Target Binding Site Detail
| Target General Information | Top | ||||
|---|---|---|---|---|---|
| Target ID | T35792 | Target Info | |||
| Target Name | Histone-lysine N-methyltransferase SMYD3 (SMYD3) | ||||
| Synonyms | SET and MYND domain-containing protein 3; Zinc finger MYND domain-containing protein 1 | ||||
| Target Type | Preclinical Target | ||||
| Gene Name | SMYD3 | ||||
| UniProt ID | |||||
| Ligand General Information | Top | ||||
|---|---|---|---|---|---|
| Ligand Name | Ademetionine | Ligand Info | |||
| Canonical SMILES | C[S+](CCC(C(=O)[O-])N)CC1C(C(C(O1)N2C=NC3=C(N=CN=C32)N)O)O | ||||
| InChI | 1S/C15H22N6O5S/c1-27(3-2-7(16)15(24)25)4-8-10(22)11(23)14(26-8)21-6-20-9-12(17)18-5-19-13(9)21/h5-8,10-11,14,22-23H,2-4,16H2,1H3,(H2-,17,18,19,24,25)/t7-,8+,10+,11+,14+,27?/m0/s1 | ||||
| InChIKey | MEFKEPWMEQBLKI-AIRLBKTGSA-N | ||||
| PubChem Compound ID | 34755 | ||||
| Drug Binding Sites of Target | Top | |||||
|---|---|---|---|---|---|---|
| PDB ID: 5V37 Crystal structure of SMYD3 with SAM and EPZ028862 | ||||||
| Method | X-ray diffraction | Resolution | 1.42 Å | Mutation | No | [1] |
| PDB Sequence |
PLKVEKFATA
12 NRGNGLRAVT22 PLRPGELLFR32 SDPLAYTVCK42 GSRGVVCDRC52 LLGKEKLMRC 62 SQCRVAKYCS72 AKCQKKAWPD82 HKRECKCLKS92 CKPRYPPDSV102 RLLGRVVFKL 112 MDGAPSESEK122 LYSFYDLESN132 INKLTEDKKE142 GLRQLVMTFQ152 HFMREEIQDA 162 SQLPPAFDLF172 EAFAKVICNS182 FTICNAEMQE192 VGVGLYPSIS202 LLNHSCDPNC 212 SIVFNGPHLL222 LRAVRDIEVG232 EELTICYLDM242 LMTSEERRKQ252 LRDQYCFECD 262 CFRCQTQDKD272 ADMLTGDEQV282 WKEVQESLKK292 IEELKAHWKW302 EQVLAMCQAI 312 ISSNSERLPD322 INIYQLKVLD332 CAMDACINLG342 LLEEALFYGT352 RTMEPYRIFF 362 PGSHPVRGVQ372 VMKVGKLQLH382 QGMFPQAMKN392 LRLAFDIMRV402 THGREHSLIE 412 DLILLLEECD422 ANIR
|
|||||
|
|
ASN13
4.340
ARG14
2.688
GLY15
3.685
ASN16
2.776
TYR124
2.756
ASP128
4.817
LEU129
4.744
GLU130
3.596
ASN132
2.830
CYS180
3.532
ASN181
3.077
|
|||||
| PDB ID: 7O2C X-RAY STRUCTURE OF SMYD3 IN COMPLEX WITH the benzodiazepine-based probe BAY-6035 | ||||||
| Method | X-ray diffraction | Resolution | 1.52 Å | Mutation | Yes | [2] |
| PDB Sequence |
EPLKVEKFAT
11 ANRGNGLRAV21 TPLRPGELLF31 RSDPLAYTVC41 KGSRGVVCDR51 CLLGKEKLMR 61 CSQCRVAKYC71 SAKCQKKAWP81 DHKRECKCLK91 SCKPRYPPDS101 VRLLGRVVFK 111 LMDGAPSESE121 KLYSFYDLES131 NINKLTEDRK141 EGLRQLVMTF151 QHFMREEIQD 161 ASQLPPAFDL171 FEAFAKVICN181 SFTICNAEMQ191 EVGVGLYPSI201 SLLNHSCDPN 211 CSIVFNGPHL221 LLRAVRDIEV231 GEELTICYLD241 MLMTSEERRK251 QLRDQYCFEC 261 DCFRCQTQDK271 DADMLTGDEQ281 VWKEVQESLK291 KIEELKAHWK301 WEQVLAMCQA 311 IISSNSERLP321 DINIYQLKVL331 DCAMDACINL341 GLLEEALFYG351 TRTMEPYRIF 361 FPGSHPVRGV371 QVMKVGKLQL381 HQGMFPQAMK391 NLRLAFDIMR401 VTHGREHSLI 411 EDLILLLEEC421 DANIRAS
|
|||||
|
|
ASN13
4.406
ARG14
2.751
GLY15
3.726
ASN16
2.798
TYR124
2.620
ASP128
4.946
LEU129
4.784
GLU130
3.655
ASN132
2.946
CYS180
3.372
ASN181
3.108
|
|||||
| PDB ID: 7O2A X-RAY STRUCTURE OF SMYD3 IN COMPLEX WITH benzodiazepine-type inhibitor compound 15 | ||||||
| Method | X-ray diffraction | Resolution | 1.57 Å | Mutation | Yes | [2] |
| PDB Sequence |
EPLKVEKFAT
11 ANRGNGLRAV21 TPLRPGELLF31 RSDPLAYTVC41 KGSRGVVCDR51 CLLGKEKLMR 61 CSQCRVAKYC71 SAKCQKKAWP81 DHKRECKCLK91 SCKPRYPPDS101 VRLLGRVVFK 111 LMDGAPSESE121 KLYSFYDLES131 NINKLTEDRK141 EGLRQLVMTF151 QHFMREEIQD 161 ASQLPPAFDL171 FEAFAKVICN181 SFTICNAEMQ191 EVGVGLYPSI201 SLLNHSCDPN 211 CSIVFNGPHL221 LLRAVRDIEV231 GEELTICYLD241 MLMTSEERRK251 QLRDQYCFEC 261 DCFRCQTQDK271 DADMLTGDEQ281 VWKEVQESLK291 KIEELKAHWK301 WEQVLAMCQA 311 IISSNSERLP321 DINIYQLKVL331 DCAMDACINL341 GLLEEALFYG351 TRTMEPYRIF 361 FPGSHPVRGV371 QVMKVGKLQL381 HQGMFPQAMK391 NLRLAFDIMR401 VTHGREHSLI 411 EDLILLLEEC421 DANIRAS
|
|||||
|
|
ASN13
4.351
ARG14
2.705
GLY15
3.713
ASN16
2.807
TYR124
2.658
ASP128
4.949
LEU129
4.824
GLU130
3.607
ASN132
2.928
CYS180
3.456
ASN181
3.167
|
|||||
| PDB ID: 7O2B X-RAY STRUCTURE OF SMYD3 in complex with benzodiazepine-type inhibitor 6 | ||||||
| Method | X-ray diffraction | Resolution | 2.03 Å | Mutation | Yes | [2] |
| PDB Sequence |
EPLKVEKFAT
11 ANRGNGLRAV21 TPLRPGELLF31 RSDPLAYTVC41 KGSRGVVCDR51 CLLGKEKLMR 61 CSQCRVAKYC71 SAKCQKKAWP81 DHKRECKCLK91 SCKPRYPPDS101 VRLLGRVVFK 111 LMDGAPSESE121 KLYSFYDLES131 NINKLTEDRK141 EGLRQLVMTF151 QHFMREEIQD 161 ASQLPPAFDL171 FEAFAKVICN181 SFTICNAEMQ191 EVGVGLYPSI201 SLLNHSCDPN 211 CSIVFNGPHL221 LLRAVRDIEV231 GEELTICYLD241 MLMTSEERRK251 QLRDQYCFEC 261 DCFRCQTQDK271 DADMLTGDEQ281 VWKEVQESLK291 KIEELKAHWK301 WEQVLAMCQA 311 IISSNSERLP321 DINIYQLKVL331 DCAMDACINL341 GLLEEALFYG351 TRTMEPYRIF 361 FPGSHPVRGV371 QVMKVGKLQL381 HQGMFPQAMK391 NLRLAFDIMR401 VTHGREHSLI 411 EDLILLLEEC421 DANIRAS
|
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .SAM or .SAM2 or .SAM3 or :3SAM;style chemicals stick;color identity;select .A:13 or .A:14 or .A:15 or .A:16 or .A:124 or .A:128 or .A:129 or .A:130 or .A:132 or .A:180 or .A:181 or .A:202 or .A:203 or .A:204 or .A:205 or .A:206 or .A:239 or .A:256 or .A:257 or .A:258 or .A:259 or .A:260; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
ASN13
4.356
ARG14
2.872
GLY15
3.824
ASN16
2.873
TYR124
2.528
ASP128
4.804
LEU129
4.742
GLU130
3.577
ASN132
3.010
CYS180
3.647
ASN181
3.195
|
|||||
| PDB ID: 5CCM Crystal structure of SMYD3 with SAM and EPZ030456 | ||||||
| Method | X-ray diffraction | Resolution | 2.30 Å | Mutation | No | [3] |
| PDB Sequence |
PLKVEKFATA
12 NRGNGLRAVT22 PLRPGELLFR32 SDPLAYTVCK42 GSRGVVCDRC52 LLGKEKLMRC 62 SQCRVAKYCS72 AKCQKKAWPD82 HKRECKCLKS92 CKPRYPPDSV102 RLLGRVVFKL 112 MDGAPSESEK122 LYSFYDLESN132 INKLTEDKKE142 GLRQLVMTFQ152 HFMREEIQDA 162 SQLPPAFDLF172 EAFAKVICNS182 FTICNAEMQE192 VGVGLYPSIS202 LLNHSCDPNC 212 SIVFNGPHLL222 LRAVRDIEVG232 EELTICYLDM242 LMTSEERRKQ252 LRDQYCFECD 262 CFRCQTQDKD272 ADMLTGDEQV282 WKEVQESLKK292 IEELKAHWKW302 EQVLAMCQAI 312 ISSNSERLPD322 INIYQLKVLD332 CAMDACINLG342 LLEEALFYGT352 RTMEPYRIFF 362 PGSHPVRGVQ372 VMKVGKLQLH382 QGMFPQAMKN392 LRLAFDIMRV402 THGREHSLIE 412 DLILLLEECD422 ANI
|
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .SAM or .SAM2 or .SAM3 or :3SAM;style chemicals stick;color identity;select .A:13 or .A:14 or .A:15 or .A:16 or .A:124 or .A:128 or .A:129 or .A:130 or .A:132 or .A:180 or .A:181 or .A:202 or .A:203 or .A:204 or .A:205 or .A:206 or .A:239 or .A:257 or .A:258 or .A:259 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
|
ASN13
4.577
ARG14
2.863
GLY15
3.604
ASN16
2.747
TYR124
2.706
ASP128
4.766
LEU129
4.816
GLU130
3.815
ASN132
2.819
CYS180
3.783
ASN181
3.216
SER202
3.010
|
|||||
| PDB ID: 6IJL Crystal structure of SmyD3 in complex with covalent inhibitor 5 | ||||||
| Method | X-ray diffraction | Resolution | 2.35 Å | Mutation | Yes | [4] |
| PDB Sequence |
PLKVEKFATA
12 NRGNGLRAVT22 PLRPGELLFR32 SDPLAYTVCK42 GSRGVVCDRC52 LLGKEKLMRC 62 SQCRVAKYCS72 AKCQKKAWPD82 HKRECKCLKS92 CKPRYPPDSV102 RLLGRVVFKL 112 MDGAPSESEK122 LYSFYDLESN132 INKLTEDRKE142 GLRQLVMTFQ152 HFMREEIQDA 162 SQLPPAFDLF172 EAFAKVICNS182 FTICNAEMQE192 VGVGLYPSIS202 LLNHSCDPNC 212 SIVFNGPHLL222 LRAVRDIEVG232 EELTICYLDM242 LMTSEERRKQ252 LRDQYCFECD 262 CFRCQTQDKD272 ADMLTGDEQV282 WKEVQESLKK292 IEELKAHWKW302 EQVLAMCQAI 312 ISSNSERLPD322 INIYQLKVLD332 CAMDACINLG342 LLEEALFYGT352 RTMEPYRIFF 362 PGSHPVRGVQ372 VMKVGKLQLH382 QGMFPQAMKN392 LRLAFDIMRV402 THGREHSLIE 412 DLILLLEECD422 ANI
|
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .SAM or .SAM2 or .SAM3 or :3SAM;style chemicals stick;color identity;select .A:13 or .A:14 or .A:15 or .A:16 or .A:17 or .A:124 or .A:128 or .A:129 or .A:130 or .A:132 or .A:180 or .A:181 or .A:202 or .A:203 or .A:204 or .A:205 or .A:206 or .A:207 or .A:239 or .A:257 or .A:258 or .A:259 or .A:260; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
ASN13
4.362
ARG14
2.653
GLY15
3.344
ASN16
2.465
GLY17
4.459
TYR124
3.107
ASP128
4.903
LEU129
4.802
GLU130
3.450
ASN132
2.316
CYS180
3.407
ASN181
3.055
|
|||||
| PDB ID: 3QWP Crystal structure of SET and MYND domain containing 3; Zinc finger MYND domain-containing protein 1 | ||||||
| Method | X-ray diffraction | Resolution | 1.53 Å | Mutation | No | [5] |
| PDB Sequence |
PLKVEKFATA
12 NRGNGLRAVT22 PLRPGELLFR32 SDPLAYTVCK42 GSRGVVCDRC52 LLGKEKLMRC 62 SQCRVAKYCS72 AKCQKKAWPD82 HKRECKCLKS92 CKPRYPPDSV102 RLLGRVVFKL 112 MDGAPSESEK122 LYSFYDLESN132 INKLTEDRKE142 GLRQLVMTFQ152 HFMREEIQDA 162 SQLPPAFDLF172 EAFAKVICNS182 FTICNAEMQE192 VGVGLYPSIS202 LLNHSCDPNC 212 SIVFNGPHLL222 LRAVRDIEVG232 EELTICYLDM242 LMTSEERRKQ252 LRDQYCFECD 262 CFRCQTQDKD272 ADMLTGDEQV282 WKEVQESLKK292 IEELKAHWKW302 EQVLAMCQAI 312 ISSNSERLPD322 INIYQLKVLD332 CAMDACINLG342 LLEEALFYGT352 RTMEPYRIFF 362 PGSHPVRGVQ372 VMKVGKLQLH382 QGMFPQAMKN392 LRLAFDIMRV402 THGREHSLIE 412 DLILLLEECD422 ANIRA
|
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .SAM or .SAM2 or .SAM3 or :3SAM;style chemicals stick;color identity;select .A:13 or .A:14 or .A:15 or .A:16 or .A:124 or .A:128 or .A:129 or .A:130 or .A:132 or .A:180 or .A:181 or .A:202 or .A:203 or .A:204 or .A:205 or .A:206 or .A:239 or .A:257 or .A:258 or .A:259 or .A:260 or .A:261; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
ASN13
4.626
ARG14
2.722
GLY15
3.737
ASN16
2.813
TYR124
2.623
ASP128
4.765
LEU129
4.809
GLU130
3.654
ASN132
2.891
CYS180
3.785
ASN181
3.247
|
|||||
| PDB ID: 3MEK Crystal Structure of Human Histone-Lysine N-methyltransferase SMYD3 in Complex with S-adenosyl-L-methionine | ||||||
| Method | X-ray diffraction | Resolution | 2.10 Å | Mutation | No | [6] |
| PDB Sequence |
PLKVEKFATA
12 NRGNGLRAVT22 PLRPGELLFR32 SDPLAYTVCK42 GSRGVVCDRC52 LLGKEKLRCS 63 QCRVAKYCSA73 KCQKKAWPDH83 KRECKCLKSC93 KPRYPPDSVR103 LLGRVVFKLD 114 GAPSESEKLY124 SFYDLESNIN134 KLTEDRKEGL144 RQLVTFQHFR156 EEIQDASQLP 166 PAFDLFEAFA176 KVICNSFTIC186 NAEQEVGVGL197 YPSISLLNHS207 CDPNCSIVFN 217 GPHLLLRAVR227 DIEVGEELTI237 CYLDLTSEER249 RKQLRDQYCF259 ECDCFRCQTQ 269 DKDADLTGDE280 QVWKEVQESL290 KKIEELKAHW300 KWEQVLACQA311 IISSNSERLP 321 DINIYQLKVL331 DCADACINLG342 LLEEALFYGT352 RTEPYRIFFP363 GSHPVRGVQV 373 KVGKLQLHQG384 FPQAKNLRLA396 FDIRVTHGRE407 HSLIEDLILL417 LEECDANI |
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .SAM or .SAM2 or .SAM3 or :3SAM;style chemicals stick;color identity;select .A:13 or .A:14 or .A:15 or .A:16 or .A:124 or .A:128 or .A:129 or .A:130 or .A:132 or .A:180 or .A:181 or .A:202 or .A:203 or .A:204 or .A:205 or .A:206 or .A:239 or .A:257 or .A:258 or .A:259 or .A:260; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
ASN13
4.507
ARG14
2.696
GLY15
3.709
ASN16
2.784
TYR124
2.716
ASP128
4.754
LEU129
4.777
GLU130
3.585
ASN132
2.882
CYS180
3.879
ASN181
3.366
|
|||||
| PDB ID: 6ZRB Crystal structure of SMYD3 conjugate with piperidine-based covalent inhibitor EM127 | ||||||
| Method | X-ray diffraction | Resolution | 1.55 Å | Mutation | Yes | [7] |
| PDB Sequence |
PLKVEKFATA
12 NRGNGLRAVT22 PLRPGELLFR32 SDPLAYTVCK42 GSRGVVCDRC52 LLGKEKLMRC 62 SQCRVAKYCS72 AKCQKKAWPD82 HKRECKCLKS92 CKPRYPPDSV102 RLLGRVVFKL 112 MDGAPSESEK122 LYSFYDLESN132 INKLTEDRKE142 GLRQLVMTFQ152 HFMREEIQDA 162 SQLPPAFDLF172 EAFAKVICNS182 FTICNAEMQE192 VGVGLYPSIS202 LLNHSCDPNC 212 SIVFNGPHLL222 LRAVRDIEVG232 EELTICYLDM242 LMTSEERRKQ252 LRDQYCFECD 262 CFRCQTQDKD272 ADMLTGDEQV282 WKEVQESLKK292 IEELKAHWKW302 EQVLAMCQAI 312 ISSNSERLPD322 INIYQLKVLD332 CAMDACINLG342 LLEEALFYGT352 RTMEPYRIFF 362 PGSHPVRGVQ372 VMKVGKLQLH382 QGMFPQAMKN392 LRLAFDIMRV402 THGREHSLIE 412 DLILLLEECD422 ANIRA
|
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .SAM or .SAM2 or .SAM3 or :3SAM;style chemicals stick;color identity;select .A:13 or .A:14 or .A:15 or .A:16 or .A:124 or .A:128 or .A:129 or .A:130 or .A:132 or .A:180 or .A:181 or .A:202 or .A:203 or .A:204 or .A:205 or .A:206 or .A:239 or .A:257 or .A:258 or .A:259 or .A:260 or .A:261; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
ASN13
4.517
ARG14
2.689
GLY15
3.716
ASN16
2.791
TYR124
2.709
ASP128
4.864
LEU129
4.822
GLU130
3.649
ASN132
2.903
CYS180
3.558
ASN181
3.241
|
|||||
| PDB ID: 7BJ1 Crystal structure of SMYD3 with diperodon S enantiomer bound to allosteric site | ||||||
| Method | X-ray diffraction | Resolution | 1.61 Å | Mutation | Yes | [8] |
| PDB Sequence |
PLKVEKFATA
12 NRGNGLRAVT22 PLRPGELLFR32 SDPLAYTVCK42 GSRGVVCDRC52 LLGKEKLMRC 62 SQCRVAKYCS72 AKCQKKAWPD82 HKRECKCLKS92 CKPRYPPDSV102 RLLGRVVFKL 112 MDGAPSESEK122 LYSFYDLESN132 INKLTEDRKE142 GLRQLVMTFQ152 HFMREEIQDA 162 SQLPPAFDLF172 EAFAKVICNS182 FTICNAEMQE192 VGVGLYPSIS202 LLNHSCDPNC 212 SIVFNGPHLL222 LRAVRDIEVG232 EELTICYLDM242 LMTSEERRKQ252 LRDQYCFECD 262 CFRCQTQDKD272 ADMLTGDEQV282 WKEVQESLKK292 IEELKAHWKW302 EQVLAMCQAI 312 ISSNSERLPD322 INIYQLKVLD332 CAMDACINLG342 LLEEALFYGT352 RTMEPYRIFF 362 PGSHPVRGVQ372 VMKVGKLQLH382 QGMFPQAMKN392 LRLAFDIMRV402 THGREHSLIE 412 DLILLLEECD422 ANIRAS
|
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .SAM or .SAM2 or .SAM3 or :3SAM;style chemicals stick;color identity;select .A:13 or .A:14 or .A:15 or .A:16 or .A:124 or .A:128 or .A:129 or .A:130 or .A:132 or .A:180 or .A:181 or .A:202 or .A:203 or .A:204 or .A:205 or .A:206 or .A:239 or .A:257 or .A:258 or .A:259 or .A:260 or .A:261; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
ASN13
4.553
ARG14
2.692
GLY15
3.774
ASN16
2.832
TYR124
2.676
ASP128
4.838
LEU129
4.806
GLU130
3.634
ASN132
2.895
CYS180
3.781
ASN181
3.348
|
|||||
| PDB ID: 6YUH Crystal structure of SMYD3 with diperodon R enantiomer bound to allosteric site | ||||||
| Method | X-ray diffraction | Resolution | 1.93 Å | Mutation | No | [9] |
| PDB Sequence |
PLKVEKFATA
12 NRGNGLRAVT22 PLRPGELLFR32 SDPLAYTVCK42 GSRGVVCDRC52 LLGKEKLMRC 62 SQCRVAKYCS72 AKCQKKAWPD82 HKRECKCLKS92 CKPRYPPDSV102 RLLGRVVFKL 112 MDGAPSESEK122 LYSFYDLESN132 INKLTEDRKE142 GLRQLVMTFQ152 HFMREEIQDA 162 SQLPPAFDLF172 EAFAKVICNS182 FTICNAEMQE192 VGVGLYPSIS202 LLNHSCDPNC 212 SIVFNGPHLL222 LRAVRDIEVG232 EELTICYLDM242 LMTSEERRKQ252 LRDQYCFECD 262 CFRCQTQDKD272 ADMLTGDEQV282 WKEVQESLKK292 IEELKAHWKW302 EQVLAMCQAI 312 ISSNSERLPD322 INIYQLKVLD332 CAMDACINLG342 LLEEALFYGT352 RTMEPYRIFF 362 PGSHPVRGVQ372 VMKVGKLQLH382 QGMFPQAMKN392 LRLAFDIMRV402 THGREHSLIE 412 DLILLLEECD422 ANIRA
|
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .SAM or .SAM2 or .SAM3 or :3SAM;style chemicals stick;color identity;select .A:13 or .A:14 or .A:15 or .A:16 or .A:17 or .A:124 or .A:128 or .A:129 or .A:130 or .A:132 or .A:180 or .A:181 or .A:202 or .A:203 or .A:204 or .A:205 or .A:206 or .A:207 or .A:239 or .A:257 or .A:258 or .A:259 or .A:260 or .A:261; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
ASN13
4.584
ARG14
2.669
GLY15
3.661
ASN16
2.707
GLY17
4.954
TYR124
2.756
ASP128
4.897
LEU129
4.839
GLU130
3.741
ASN132
2.963
CYS180
3.729
ASN181
3.273
|
|||||
| PDB ID: 6P7Z Co-crystal Structure of human SMYD3 with Isoxazole Amides Inhibitors | ||||||
| Method | X-ray diffraction | Resolution | 1.19 Å | Mutation | No | [10] |
| PDB Sequence |
PLKVEKFATA
12 NRGNGLRAVT22 PLRPGELLFR32 SDPLAYTVCK42 GSRGVVCDRC52 LLGKEKLMRC 62 SQCRVAKYCS72 AKCQKKAWPD82 HKRECKCLKS92 CPRYPPDSVR103 LLGRVVFKLM 113 DGAPSESEKL123 YSFYDLESNI133 NKLTEDKKEG143 LRQLVMTFQH153 FMREEIQDAS 163 QLPPAFDLFE173 AFAKVICNSF183 TICNAEMQEV193 GVGLYPSISL203 LNHSCDPNCS 213 IVFNGPHLLL223 RAVRDIEVGE233 ELTICYLDML243 MTSEERRKQL253 RDQYCFECDC 263 FRCQTQDKDA273 DMLTGDEQVW283 KEVQESLKKI293 EELKAHWKWE303 QVLAMCQAII 313 SSNSERLPDI323 NIYQLKVLDC333 AMDACINLGL343 LEEALFYGTR353 TMEPYRIFFP 363 GSHPVRGVQV373 MKVGKLQLHQ383 GMFPQAMKNL393 RLAFDIMRVT403 HGREHSLIED 413 LILLLEECDA423 NIRAS
|
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .SAM or .SAM2 or .SAM3 or :3SAM;style chemicals stick;color identity;select .A:13 or .A:14 or .A:15 or .A:16 or .A:124 or .A:128 or .A:129 or .A:130 or .A:132 or .A:180 or .A:181 or .A:202 or .A:203 or .A:204 or .A:205 or .A:206 or .A:239 or .A:257 or .A:258 or .A:259 or .A:260 or .A:261; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
ASN13
4.419
ARG14
2.652
GLY15
3.715
ASN16
2.798
TYR124
2.647
ASP128
4.871
LEU129
4.743
GLU130
3.654
ASN132
2.897
CYS180
3.735
ASN181
3.259
|
|||||
| PDB ID: 6PAF Co-crystal Structure of human SMYD3 with Isoxazole Amides Inhibitors | ||||||
| Method | X-ray diffraction | Resolution | 1.24 Å | Mutation | No | [10] |
| PDB Sequence |
PLKVEKFATA
12 NRGNGLRAVT22 PLRPGELLFR32 SDPLAYTVCK42 GSRGVVCDRC52 LLGKKLMRCS 63 QCRVAKYCSA73 KCQKKAWPDH83 KRECKCLKSC93 RYPPDSVRLL105 GRVVFKLMDG 115 APSESEKLYS125 FYDLESNINK135 LTEDKKEGLR145 QLVMTFQHFM155 REEIQDASQL 165 PPAFDLFEAF175 AKVICNSFTI185 CNAEMQEVGV195 GLYPSISLLN205 HSCDPNCSIV 215 FNGPHLLLRA225 VRDIEVGEEL235 TICYLDMLMT245 SEERRKQLRD255 QYCFECDCFR 265 CQTQDKDADM275 LTGDEQVWKE285 VQESLKKIEE295 LKAHWKWEQV305 LAMCQAIISS 315 NSERLPDINI325 YQLKVLDCAM335 DACINLGLLE345 EALFYGTRTM355 EPYRIFFPGS 365 HPVRGVQVMK375 VGKLQLHQGM385 FPQAMKNLRL395 AFDIMRVTHG405 REHSLIEDLI 415 LLLEECDANI425 RAS
|
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .SAM or .SAM2 or .SAM3 or :3SAM;style chemicals stick;color identity;select .A:13 or .A:14 or .A:15 or .A:16 or .A:124 or .A:128 or .A:129 or .A:130 or .A:132 or .A:180 or .A:181 or .A:202 or .A:203 or .A:204 or .A:205 or .A:206 or .A:239 or .A:257 or .A:258 or .A:259 or .A:260 or .A:261; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
ASN13
4.445
ARG14
2.687
GLY15
3.666
ASN16
2.762
TYR124
2.679
ASP128
4.960
LEU129
4.750
GLU130
3.601
ASN132
2.946
CYS180
3.493
ASN181
3.234
|
|||||
| PDB ID: 5CCL Crystal structure of SMYD3 with SAM and oxindole compound | ||||||
| Method | X-ray diffraction | Resolution | 1.50 Å | Mutation | No | [3] |
| PDB Sequence |
PLKVEKFATA
12 NRGNGLRAVT22 PLRPGELLFR32 SDPLAYTVCK42 GSRGVVCDRC52 LLGKEKLMRC 62 SQCRVAKYCS72 AKCQKKAWPD82 HKRECKCLKS92 CKPRYPPDSV102 RLLGRVVFKL 112 MDGAPSESEK122 LYSFYDLESN132 INKLTEDKKE142 GLRQLVMTFQ152 HFMREEIQDA 162 SQLPPAFDLF172 EAFAKVICNS182 FTICNAEMQE192 VGVGLYPSIS202 LLNHSCDPNC 212 SIVFNGPHLL222 LRAVRDIEVG232 EELTICYLDM242 LMTSEERRKQ252 LRDQYCFECD 262 CFRCQTQDKD272 ADMLTGDEQV282 WKEVQESLKK292 IEELKAHWKW302 EQVLAMCQAI 312 ISSNSERLPD322 INIYQLKVLD332 CAMDACINLG342 LLEEALFYGT352 RTMEPYRIFF 362 PGSHPVRGVQ372 VMKVGKLQLH382 QGMFPQAMKN392 LRLAFDIMRV402 THGREHSLIE 412 DLILLLEECD422 ANIRA
|
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .SAM or .SAM2 or .SAM3 or :3SAM;style chemicals stick;color identity;select .A:13 or .A:14 or .A:15 or .A:16 or .A:17 or .A:124 or .A:128 or .A:129 or .A:130 or .A:132 or .A:180 or .A:181 or .A:202 or .A:203 or .A:204 or .A:205 or .A:206 or .A:239 or .A:257 or .A:258 or .A:259 or .A:260 or .A:261; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
ASN13
4.801
ARG14
2.711
GLY15
3.680
ASN16
2.743
GLY17
4.999
TYR124
2.678
ASP128
4.688
LEU129
4.782
GLU130
3.637
ASN132
2.938
CYS180
3.567
ASN181
3.178
|
|||||
| PDB ID: 6P6K Co-crystal Structure of human SMYD3 with Isoxazole Amides Inhibitors | ||||||
| Method | X-ray diffraction | Resolution | 1.55 Å | Mutation | No | [10] |
| PDB Sequence |
PLKVEKFATA
12 NRGNGLRAVT22 PLRPGELLFR32 SDPLAYTVCK42 GSRGVVCDRC52 LLGKKLMRCS 63 QCRVAKYCSA73 KCQKKAWPDH83 KRECKCLKSC93 PRYPPDSVRL104 LGRVVFKLMD 114 GAPSESEKLY124 SFYDLESNIN134 KLTEDKKEGL144 RQLVMTFQHF154 MREEIQDASQ 164 LPPAFDLFEA174 FAKVICNSFT184 ICNAEMQEVG194 VGLYPSISLL204 NHSCDPNCSI 214 VFNGPHLLLR224 AVRDIEVGEE234 LTICYLDMLM244 TSEERRKQLR254 DQYCFECDCF 264 RCQTQDKDAD274 MLTGDEQVWK284 EVQESLKKIE294 ELKAHWKWEQ304 VLAMCQAIIS 314 SNSERLPDIN324 IYQLKVLDCA334 MDACINLGLL344 EEALFYGTRT354 MEPYRIFFPG 364 SHPVRGVQVM374 KVGKLQLHQG384 MFPQAMKNLR394 LAFDIMRVTH404 GREHSLIEDL 414 ILLLEECDAN424 IRAS
|
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .SAM or .SAM2 or .SAM3 or :3SAM;style chemicals stick;color identity;select .A:13 or .A:14 or .A:15 or .A:16 or .A:124 or .A:129 or .A:130 or .A:132 or .A:180 or .A:181 or .A:202 or .A:203 or .A:204 or .A:205 or .A:206 or .A:239 or .A:257 or .A:258 or .A:259 or .A:260; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
||||||
| PDB ID: 5XXJ Crystal structure of SmyD3 in complex with covalent inhibitor 3 | ||||||
| Method | X-ray diffraction | Resolution | 1.69 Å | Mutation | No | [11] |
| PDB Sequence |
PLKVEKFATA
12 NRGNGLRAVT22 PLRPGELLFR32 SDPLAYTVCK42 GSRGVVCDRC52 LLGKEKLMRC 62 SQCRVAKYCS72 AKCQKKAWPD82 HKRECKCLKS92 CKPRYPPDSV102 RLLGRVVFKL 112 MDGAPSESEK122 LYSFYDLESN132 INKLTEDRKE142 GLRQLVMTFQ152 HFMREEIQDA 162 SQLPPAFDLF172 EAFAKVICNS182 FTICNAEMQE192 VGVGLYPSIS202 LLNHSCDPNC 212 SIVFNGPHLL222 LRAVRDIEVG232 EELTICYLDM242 LMTSEERRKQ252 LRDQYCFECD 262 CFRCQTQDKD272 ADMLTGDEQV282 WKEVQESLKK292 IEELKAHWKW302 EQVLAMCQAI 312 ISSNSERLPD322 INIYQLKVLD332 CAMDACINLG342 LLEEALFYGT352 RTMEPYRIFF 362 PGSHPVRGVQ372 VMKVGKLQLH382 QGMFPQAMKN392 LRLAFDIMRV402 THGREHSLIE 412 DLILLLEECD422 ANI
|
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .SAM or .SAM2 or .SAM3 or :3SAM;style chemicals stick;color identity;select .A:13 or .A:14 or .A:15 or .A:16 or .A:124 or .A:128 or .A:129 or .A:130 or .A:132 or .A:180 or .A:181 or .A:202 or .A:203 or .A:204 or .A:205 or .A:206 or .A:207 or .A:239 or .A:257 or .A:258 or .A:259 or .A:260; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
ASN13
4.555
ARG14
2.778
GLY15
3.747
ASN16
2.823
TYR124
2.686
ASP128
4.859
LEU129
4.839
GLU130
3.622
ASN132
2.837
CYS180
3.631
ASN181
3.275
|
|||||
| PDB ID: 5YJO Crystal structure of SmyD3 in complex with covalent inhibitor 4 | ||||||
| Method | X-ray diffraction | Resolution | 2.13 Å | Mutation | Yes | [4] |
| PDB Sequence |
PLKVEKFATA
12 NRGNGLRAVT22 PLRPGELLFR32 SDPLAYTVCK42 GSRGVVCDRC52 LLGKEKLMRC 62 SQCRVAKYCS72 AKCQKKAWPD82 HKRECKCLKS92 CKPRYPPDSV102 RLLGRVVFKL 112 MDGAPSESEK122 LYSFYDLESN132 INKLTEDRKE142 GLRQLVMTFQ152 HFMREEIQDA 162 SQLPPAFDLF172 EAFAKVICNS182 FTICNAEMQE192 VGVGLYPSIS202 LLNHSCDPNC 212 SIVFNGPHLL222 LRAVRDIEVG232 EELTICYLDM242 LMTSEERRKQ252 LRDQYCFECD 262 CFRCQTQDKD272 ADMLTGDEQV282 WKEVQESLKK292 IEELKAHWKW302 EQVLAMCQAI 312 ISSNSERLPD322 INIYQLKVLD332 CAMDACINLG342 LLEEALFYGT352 RTMEPYRIFF 362 PGSHPVRGVQ372 VMKVGKLQLH382 QGMFPQAMKN392 LRLAFDIMRV402 THGREHSLIE 412 DLILLLEECD422 ANI
|
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .SAM or .SAM2 or .SAM3 or :3SAM;style chemicals stick;color identity;select .A:13 or .A:14 or .A:15 or .A:16 or .A:124 or .A:128 or .A:129 or .A:130 or .A:132 or .A:180 or .A:181 or .A:202 or .A:203 or .A:204 or .A:205 or .A:206 or .A:239 or .A:257 or .A:258 or .A:259 or .A:260; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
ASN13
4.275
ARG14
2.574
GLY15
3.766
ASN16
2.787
TYR124
3.048
ASP128
4.844
LEU129
4.812
GLU130
3.644
ASN132
2.604
CYS180
3.570
ASN181
3.344
|
|||||
| PDB ID: 5XXG Crystal structure of SmyD3 in complex with covalent inhibitor 2 | ||||||
| Method | X-ray diffraction | Resolution | 2.14 Å | Mutation | No | [12] |
| PDB Sequence |
PLKVEKFATA
12 NRGNGLRAVT22 PLRPGELLFR32 SDPLAYTVCK42 GSRGVVCDRC52 LLGKEKLMRC 62 SQCRVAKYCS72 AKCQKKAWPD82 HKRECKCLKS92 CKPRYPPDSV102 RLLGRVVFKL 112 MDGAPSESEK122 LYSFYDLESN132 INKLTEDRKE142 GLRQLVMTFQ152 HFMREEIQDA 162 SQLPPAFDLF172 EAFAKVICNS182 FTICNAEMQE192 VGVGLYPSIS202 LLNHSCDPNC 212 SIVFNGPHLL222 LRAVRDIEVG232 EELTICYLDM242 LMTSEERRKQ252 LRDQYCFECD 262 CFRCQTQDKD272 ADMLTGDEQV282 WKEVQESLKK292 IEELKAHWKW302 EQVLAMCQAI 312 ISSNSERLPD322 INIYQLKVLD332 CAMDACINLG342 LLEEALFYGT352 RTMEPYRIFF 362 PGSHPVRGVQ372 VMKVGKLQLH382 QGMFPQAMKN392 LRLAFDIMRV402 THGREHSLIE 412 DLILLLEECD422 ANI
|
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .SAM or .SAM2 or .SAM3 or :3SAM;style chemicals stick;color identity;select .A:13 or .A:14 or .A:15 or .A:16 or .A:124 or .A:128 or .A:129 or .A:130 or .A:132 or .A:180 or .A:181 or .A:202 or .A:203 or .A:204 or .A:205 or .A:206 or .A:207 or .A:239 or .A:257 or .A:258 or .A:259 or .A:260; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
ASN13
4.454
ARG14
2.680
GLY15
3.868
ASN16
2.759
TYR124
2.750
ASP128
4.911
LEU129
4.815
GLU130
3.693
ASN132
2.830
CYS180
3.674
ASN181
3.207
|
|||||
| PDB ID: 5XXD Crystal structure of SmyD3 in complex with covalent inhibitor 1 | ||||||
| Method | X-ray diffraction | Resolution | 2.31 Å | Mutation | No | [13] |
| PDB Sequence |
PLKVEKFATA
12 NRGNGLRAVT22 PLRPGELLFR32 SDPLAYTVCK42 GSRGVVCDRC52 LLGKEKLMRC 62 SQCRVAKYCS72 AKCQKKAWPD82 HKRECKCLKS92 CKPRYPPDSV102 RLLGRVVFKL 112 MDGAPSESEK122 LYSFYDLESN132 INKLTEDRKE142 GLRQLVMTFQ152 HFMREEIQDA 162 SQLPPAFDLF172 EAFAKVICNS182 FTICNAEMQE192 VGVGLYPSIS202 LLNHSCDPNC 212 SIVFNGPHLL222 LRAVRDIEVG232 EELTICYLDM242 LMTSEERRKQ252 LRDQYCFECD 262 CFRCQTQDKD272 ADMLTGDEQV282 WKEVQESLKK292 IEELKAHWKW302 EQVLAMCQAI 312 ISSNSERLPD322 INIYQLKVLD332 CAMDACINLG342 LLEEALFYGT352 RTMEPYRIFF 362 PGSHPVRGVQ372 VMKVGKLQLH382 QGMFPQAMKN392 LRLAFDIMRV402 THGREHSLIE 412 DLILLLEECD422 ANI
|
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .SAM or .SAM2 or .SAM3 or :3SAM;style chemicals stick;color identity;select .A:13 or .A:14 or .A:15 or .A:16 or .A:124 or .A:128 or .A:129 or .A:130 or .A:132 or .A:180 or .A:181 or .A:202 or .A:203 or .A:204 or .A:205 or .A:206 or .A:207 or .A:239 or .A:257 or .A:258 or .A:259 or .A:260; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
ASN13
4.681
ARG14
2.650
GLY15
3.789
ASN16
2.759
TYR124
3.023
ASP128
4.852
LEU129
4.836
GLU130
3.628
ASN132
2.475
CYS180
3.504
ASN181
3.259
|
|||||
| References | Top | ||||
|---|---|---|---|---|---|
| REF 1 | 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. | ||||
| REF 2 | Discovery of the SMYD3 Inhibitor BAY-6035 Using Thermal Shift Assay (TSA)-Based High-Throughput Screening. SLAS Discov. 2021 Sep;26(8):947-960. | ||||
| REF 3 | Novel Oxindole Sulfonamides and Sulfamides: EPZ031686, the First Orally Bioavailable Small Molecule SMYD3 Inhibitor. ACS Med Chem Lett. 2015 Aug 27;7(2):134-8. | ||||
| REF 4 | Discovery of Irreversible Inhibitors Targeting Histone Methyltransferase, SMYD3. ACS Med Chem Lett. 2019 May 23;10(6):978-984. | ||||
| REF 5 | The Crystal Structure of human Histone-lysine N-methyltransferase SMYD3 | ||||
| REF 6 | Crystal Structure of Human Histone-Lysine N-methyltransferase SMYD3 in Complex with S-adenosyl-L-methionine | ||||
| REF 7 | Discovery of the 4-aminopiperidine-based compound EM127 for the site-specific covalent inhibition of SMYD3. doi:10.1016/j.ejmech.2022.114683. | ||||
| REF 8 | Discovery of an Allosteric Ligand Binding Site in SMYD3 Lysine Methyltransferase. doi:10.1002/cbic.202000736. | ||||
| REF 9 | Discovery of an Allosteric Ligand Binding Site in SMYD3 Lysine Methyltransferase. Chembiochem. 2021 May 4;22(9):1597-1608. | ||||
| REF 10 | Discovery of Isoxazole Amides as Potent and Selective SMYD3 Inhibitors. ACS Med Chem Lett. 2019 Dec 27;11(2):133-140. | ||||
| REF 11 | Crystal structure of SmyD3 in complex with covalent inhibitor 3 | ||||
| REF 12 | Crystal structure of SmyD3 in complex with covalent inhibitor 2 | ||||
| REF 13 | Crystal structure of SmyD3 in complex with covalent inhibitor 1 | ||||
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