Target Binding Site Detail
| 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 | |||||
| Ligand General Information | Top | ||||
|---|---|---|---|---|---|
| Ligand Name | Alpha-ketoglutaric acid | Ligand Info | |||
| Canonical SMILES | C(CC(=O)O)C(=O)C(=O)O | ||||
| InChI | 1S/C5H6O5/c6-3(5(9)10)1-2-4(7)8/h1-2H2,(H,7,8)(H,9,10) | ||||
| InChIKey | KPGXRSRHYNQIFN-UHFFFAOYSA-N | ||||
| PubChem Compound ID | 51 | ||||
| Drug Binding Sites of Target | Top | |||||
|---|---|---|---|---|---|---|
| PDB ID: 5TVR JMJD2A in complex with Ni(II) and alpha-Ketoglutarate | ||||||
| Method | X-ray diffraction | Resolution | 2.09 Å | Mutation | No | [1] |
| 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 PTPEAAEF
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| PDB ID: 2Q8C Crystal structure of JMJD2A in ternary complex with an histone H3K9me3 peptide and 2-oxoglutarate | ||||||
| Method | X-ray diffraction | Resolution | 2.05 Å | Mutation | No | [2] |
| 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
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| PDB ID: 2GP5 Crystal structure of catalytic core domain of jmjd2A complexed with alpha-Ketoglutarate | ||||||
| Method | X-ray diffraction | Resolution | 2.28 Å | Mutation | No | [3] |
| 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
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| References | Top | ||||
|---|---|---|---|---|---|
| REF 1 | The small molecule JIB-04 disrupts O(2) binding in the Fe-dependent histone demethylase KDM4A/JMJD2A. Chem Commun (Camb). 2017 Feb 9;53(13):2174-2177. | ||||
| REF 2 | Specificity and mechanism of JMJD2A, a trimethyllysine-specific histone demethylase. Nat Struct Mol Biol. 2007 Aug;14(8):689-95. | ||||
| REF 3 | Structural insights into histone demethylation by JMJD2 family members. Cell. 2006 May 19;125(4):691-702. | ||||
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