Binding Site Information of Target
| Target General Information | Top | ||||
|---|---|---|---|---|---|
| Target ID | T15797 | Target Info | |||
| Target Name | SET and MYND domain-containing protein 2 (SMYD2) | ||||
| Synonyms | Nlysine methyltransferase SMYD2; N-lysine methyltransferase SMYD2; Lysine Nmethyltransferase 3C; Lysine N-methyltransferase 3C; KMT3C; Histone methyltransferase SMYD2; HSKMB; HSKM-B | ||||
| Target Type | Preclinical Target | ||||
| Gene Name | SMYD2 | ||||
| Biochemical Class | Methyltransferase | ||||
| UniProt ID | |||||
| Drug Binding Sites of Target | Top | |||||
|---|---|---|---|---|---|---|
| Ligand Name: Ademetionine | Ligand Info | |||||
| Structure Description | SMYD2 in complex with small molecule inhibitor compound-2 | PDB:5ARF | ||||
| Method | X-ray diffraction | Resolution | 1.92 Å | Mutation | No | [1] |
| PDB Sequence |
LGGLERFCSP
15 GKGRGLRALQ25 PFQVGDLLFS35 CPAYAYVLTV45 NERGNHCEYC55 FTRKEGLSKC 65 GRCKQAFYCN75 VECQKEDWPM85 HKLECSPMVV95 FGENWNPSET105 VRLTARILAK 115 QKIHPERTPS125 EKLLAVKEFE135 SHLDKLDNEK145 KDLIQSDIAA155 LHHFYSKHLG 165 FPDNDSLVVL175 FAQVNCNGFT185 IEDEELSHLG195 SAIFPDVALM205 NHSCCPNVIV 215 TYKGTLAEVR225 AVQEIKPGEE235 VFTSYIDLLY245 PTEDRNDRLR255 DSYFFTCECQ 265 ECTTKDKDKA275 KVEIRKLSDP285 PKAEAIRDMV295 RYARNVIEEF305 RRAKHYKSPS 315 ELLEICELSQ325 EKMSSVFEDS335 NVYMLHMMYQ345 AMGVCLYMQD355 WEGALQYGQK 365 IIKPYSKHYP375 LYSLNVASMW385 LKLGRLYMGL395 EHKAAGEKAL405 KKAIAIMEVA 415 HGKDHPYISE425 IKQEI
|
|||||
|
|
GLY16
3.297
LYS17
2.882
GLY18
3.932
ARG19
2.058
GLY20
4.258
LEU129
4.875
GLU135
3.341
HIS137
3.020
CYS181
3.590
ASN182
2.978
ALA203
2.634
|
|||||
| Click to View More Binding Site Information of This Target and Ligand Pair | ||||||
| Ligand Name: BAY 598 | Ligand Info | |||||
| Structure Description | SMYD2 in complex with SGC probe BAY-598 | PDB:5ARG | ||||
| Method | X-ray diffraction | Resolution | 1.99 Å | Mutation | No | [1] |
| PDB Sequence |
LGGLERFCSP
15 GKGRGLRALQ25 PFQVGDLLFS35 CPAYAYVLTV45 NERGNHCEYC55 FTRKEGLSKC 65 GRCKQAFYCN75 VECQKEDWPM85 HKLECSPMVV95 FGENWNPSET105 VRLTARILAK 115 QKIHPERTPS125 EKLLAVKEFE135 SHLDKLDNEK145 KDLIQSDIAA155 LHHFYSKHLG 165 FPDNDSLVVL175 FAQVNCNGFT185 IEDEELSHLG195 SAIFPDVALM205 NHSCCPNVIV 215 TYKGTLAEVR225 AVQEIKPGEE235 VFTSYIDLLY245 PTEDRNDRLR255 DSYFFTCECQ 265 ECTTKDKDKA275 KVEIRKLSDP285 PKAEAIRDMV295 RYARNVIEEF305 RRAKHYKSPS 315 ELLEICELSQ325 EKMSSVFEDS335 NVYMLHMMYQ345 AMGVCLYMQD355 WEGALQYGQK 365 IIKPYSKHYP375 LYSLNVASMW385 LKLGRLYMGL395 EHKAAGEKAL405 KKAIAIMEVA 415 HGKDHPYISE425 IKQEIE
|
|||||
|
|
GLU104
3.440
THR105
3.358
LEU108
3.492
VAL179
3.194
ASN180
3.792
CYS181
4.205
ASN182
3.517
GLY183
2.607
PHE184
3.423
THR185
2.574
ILE186
4.587
GLU187
3.861
|
|||||
| Ligand Name: AZ505 | Ligand Info | |||||
| Structure Description | Structural Basis of Substrate Methylation and Inhibition of SMYD2 | PDB:3S7B | ||||
| Method | X-ray diffraction | Resolution | 2.42 Å | Mutation | No | [2] |
| PDB Sequence |
GLGGLERFCS
14 PGKGRGLRAL24 QPFQVGDLLF34 SCPAYAYVLT44 VNERGNHCEY54 CFTRKEGLSK 64 CGRCKQAFYC74 NVECQKEDWP84 MHKLECSPMV94 VFGENWNPSE104 TVRLTARILA 114 KQKIHPERTP124 SEKLLAVKEF134 ESHLDKLDNE144 KKDLIQSDIA154 ALHHFYSKHL 164 EFPDNDSLVV174 LFAQVNCNGF184 TIEDEELSHL194 GSAIFPDVAL204 MNHSCCPNVI 214 VTYKGTLAEV224 RAVQEIKPGE234 EVFTSYIDLL244 YPTEDRNDRL254 RDSYFFTCEC 264 QECTTKDKDK274 AKVEIRKLSD284 PPKAEAIRDM294 VRYARNVIEE304 FRRAKHYKSP 314 SELLEICELS324 QEKMSSVFED334 SNVYMLHMMY344 QAMGVCLYMQ354 DWEGALQYGQ 364 KIIKPYSKHY374 PLYSLNVASM384 WLKLGRLYMG394 LEHKAAGEKA404 LKKAIAIMEV 414 AHGKDHPYIS424 EIKQEIESH
|
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .NH5 or .NH52 or .NH53 or :3NH5;style chemicals stick;color identity;select .A:105 or .A:108 or .A:141 or .A:145 or .A:148 or .A:149 or .A:176 or .A:177 or .A:179 or .A:180 or .A:181 or .A:182 or .A:183 or .A:184 or .A:185 or .A:196 or .A:202 or .A:203 or .A:205 or .A:215 or .A:238 or .A:239 or .A:240 or .A:256 or .A:257 or .A:258 or .A:259; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
THR105
3.209
LEU108
4.209
LEU141
3.858
LYS145
3.702
LEU148
4.356
ILE149
3.661
PHE176
4.870
ALA177
3.866
VAL179
3.872
ASN180
3.310
CYS181
3.639
ASN182
3.582
GLY183
2.957
PHE184
3.499
|
|||||
| Ligand Name: LLY-507 | Ligand Info | |||||
| Structure Description | Crystal Structure of Protein Lysine Methyltransferase SMYD2 in complex with LLY-507, a Cell-Active, Potent and Selective Inhibitor | PDB:4WUY | ||||
| Method | X-ray diffraction | Resolution | 1.63 Å | Mutation | No | [3] |
| PDB Sequence |
GLGGLERFCS
14 PGKGRGLRAL24 QPFQVGDLLF34 SCPAYAYVLT44 VNERGNHCEY54 CFTRKEGLSK 64 CGRCKQAFYC74 NVECQKEDWP84 MHKLECSPMV94 VFGENWNPSE104 TVRLTARILA 114 KQKIHPERTP124 SEKLLAVKEF134 ESHLDKLDNE144 KKDLIQSDIA154 ALHHFYSKHL 164 GFPDNDSLVV174 LFAQVNCNGF184 TIEDEELSHL194 GSAIFPDVAL204 MNHSCCPNVI 214 VTYKGTLAEV224 RAVQEIKPGE234 EVFTSYIDLL244 YPTEDRNDRL254 RDSYFFTCEC 264 QECTTKDKDK274 AKVEIRKAEA290 IRDMVRYARN300 VIEEFRELLE319 ICELSQEKMS 329 SVFEDSNVYM339 LHMMYQAMGV349 CLYMQDWEGA359 LQYGQKIIKP369 YSKHYPLYSL 379 NVASMWLKLG389 RLYMGLEHKA399 AGEKALKKAI409 AIMEVAHGKD419 HPYISEIKQE 429 IESH
|
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .3UJ or .3UJ2 or .3UJ3 or :33UJ;style chemicals stick;color identity;select .A:105 or .A:108 or .A:136 or .A:141 or .A:145 or .A:148 or .A:149 or .A:177 or .A:179 or .A:180 or .A:181 or .A:182 or .A:183 or .A:184 or .A:185 or .A:196 or .A:203 or .A:239 or .A:240 or .A:256 or .A:257 or .A:258 or .A:259; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
THR105
3.808
LEU108
4.331
SER136
3.833
LEU141
3.535
LYS145
3.556
LEU148
4.168
ILE149
3.721
ALA177
3.599
VAL179
3.919
ASN180
2.936
CYS181
3.122
ASN182
3.349
|
|||||
| Ligand Name: A-893 | Ligand Info | |||||
| Structure Description | The Discovery of A-893, A New Cell-Active Benzoxazinone Inhibitor of Lysine Methyltransferase SMYD2 | PDB:4YND | ||||
| Method | X-ray diffraction | Resolution | 2.79 Å | Mutation | No | [4] |
| PDB Sequence |
AEGLGGLERF
12 CSPGKGRGLR22 ALQPFQVGDL32 LFSCPAYAYV42 LTVNERGNHC52 EYCFTRKEGL 62 SKCGRCKQAF72 YCNVECQKED82 WPMHKLECSP92 MVVFGENWNP102 SETVRLTARI 112 LAKQKIHPER122 TPSEKLLAVK132 EFESHLDKLD142 NEKKDLIQSD152 IAALHHFYSK 162 HLGFPDNDSL172 VVLFAQVNCN182 GFTIEDEELS192 HLGSAIFPDV202 ALMNHSCCPN 212 VIVTYKGTLA222 EVRAVQEIKP232 GEEVFTSYID242 LLYPTEDRND252 RLRDSYFFTC 262 ECQECTTKDK272 DKAKVEIRKL282 SDPPKAEAIR292 DMVRYARNVI302 EEFRRAKHYK 312 SPSELLEICE322 LSQEKMSSVF332 EDSNVYMLHM342 MYQAMGVCLY352 MQDWEGALQY 362 GQKIIKPYSK372 HYPLYSLNVA382 SMWLKLGRLY392 MGLEHKAAGE402 KALKKAIAIM 412 EVAHGKDHPY422 ISEIKQEI
|
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .4GQ or .4GQ2 or .4GQ3 or :34GQ;style chemicals stick;color identity;select .A:104 or .A:105 or .A:108 or .A:141 or .A:145 or .A:148 or .A:149 or .A:176 or .A:177 or .A:179 or .A:180 or .A:181 or .A:182 or .A:183 or .A:184 or .A:185 or .A:196 or .A:202 or .A:203 or .A:205 or .A:238 or .A:239 or .A:240 or .A:241 or .A:256 or .A:257 or .A:258 or .A:259; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
GLU104
4.891
THR105
3.343
LEU108
4.470
LEU141
3.586
LYS145
3.655
LEU148
4.220
ILE149
3.637
PHE176
4.958
ALA177
3.996
VAL179
3.443
ASN180
3.041
CYS181
3.995
ASN182
3.547
GLY183
3.229
|
|||||
| Ligand Name: N-[(4S)-5-(4-chlorophenyl)-2-[N-cyano-N'-[3-(difluoromethoxy)phenyl]carbamimidoyl]-3,4-dihydropyrazol-4-yl]-N-ethyl-2-hydroxyacetamide | Ligand Info | |||||
| Structure Description | SMYD2 in complex with small molecule inhibitor compound-2 | PDB:5ARF | ||||
| Method | X-ray diffraction | Resolution | 1.92 Å | Mutation | No | [1] |
| PDB Sequence |
LGGLERFCSP
15 GKGRGLRALQ25 PFQVGDLLFS35 CPAYAYVLTV45 NERGNHCEYC55 FTRKEGLSKC 65 GRCKQAFYCN75 VECQKEDWPM85 HKLECSPMVV95 FGENWNPSET105 VRLTARILAK 115 QKIHPERTPS125 EKLLAVKEFE135 SHLDKLDNEK145 KDLIQSDIAA155 LHHFYSKHLG 165 FPDNDSLVVL175 FAQVNCNGFT185 IEDEELSHLG195 SAIFPDVALM205 NHSCCPNVIV 215 TYKGTLAEVR225 AVQEIKPGEE235 VFTSYIDLLY245 PTEDRNDRLR255 DSYFFTCECQ 265 ECTTKDKDKA275 KVEIRKLSDP285 PKAEAIRDMV295 RYARNVIEEF305 RRAKHYKSPS 315 ELLEICELSQ325 EKMSSVFEDS335 NVYMLHMMYQ345 AMGVCLYMQD355 WEGALQYGQK 365 IIKPYSKHYP375 LYSLNVASMW385 LKLGRLYMGL395 EHKAAGEKAL405 KKAIAIMEVA 415 HGKDHPYISE425 IKQEI
|
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .I9H or .I9H2 or .I9H3 or :3I9H;style chemicals stick;color identity;select .A:104 or .A:105 or .A:108 or .A:179 or .A:180 or .A:182 or .A:183 or .A:184 or .A:185 or .A:186 or .A:187 or .A:196 or .A:197 or .A:202 or .A:203 or .A:205 or .A:217 or .A:238 or .A:239 or .A:240 or .A:241 or .A:242 or .A:258; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
GLU104
3.425
THR105
3.253
LEU108
3.573
VAL179
3.247
ASN180
3.542
ASN182
4.375
GLY183
2.959
PHE184
3.452
THR185
2.688
ILE186
4.740
GLU187
3.832
SER196
3.041
|
|||||
| Ligand Name: [3-(6-Amino-2-methylpurin-9-yl)azetidin-1-yl]-[5-[(4-cycloheptylpiperazin-1-yl)methyl]-1-methylpyrazol-3-yl]methanone | Ligand Info | |||||
| Structure Description | SET and MYND Domain Containing protein 2 | PDB:5WCG | ||||
| Method | X-ray diffraction | Resolution | 2.02 Å | Mutation | No | [5] |
| PDB Sequence |
RAELGGLERF
12 CSPGKGRGLR22 ALQPFQVGDL32 LFSCPAYAYV42 LTVNERGNHC52 EYCFTRKEGL 62 SKCGRCKQAF72 YCNVECQKED82 WPMHKLECSP92 MVVFGENWNP102 SETVRLTARI 112 LAKQKIHPER122 TPSEKLLAVK132 EFESHLDKLD142 NEKKDLIQSD152 IAALHHFYSK 162 HLEFPDNDSL172 VVLFAQVNCN182 GFTIEDEELS192 HLGSAIFPDV202 ALMNHSCCPN 212 VIVTYKGTLA222 EVRAVQEIKP232 GEEVFTSYID242 LLYPTEDRND252 RLRDSYFFTC 262 ECQECTTKDK272 DKAKVEIRKL282 SDPPKAEAIR292 DMVRYARNVI302 EEFRRAKHYK 312 SPSELLEICE322 LSQEKMSSVF332 EDSNVYMLHM342 MYQAMGVCLY352 MQDWEGALQY 362 GQKIIKPYSK372 HYPLYSLNVA382 SMWLKLGRLY392 MGLEHKAAGE402 KALKKAIAIM 412 EVAHGKDHPY422 ISEIKQEIES432
|
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .A4M or .A4M2 or .A4M3 or :3A4M;style chemicals stick;color identity;select .A:16 or .A:17 or .A:135 or .A:137 or .A:181 or .A:182 or .A:183 or .A:184 or .A:185 or .A:203 or .A:206 or .A:207 or .A:239 or .A:240 or .A:258 or .A:260 or .A:261 or .A:262; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
||||||
| Ligand Name: N(6)-Methyllysine | Ligand Info | |||||
| Structure Description | Structural Basis of Substrate Methylation and Inhibition of SMYD2 | PDB:3S7D | ||||
| Method | X-ray diffraction | Resolution | 2.30 Å | Mutation | No | [2] |
| PDB Sequence |
GLGGLERFCS
14 PGKGRGLRAL24 QPFQVGDLLF34 SCPAYAYVLT44 VNERGNHCEY54 CFTRKEGLSK 64 CGRCKQAFYC74 NVECQKEDWP84 MHKLECSPMV94 VFGENWNPSE104 TVRLTARILA 114 KQKIHPERTP124 SEKLLAVKEF134 ESHLDKLDNE144 KKDLIQSDIA154 ALHHFYSKHL 164 EFPDNDSLVV174 LFAQVNCNGF184 TIEDEELSHL194 GSAIFPDVAL204 MNHSCCPNVI 214 VTYKGTLAEV224 RAVQEIKPGE234 EVFTSYIDLL244 YPTEDRNDRL254 RDSYFFTCEC 264 QECTTKDKDK274 AKVEIRKLSD284 PPKAEAIRDM294 VRYARNVIEE304 FRRAKHYKSP 314 SELLEICELS324 QEKMSSVFED334 SNVYMLHMMY344 QAMGVCLYMQ354 DWEGALQYGQ 364 KIIKPYSKHY374 PLYSLNVASM384 WLKLGRLYMG394 LEHKAAGEKA404 LKKAIAIMEV 414 AHGKDHPYIS424 EIKQEIESH
|
|||||
|
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:181 or .A:182 or .A:183 or .A:184 or .A:185 or .A:202 or .A:203 or .A:204 or .A:205 or .A:217 or .A:240 or .A:258; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
||||||
| Ligand Name: [3-(4-amino-6-methyl-1H-imidazo[4,5-c]pyridin-1-yl)azetidin-1-yl][1-({1-[(1R)-cyclohept-2-en-1-yl]piperidin-4-yl}methyl)-1H-pyrrol-3-yl]methanone | Ligand Info | |||||
| Structure Description | Crystal structure of human SET and MYND Domain Containing protein 2 with MTF1497 | PDB:6CBX | ||||
| Method | X-ray diffraction | Resolution | 1.94 Å | Mutation | No | [6] |
| PDB Sequence |
GLGGLERFCS
14 PGKGRGLRAL24 QPFQVGDLLF34 SCPAYAYVLT44 VNERGNHCEY54 CFTRKEGLSK 64 CGRCKQAFYC74 NVECQKEDWP84 MHKLECSPMV94 VFGENWNPSE104 TVRLTARILA 114 KQKIHPERTP124 SEKLLAVKEF134 ESHLDKLDNE144 KKDLIQSDIA154 ALHHFYSKHL 164 EFPDNDSLVV174 LFAQVNCNGF184 TIEDEELSHL194 GSAIFPDVAL204 MNHSCCPNVI 214 VTYKGTLAEV224 RAVQEIKPGE234 EVFTSYIDLL244 YPTEDRNDRL254 RDSYFFTCEC 264 QECTTKDKDK274 AKVEIRKLSD284 PPKAEAIRDM294 VRYARNVIEE304 FRRAKHYKSP 314 SELLEICELS324 QEKMSSVFED334 SNVYMLHMMY344 QAMGVCLYMQ354 DWEGALQYGQ 364 KIIKPYSKHY374 PLYSLNVASM384 WLKLGRLYMG394 LEHKAAGEKA404 LKKAIAIMEV 414 AHGKDHPYIS424 EIKQEIES
|
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .EW1 or .EW12 or .EW13 or :3EW1;style chemicals stick;color identity;select .A:16 or .A:17 or .A:135 or .A:137 or .A:181 or .A:182 or .A:183 or .A:184 or .A:185 or .A:203 or .A:205 or .A:206 or .A:207 or .A:239 or .A:240 or .A:258 or .A:260 or .A:261 or .A:262 or .A:263; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
||||||
| Ligand Name: [3-(4-amino-6-methylimidazo[4,5-c]pyridin-1-yl)-3-methylazetidin-1-yl]-[1-[[1-[(1R)-cyclohept-2-en-1-yl]piperidin-4-yl]methyl]pyrrol-3-yl]methanone | Ligand Info | |||||
| Structure Description | Crystal structure of human SET and MYND Domain Containing protein 2 with MTF9975 | PDB:6CBY | ||||
| Method | X-ray diffraction | Resolution | 2.55 Å | Mutation | No | [7] |
| PDB Sequence |
GLGGLERFCS
14 PGKGRGLRAL24 QPFQVGDLLF34 SCPAYAYVLT44 VNERGNHCEY54 CFTRKEGLSK 64 CGRCKQAFYC74 NVECQKEDWP84 MHKLECSPMV94 VFGENWNPSE104 TVRLTARILA 114 KQKIHPERTP124 SEKLLAVKEF134 ESHLDKLDNE144 KKDLIQSDIA154 ALHHFYSKHL 164 EFPDNDSLVV174 LFAQVNCNGF184 TIEDEELSHL194 GSAIFPDVAL204 MNHSCCPNVI 214 VTYKGTLAEV224 RAVQEIKPGE234 EVFTSYIDLL244 YPTEDRNDRL254 RDSYFFTCEC 264 QECTTKDKDK274 AKVEIRKLSD284 PPKAEAIRDM294 VRYARNVIEE304 FRRAKHYKSP 314 SELLEICELS324 QEKMSSVFED334 SNVYMLHMMY344 QAMGVCLYMQ354 DWEGALQYGQ 364 KIIKPYSKHY374 PLYSLNVASM384 WLKLGRLYMG394 LEHKAAGEKA404 LKKAIAIMEV 414 AHGKDHPYIS424 EIKQEIES
|
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .EW4 or .EW42 or .EW43 or :3EW4;style chemicals stick;color identity;select .A:16 or .A:17 or .A:18 or .A:19 or .A:135 or .A:137 or .A:181 or .A:182 or .A:183 or .A:184 or .A:185 or .A:203 or .A:206 or .A:207 or .A:237 or .A:239 or .A:240 or .A:258 or .A:260 or .A:261 or .A:262 or .A:263; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
GLY16
3.446
LYS17
3.422
GLY18
4.138
ARG19
4.622
GLU135
4.209
HIS137
2.770
CYS181
3.244
ASN182
3.428
GLY183
3.245
PHE184
3.828
THR185
3.432
|
|||||
| Ligand Name: (R,R)-2,3-butanediol | Ligand Info | |||||
| Structure Description | SMYD2 in complex with AZ370 | PDB:5KJK | ||||
| Method | X-ray diffraction | Resolution | 1.93 Å | Mutation | Yes | [8] |
| PDB Sequence |
GLGGLERFCS
14 PGKGRGLRAL24 QPFQVGDLLF34 SCPAYAYVLT44 VNERGNHCEY54 CFTRKEGLSK 64 CGRCKQAFYC74 NVECQKEDWP84 MHKLECSPMV94 VFGENWNPSE104 TVRLTARILA 114 KQKIHPERTP124 SEKLLAVKEF134 ESHLDKLDNE144 KKDLIQSDIA154 ALHHFYSKHL 164 EFPDNDSLVV174 LFAQVNCNGF184 TIEDEELSHL194 GSAIFPDVAL204 MNHSCCPNVI 214 VTYKGTLAEV224 RAVQEIKPGE234 EVFTSYIDLL244 YPTEDRNDRL254 RDSYFFTCEC 264 QECTTKDKDK274 AKVEIRKLSD284 PPKAEAIRDM294 VRYARNVIEE304 FRRAKHYKSP 314 SELLEICELS324 QEKMSSVFED334 SNVYMLHMMY344 QAMGVCLYMQ354 DWEGALQYGQ 364 KIIKPYSKHY374 PLYSLNVASM384 WLKLGRLYMG394 LEHKAAGEKA404 LKKAIAIMEV 414 AHGKDHPYIS424 EIKQEIESH
|
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .BU3 or .BU32 or .BU33 or :3BU3;style chemicals stick;color identity;select .A:5 or .A:65 or .A:67 or .A:79 or .A:80 or .A:83 or .A:122 or .A:126 or .A:127 or .A:247 or .A:248 or .A:251 or .A:252 or .A:255 or .A:261 or .A:270 or .A:356 or .A:390 or .A:391 or .A:394 or .A:395; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
GLY5
3.171
CYS65
4.926
ARG67
3.430
GLN79
3.598
LYS80
4.340
TRP83
3.603
ARG122
3.438
GLU126
4.675
LYS127
3.620
THR247
3.303
GLU248
3.425
|
|||||
| Click to View More Binding Site Information of This Target and Ligand Pair | ||||||
| Ligand Name: 2-[2-[1-[2-(3,4-Dichlorophenyl)ethyl]azetidin-3-Yl]oxyphenyl]-~{n}-(3-Pyrrolidin-1-Ylpropyl)pyridine-4-Carboxamide | Ligand Info | |||||
| Structure Description | SMYD2 in complex with AZ370 | PDB:5KJK | ||||
| Method | X-ray diffraction | Resolution | 1.93 Å | Mutation | Yes | [8] |
| PDB Sequence |
GLGGLERFCS
14 PGKGRGLRAL24 QPFQVGDLLF34 SCPAYAYVLT44 VNERGNHCEY54 CFTRKEGLSK 64 CGRCKQAFYC74 NVECQKEDWP84 MHKLECSPMV94 VFGENWNPSE104 TVRLTARILA 114 KQKIHPERTP124 SEKLLAVKEF134 ESHLDKLDNE144 KKDLIQSDIA154 ALHHFYSKHL 164 EFPDNDSLVV174 LFAQVNCNGF184 TIEDEELSHL194 GSAIFPDVAL204 MNHSCCPNVI 214 VTYKGTLAEV224 RAVQEIKPGE234 EVFTSYIDLL244 YPTEDRNDRL254 RDSYFFTCEC 264 QECTTKDKDK274 AKVEIRKLSD284 PPKAEAIRDM294 VRYARNVIEE304 FRRAKHYKSP 314 SELLEICELS324 QEKMSSVFED334 SNVYMLHMMY344 QAMGVCLYMQ354 DWEGALQYGQ 364 KIIKPYSKHY374 PLYSLNVASM384 WLKLGRLYMG394 LEHKAAGEKA404 LKKAIAIMEV 414 AHGKDHPYIS424 EIKQEIESH
|
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .6T1 or .6T12 or .6T13 or :36T1;style chemicals stick;color identity;select .A:105 or .A:108 or .A:141 or .A:145 or .A:148 or .A:149 or .A:177 or .A:179 or .A:180 or .A:181 or .A:182 or .A:183 or .A:184 or .A:185 or .A:196 or .A:203 or .A:239 or .A:240 or .A:256 or .A:257 or .A:258 or .A:259; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
THR105
3.369
LEU108
4.234
LEU141
3.736
LYS145
3.652
LEU148
4.343
ILE149
3.601
ALA177
3.980
VAL179
3.718
ASN180
2.690
CYS181
3.619
ASN182
3.588
|
|||||
| Ligand Name: 6-[2-[4-[2-(3,4-Dichlorophenyl)ethyl]piperazin-1-Yl]phenyl]-~{n}-(3-Pyrrolidin-1-Ylpropyl)-2~{h}-Pyrazolo[3,4-B]pyridine-4-Carboxamide | Ligand Info | |||||
| Structure Description | SMYD2 in complex with AZ931 | PDB:5KJM | ||||
| Method | X-ray diffraction | Resolution | 2.19 Å | Mutation | Yes | [8] |
| PDB Sequence |
GLGGLERFCS
14 PGKGRGLRAL24 QPFQVGDLLF34 SCPAYAYVLT44 VNERGNHCEY54 CFTRKEGLSK 64 CGRCKQAFYC74 NVECQKEDWP84 MHKLECSPMV94 VFGENWNPSE104 TVRLTARILA 114 KQKIHPERTP124 SEKLLAVKEF134 ESHLDKLDNE144 KKDLIQSDIA154 ALHHFYSKHL 164 EFPDNDSLVV174 LFAQVNCNGF184 TIEDEELSHL194 GSAIFPDVAL204 MNHSCCPNVI 214 VTYKGTLAEV224 RAVQEIKPGE234 EVFTSYIDLL244 YPTEDRNDRL254 RDSYFFTCEC 264 QECTTKDKDK274 AKVEIRKLSD284 PPKAEAIRDM294 VRYARNVIEE304 FRRAKHYKSP 314 SELLEICELS324 QEKMSSVFED334 SNVYMLHMMY344 QAMGVCLYMQ354 DWEGALQYGQ 364 KIIKPYSKHY374 PLYSLNVASM384 WLKLGRLYMG394 LEHKAAGEKA404 LKKAIAIMEV 414 AHGKDHPYIS424 EIKQEIESH
|
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .6TM or .6TM2 or .6TM3 or :36TM;style chemicals stick;color identity;select .A:105 or .A:108 or .A:141 or .A:145 or .A:148 or .A:149 or .A:177 or .A:179 or .A:180 or .A:181 or .A:182 or .A:183 or .A:184 or .A:185 or .A:196 or .A:197 or .A:203 or .A:239 or .A:240 or .A:256 or .A:257 or .A:258 or .A:259; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
THR105
3.497
LEU108
3.884
LEU141
3.776
LYS145
3.710
LEU148
4.159
ILE149
3.662
ALA177
4.659
VAL179
3.605
ASN180
3.161
CYS181
3.598
ASN182
3.553
GLY183
3.288
|
|||||
| Ligand Name: 5-[2-[4-[2-(1~{h}-Indol-3-Yl)ethyl]piperazin-1-Yl]phenyl]-~{n}-(3-Pyrrolidin-1-Ylpropyl)pyridine-3-Carboxamide | Ligand Info | |||||
| Structure Description | SMYD2 in complex with AZ506 | PDB:5KJN | ||||
| Method | X-ray diffraction | Resolution | 2.72 Å | Mutation | Yes | [8] |
| PDB Sequence |
GLGGLERFCS
14 PGKGRGLRAL24 QPFQVGDLLF34 SCPAYAYVLT44 VNERGNHCEY54 CFTRKEGLSK 64 CGRCKQAFYC74 NVECQKEDWP84 MHKLECSPMV94 VFGENWNPSE104 TVRLTARILA 114 KQKIHPERTP124 SEKLLAVKEF134 ESHLDKLDNE144 KKDLIQSDIA154 ALHHFYSKHL 164 EFPDNDSLVV174 LFAQVNCNGF184 TIEDEELSHL194 GSAIFPDVAL204 MNHSCCPNVI 214 VTYKGTLAEV224 RAVQEIKPGE234 EVFTSYIDLL244 YPTEDRNDRL254 RDSYFFTCEC 264 QECTTKDKDK274 AKVEIRKLSD284 PPKAEAIRDM294 VRYARNVIEE304 FRRAKHYKSP 314 SELLEICELS324 QEKMSSVFED334 SNVYMLHMMY344 QAMGVCLYMQ354 DWEGALQYGQ 364 KIIKPYSKHY374 PLYSLNVASM384 WLKLGRLYMG394 LEHKAAGEKA404 LKKAIAIMEV 414 AHGKDHPYIS424 EIKQEIESH
|
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .6TL or .6TL2 or .6TL3 or :36TL;style chemicals stick;color identity;select .A:105 or .A:108 or .A:141 or .A:145 or .A:148 or .A:149 or .A:177 or .A:179 or .A:180 or .A:181 or .A:182 or .A:183 or .A:184 or .A:185 or .A:196 or .A:203 or .A:217 or .A:239 or .A:240 or .A:256 or .A:257 or .A:258 or .A:259; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
THR105
4.166
LEU108
4.265
LEU141
4.039
LYS145
3.480
LEU148
4.037
ILE149
3.737
ALA177
4.410
VAL179
3.696
ASN180
2.935
CYS181
3.795
ASN182
3.508
GLY183
3.087
|
|||||
| Ligand Name: N-[1-({1-[(4-chlorophenyl)methyl]-1H-pyrazol-4-yl}methyl)azetidin-3-yl]-1-cyclopropyl-1H-1,2,3-triazole-4-carboxamide | Ligand Info | |||||
| Structure Description | Crystal structure of SMYD2 with SAM and EPZ033294 | PDB:5V3H | ||||
| Method | X-ray diffraction | Resolution | 2.69 Å | Mutation | No | [9] |
| PDB Sequence |
KDDDDKMRAE
4 GLGGLERFCS14 PGKGRGLRAL24 QPFQVGDLLF34 SCPAYAYVLT44 VNERGNHCEY 54 CFTRKEGLSK64 CGRCKQAFYC74 NVECQKEDWP84 MHKLECSPMV94 VFGENWNPSE 104 TVRLTARILA114 KQKIHPERTP124 SEKLLAVKEF134 ESHLDKLDNE144 KKDLIQSDIA 154 ALHHFYSKHL164 GFPDNDSLVV174 LFAQVNCNGF184 TIEDEELSHL194 GSAIFPDVAL 204 MNHSCCPNVI214 VTYKGTLAEV224 RAVQEIKPGE234 EVFTSYIDLL244 YPTEDRNDRL 254 RDSYFFTCEC264 QECTTKDKDK274 AKVEIRKLSD284 PPKAEAIRDM294 VRYARNVIEE 304 FRRAKHYKSP314 SELLEICELS324 QEKMSSVFED334 SNVYMLHMMY344 QAMGVCLYMQ 354 DWEGALQYGQ364 KIIKPYSKHY374 PLYSLNVASM384 WLKLGRLYMG394 LEHKAAGEKA 404 LKKAIAIMEV414 AHGKDHPYIS424 EIKQEIES
|
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .8WG or .8WG2 or .8WG3 or :38WG;style chemicals stick;color identity;select .A:104 or .A:105 or .A:108 or .A:179 or .A:180 or .A:181 or .A:182 or .A:183 or .A:184 or .A:185 or .A:187 or .A:188 or .A:189 or .A:191 or .A:196 or .A:215 or .A:216 or .A:217 or .A:239 or .A:240 or .A:241 or .A:242 or .A:245 or .A:253 or .A:258 or .A:341 or .A:379 or .A:382 or .A:383 or .A:386 or .A:412 or .A:416 or .A:422; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
GLU104
4.006
THR105
3.857
LEU108
3.578
VAL179
3.908
ASN180
3.798
CYS181
3.752
ASN182
4.411
GLY183
3.460
PHE184
3.391
THR185
3.108
GLU187
2.492
ASP188
3.329
GLU189
3.520
LEU191
3.936
SER196
3.606
VAL215
3.631
THR216
4.525
|
|||||
| References | Top | ||||
|---|---|---|---|---|---|
| REF 1 | Discovery and Characterization of a Highly Potent and Selective Aminopyrazoline-Based in Vivo Probe (BAY-598) for the Protein Lysine Methyltransferase SMYD2. J Med Chem. 2016 May 26;59(10):4578-600. | ||||
| REF 2 | Structural basis of substrate methylation and inhibition of SMYD2. Structure. 2011 Sep 7;19(9):1262-73. | ||||
| REF 3 | LLY-507, a Cell-active, Potent, and Selective Inhibitor of Protein-lysine Methyltransferase SMYD2. J Biol Chem. 2015 May 29;290(22):13641-53. | ||||
| REF 4 | Discovery of A-893, A New Cell-Active Benzoxazinone Inhibitor of Lysine Methyltransferase SMYD2. ACS Med Chem Lett. 2015 Apr 29;6(6):695-700. | ||||
| REF 5 | The crystal structure of SMYD2 in complex with compound MTF003 | ||||
| REF 6 | Crystal structure of human SET and MYND Domain Containing protein 2 with MTF1497 | ||||
| REF 7 | Crystal structure of human SET and MYND Domain Containing protein 2 with MTF9975 | ||||
| REF 8 | Design, Synthesis, and Biological Activity of Substrate Competitive SMYD2 Inhibitors. J Med Chem. 2016 Dec 22;59(24):11079-11097. | ||||
| REF 9 | Small molecule inhibitors and CRISPR/Cas9 mutagenesis demonstrate that SMYD2 and SMYD3 activity are dispensable for autonomous cancer cell proliferation. PLoS One. 2018 Jun 1;13(6):e0197372. | ||||
If You Find Any Error in Data or Bug in Web Service, Please Kindly Report It to Dr. Zhou and Dr. Zhang.