126 FNPPIYGADV136 NGTLYEKHVD146 EWNIGRLRTI156 LDLVEKESGI 166 TIEGVNTPYL176 YFGMWKTSFA186 WHTEDMDLYS196 INYLHFGEPK206 SWYSVPPEHG 216 KRLERLAKGF226 FPGSAQSCEA236 FLRHKMTLIS246 PLMLKKYGIP256 FDKVTQEAGE 266 FMITFPYGYH276 AGFNHGFNCA286 ESTNFATRRW296 IEYGKQAVLC306 SCRVKISMDV 319 FVRKFQPERY329 KLWKAGKDNT339 VIDHTLPTPE349 AAEFL
|
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .QC2 or .QC22 or .QC23 or :3QC2;style chemicals stick;color identity;select .A:84 or .A:132 or .A:134 or .A:135 or .A:177 or .A:184 or .A:185 or .A:186 or .A:188 or .A:190 or .A:198 or .A:206 or .A:208 or .A:241 or .A:276 or .A:280; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
||||||
| Ligand Name: 3,4-Dihydroxybenzoic acid | Ligand Info | |||||
| Structure Description | Crystal structure of JMJD2A complexed with 3,4-dihydroxybenzoic acid | PDB:7EQV | ||||
| Method | X-ray diffraction | Resolution | 2.60 Å | Mutation | No | [26] |
| PDB Sequence |
LNPSARIMTF
17 YPTMEEFRNF27 SRYIAYIESQ37 GAHRAGLAKV47 VPPKEWKPRA57 SYDDIDDLVI 67 PAPIQQLVTG77 QSGLFTQYNI87 QKKAMTVREF97 RKIANSDKYC107 TPRYSEFEEL 117 ERKYWKNLTF127 NPPIYGADVN137 GTLYEKHVDE147 WNIGRLRTIL157 DLVEKESGIT 167 IEGVNTPYLY177 FGMWKTSFAW187 HTEDMDLYSI197 NYLHFGEPKS207 WYSVPPEHGK 217 RLERLAKGFF227 PGSAQSCEAF237 LRHKMTLISP247 LMLKKYGIPF257 DKVTQEAGEF 267 MITFPYGYHA277 GFNHGFNCAE287 STNFATRRWI297 EYGKQAVLCS307 CRKDMVKISM 317 DVFVRKFQPE327 RYKLWKAGKD337 NTVIDHTLPT347
|
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .DHB or .DHB2 or .DHB3 or :3DHB;style chemicals stick;color identity;select .A:132 or .A:177 or .A:184 or .A:185 or .A:188 or .A:190 or .A:196 or .A:198 or .A:206 or .A:208 or .A:241 or .A:276 or .A:280; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
||||||
| Ligand Name: O-benzyl-N-(carboxycarbonyl)-D-tyrosine | Ligand Info | |||||
| Structure Description | STRUCTURE OF JMJD2A COMPLEXED WITH INHIBITOR 10A | PDB:2WWJ | ||||
| Method | X-ray diffraction | Resolution | 2.60 Å | Mutation | No | [27] |
| PDB Sequence |
LNPSARIMTF
17 YPTMEEFRNF27 SRYIAYIESQ37 GAHRAGLAKV47 VPPKEWKPRA57 SYDDIDDLVI 67 PAPIQQLVTG77 QSGLFTQYNI87 QKKAMTVREF97 RKIANSDKYC107 TPRYSEFEEL 117 ERKYWKNLTF127 NPPIYGADVN137 GTLYEKHVDE147 WNIGRLRTIL157 DLVEKESGIT 167 IEGVNTPYLY177 FGMWKTSFAW187 HTEDMDLYSI197 NYLHFGEPKS207 WYSVPPEHGK 217 RLERLAKGFF227 PGSAQSCEAF237 LRHKMTLISP247 LMLKKYGIPF257 DKVTQEAGEF 267 MITFPYGYHA277 GFNHGFNCAE287 STNFATRRWI297 EYGKQAVLCS307 CRKDMVKISM 317 DVFVRKFQPE327 RYKLWKAGKD337 NTVIDHTLPT347 PEAAEF
|
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .Y28 or .Y282 or .Y283 or :3Y28;style chemicals stick;color identity;select .A:71 or .A:73 or .A:84 or .A:86 or .A:132 or .A:134 or .A:135 or .A:177 or .A:184 or .A:185 or .A:186 or .A:188 or .A:190 or .A:196 or .A:197 or .A:198 or .A:206 or .A:208 or .A:240 or .A:241 or .A:270 or .A:276 or .A:280 or .A:286 or .A:288; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
ILE71
3.508
GLN73
4.362
GLN84
3.633
ASN86
3.446
TYR132
2.360
ALA134
4.436
ASP135
4.029
TYR177
3.691
SER184
3.874
PHE185
3.410
ALA186
3.679
HIS188
3.214
GLU190
3.073
|
|||||
| Ligand Name: N(6)-Methyllysine | Ligand Info | |||||
| Structure Description | The complex structure of JMJD2A and monomethylated H3K36 peptide | PDB:2PXJ | ||||
| Method | X-ray diffraction | Resolution | 2.00 Å | Mutation | No | [28] |
| PDB Sequence |
ASESETLNPS
11 ARIMTFYPTM21 EEFRNFSRYI31 AYIESQGAHR41 AGLAKVVPPK51 EWKPRASYDD 61 IDDLVIPAPI71 QQLVTGQSGL81 FTQYNIQKKA91 MTVREFRKIA101 NSDKYCTPRY 111 SEFEELERKY121 WKNLTFNPPI131 YGADVNGTLY141 EKHVDEWNIG151 RLRTILDLVE 161 KESGITIEGV171 NTPYLYFGMW181 KTSFAWHTED191 MDLYSINYLH201 FGEPKSWYSV 211 PPEHGKRLER221 LAKGFFPGSA231 QSCEAFLRHK241 MTLISPLMLK251 KYGIPFDKVT 261 QEAGEFMITF271 PYGYHAGFNH281 GFNCAESTNF291 ATRRWIEYGK301 QAVLCSCRKD 311 MVKISMDVFV321 RKFQPERYKL331 WKAGKDNTVI341 DHTLPTP
|
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .MLZ or .MLZ2 or .MLZ3 or :3MLZ;style chemicals stick;color identity;select .A:135 or .A:168 or .A:169 or .A:170 or .A:171 or .A:175 or .A:177 or .A:190 or .A:191 or .A:196 or .A:241 or .A:288 or .A:289 or .A:290 or .A:313; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
||||||
| Click to View More Binding Site Information of This Target and Ligand Pair | ||||||
| Ligand Name: Mesotartaric acid | Ligand Info | |||||
| Structure Description | Crystal structure of double tudor domain of human lysine demethylase KDM4A | PDB:5D6W | ||||
| Method | X-ray diffraction | Resolution | 1.99 Å | Mutation | No | [29] |
| PDB Sequence |
QSITAGQKVI
906 SKHKNGRFYQ916 CEVVRLTTET926 FYEVNFDDGS936 FSDNLYPEDI946 VSQDCLQFGP 956 PAEGEVVQVR966 WTDGQVYGAK976 FVASHPIQMY986 QVEFEDGSQL996 VVKRDDVYTL 1006 DEELP
|
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .SRT or .SRT2 or .SRT3 or :3SRT;style chemicals stick;color identity;select .A:910 or .A:992 or .A:993 or .A:994 or .A:995; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
||||||
| Ligand Name: Kdm4-IN-4 | Ligand Info | |||||
| Structure Description | Crystal structure of KDM4A tandem TUDOR domain in complex with a tri-methyl lysine competitive inhibitor | PDB:5VAR | ||||
| Method | X-ray diffraction | Resolution | 1.83 Å | Mutation | No | [30] |
| PDB Sequence |
QSITAGQKVI
906 SKHKNGRFYQ916 CEVVRLTTET926 FYEVNFDDGS936 FSDNLYPEDI946 VSQDCLQFGP 956 PAEGEVVQVR966 WTDGQVYGAK976 FVASHPIQMY986 QVEFEDGSQL996 VVKRDDVY |
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .92Y or .92Y2 or .92Y3 or :392Y;style chemicals stick;color identity;select .A:932 or .A:933 or .A:934 or .A:936 or .A:937 or .A:938 or .A:967 or .A:973 or .A:974; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
||||||
| References | Top | ||||
|---|---|---|---|---|---|
| REF 1 | Crystal Structure of Human Jmjd2A in Complex with Pyruvate | ||||
| REF 2 | Crystal Structure of Human Jmjd2A in Complex with Succinate | ||||
| REF 3 | Studies on the catalytic domains of multiple JmjC oxygenases using peptide substrates. Epigenetics. 2014 Dec;9(12):1596-603. | ||||
| REF 4 | Arginine demethylation is catalysed by a subset of JmjC histone lysine demethylases. Nat Commun. 2016 Jun 23;7:11974. | ||||
| REF 5 | Plant growth regulator daminozide is a selective inhibitor of human KDM2/7 histone demethylases. J Med Chem. 2012 Jul 26;55(14):6639-43. | ||||
| REF 6 | Inhibitor scaffolds for 2-oxoglutarate-dependent histone lysine demethylases. J Med Chem. 2008 Nov 27;51(22):7053-6. | ||||
| REF 7 | 5-Carboxy-8-hydroxyquinoline is a Broad Spectrum 2-Oxoglutarate Oxygenase Inhibitor which Causes Iron Translocation. Chem Sci. 2013 Aug 1;4(8):3110-3117. | ||||
| REF 8 | Highly selective inhibition of histone demethylases by de novo macrocyclic peptides. Nat Commun. 2017 Apr 6;8:14773. | ||||
| REF 9 | Quantitative high-throughput screening identifies 8-hydroxyquinolines as cell-active histone demethylase inhibitors. PLoS One. 2010 Nov 23;5(11):e15535. | ||||
| REF 10 | Specificity and mechanism of JMJD2A, a trimethyllysine-specific histone demethylase. Nat Struct Mol Biol. 2007 Aug;14(8):689-95. | ||||
| REF 11 | Crystal structures of histone demethylase JMJD2A reveal basis for substrate specificity. Nature. 2007 Jul 5;448(7149):87-91. | ||||
| REF 12 | Inhibition of histone demethylases by 4-carboxy-2,2'-bipyridyl compounds. ChemMedChem. 2011 May 2;6(5):759-764. | ||||
| REF 13 | Docking and Linking of Fragments To Discover Jumonji Histone Demethylase Inhibitors. J Med Chem. 2016 Feb 25;59(4):1580-98. | ||||
| REF 14 | The oncometabolite 2-hydroxyglutarate inhibits histone lysine demethylases. EMBO Rep. 2011 May;12(5):463-9. | ||||
| REF 15 | Linking of 2-oxoglutarate and substrate binding sites enables potent and highly selective inhibition of JmjC histone demethylases. Angew Chem Int Ed Engl. 2012 Feb 13;51(7):1631-4. | ||||
| REF 16 | Crystal Structure of JMJD2A Complexed with Inhibitor | ||||
| REF 17 | Crystal Structure of JMJD2A Complexed with Inhibitor | ||||
| REF 18 | Crystal Structure of Human Jmjd2A in Complex with D-Threo-Isocitrate | ||||
| REF 19 | Design of KDM4 Inhibitors with Antiproliferative Effects in Cancer Models. ACS Med Chem Lett. 2017 Jul 27;8(8):869-874. | ||||
| REF 20 | 8-Substituted Pyrido[3,4-d]pyrimidin-4(3H)-one Derivatives As Potent, Cell Permeable, KDM4 (JMJD2) and KDM5 (JARID1) Histone Lysine Demethylase Inhibitors. J Med Chem. 2016 Feb 25;59(4):1388-409. | ||||
| REF 21 | C8-substituted pyrido[3,4-d]pyrimidin-4(3H)-ones: Studies towards the identification of potent, cell penetrant Jumonji C domain containing histone lysine demethylase 4 subfamily (KDM4) inhibitors, compound profiling in cell-based target engagement assays. Eur J Med Chem. 2019 Sep 1;177:316-337. | ||||
| REF 22 | Optimisation of a triazolopyridine based histone demethylase inhibitor yields a potent and selective KDM2A (FBXL11) inhibitor. Medchemcomm. 2014 Dec 1;5(12):1879-1886. | ||||
| REF 23 | Structural analysis of human KDM5B guides histone demethylase inhibitor development. Nat Chem Biol. 2016 Jul;12(7):539-45. | ||||
| REF 24 | Substituted 2-(2-aminopyrimidin-4-yl)pyridine-4-carboxylates as potent inhibitors of JumonjiC domain-containing histone demethylases. Future Med Chem. 2016 Sep;8(13):1553-71. | ||||
| REF 25 | Structure-based design and discovery of potent and selective KDM5 inhibitors. Bioorg Med Chem Lett. 2018 May 15;28(9):1490-1494. | ||||
| REF 26 | Natural product myricetin is a pan-KDM4 inhibitor which with poly lactic-co-glycolic acid formulation effectively targets castration-resistant prostate cancer. J Biomed Sci. 2022 May 9;29(1):29. | ||||
| REF 27 | Selective inhibitors of the JMJD2 histone demethylases: combined nondenaturing mass spectrometric screening and crystallographic approaches. J Med Chem. 2010 Feb 25;53(4):1810-8. | ||||
| REF 28 | Structural basis of the recognition of a methylated histone tail by JMJD2A. Proc Natl Acad Sci U S A. 2007 Jun 26;104(26):10818-23. | ||||
| REF 29 | Reader domain specificity and lysine demethylase-4 family function. Nat Commun. 2016 Nov 14;7:13387. | ||||
| REF 30 | Targeting lysine specific demethylase 4A (KDM4A) tandem TUDOR domain - A fragment based approach. Bioorg Med Chem Lett. 2018 Jun 1;28(10):1708-1713. | ||||
If You Find Any Error in Data or Bug in Web Service, Please Kindly Report It to Dr. Zhou and Dr. Zhang.