Binding Site Information of Target
| 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 | |||||
| Drug Binding Sites of Target | Top | |||||
|---|---|---|---|---|---|---|
| Ligand Name: Ademetionine | Ligand Info | |||||
| Structure Description | Co-crystal Structure of human SMYD3 with Isoxazole Amides Inhibitors | PDB:6P7Z | ||||
| Method | X-ray diffraction | Resolution | 1.19 Å | Mutation | No | [1] |
| 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
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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
|
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| Click to View More Binding Site Information of This Target and Ligand Pair | ||||||
| Ligand Name: GSK2807 | Ligand Info | |||||
| Structure Description | Co-crystal structure of human SMYD3 with an aza-SAH compound | PDB:5HI7 | ||||
| Method | X-ray diffraction | Resolution | 2.15 Å | Mutation | No | [2] |
| 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 ANIRAS
|
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ARG14
2.879
GLY15
3.414
ASN16
2.126
GLY17
4.714
TYR124
2.265
ASP128
4.788
LEU129
4.149
GLU130
2.826
ASN132
1.845
LYS135
4.076
CYS180
3.171
ASN181
2.776
SER182
3.599
PHE183
3.288
|
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| Ligand Name: Sinefungin | Ligand Info | |||||
| Structure Description | Crystal structure of SmyD3 in complex with methyltransferase inhibitor sinefungin | PDB:3PDN | ||||
| Method | X-ray diffraction | Resolution | 1.70 Å | Mutation | No | [3] |
| 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
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .SFG or .SFG2 or .SFG3 or :3SFG;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
4.372
ARG14
2.725
GLY15
3.714
ASN16
2.795
TYR124
2.647
ASP128
4.838
LEU129
4.785
GLU130
3.567
ASN132
2.919
CYS180
3.697
ASN181
3.029
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| Click to View More Binding Site Information of This Target and Ligand Pair | ||||||
| Ligand Name: N-{(3-endo)-8-[(trans-4-aminocyclohexyl)sulfonyl]-8-azabicyclo[3.2.1]octan-3-yl}-5-cyclopropyl-1,2-oxazole-3-carboxamide | Ligand Info | |||||
| Structure Description | Crystal structure of SMYD3 with SAM and EPZ028862 | PDB:5V37 | ||||
| Method | X-ray diffraction | Resolution | 1.42 Å | Mutation | No | [4] |
| 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
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .8WD or .8WD2 or .8WD3 or :38WD;style chemicals stick;color identity;select .A:180 or .A:181 or .A:182 or .A:183 or .A:184 or .A:186 or .A:190 or .A:192 or .A:202 or .A:214 or .A:237 or .A:238 or .A:239 or .A:240 or .A:241 or .A:242 or .A:257 or .A:297 or .A:332 or .A:366 or .A:368; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
CYS180
3.538
ASN181
3.498
SER182
3.473
PHE183
3.398
THR184
2.782
CYS186
4.401
MET190
3.423
GLU192
3.627
SER202
4.652
ILE214
4.360
ILE237
3.518
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| Ligand Name: (2S)-1-[[(1R,5S)-3-azabicyclo[3.1.0]hexan-3-yl]carbonyl]-N-(2-cyclopropylethyl)-2-methyl-4-oxidanylidene-3,5-dihydro-2H-1,5-benzodiazepine-7-carboxamide | Ligand Info | |||||
| Structure Description | X-RAY STRUCTURE OF SMYD3 IN COMPLEX WITH the benzodiazepine-based probe BAY-6035 | PDB:7O2C | ||||
| Method | X-ray diffraction | Resolution | 1.52 Å | Mutation | Yes | [5] |
| 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
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .UZK or .UZK2 or .UZK3 or :3UZK;style chemicals stick;color identity;select .A:180 or .A:181 or .A:182 or .A:183 or .A:184 or .A:185 or .A:186 or .A:190 or .A:192 or .A:202 or .A:204 or .A:214 or .A:216 or .A:237 or .A:238 or .A:239 or .A:240 or .A:241 or .A:257 or .A:366 or .A:367 or .A:368; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
CYS180
3.723
ASN181
4.434
SER182
3.656
PHE183
3.185
THR184
2.778
ILE185
4.556
CYS186
3.063
MET190
3.996
GLU192
4.370
SER202
4.812
LEU204
4.707
|
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| Ligand Name: (2S)-1-(4-azanylpiperidin-1-yl)carbonyl-N-(2-cyclopropylethyl)-2-methyl-4-oxidanylidene-3,5-dihydro-2H-1,5-benzodiazepine-7-carboxamide | Ligand Info | |||||
| Structure Description | X-RAY STRUCTURE OF SMYD3 IN COMPLEX WITH benzodiazepine-type inhibitor compound 15 | PDB:7O2A | ||||
| Method | X-ray diffraction | Resolution | 1.57 Å | Mutation | Yes | [5] |
| 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
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|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .UZT or .UZT2 or .UZT3 or :3UZT;style chemicals stick;color identity;select .A:180 or .A:181 or .A:182 or .A:183 or .A:184 or .A:185 or .A:186 or .A:190 or .A:192 or .A:202 or .A:204 or .A:214 or .A:215 or .A:216 or .A:237 or .A:238 or .A:239 or .A:240 or .A:241 or .A:257 or .A:366 or .A:367 or .A:368; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
CYS180
3.576
ASN181
4.298
SER182
3.677
PHE183
3.259
THR184
2.808
ILE185
4.512
CYS186
3.156
MET190
4.016
GLU192
2.472
SER202
4.815
LEU204
4.730
ILE214
3.733
|
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| Ligand Name: (2S)-N-butyl-1-(2-fluorophenyl)carbonyl-2-methyl-4-oxidanylidene-3,5-dihydro-2H-1,5-benzodiazepine-7-carboxamide | Ligand Info | |||||
| Structure Description | X-RAY STRUCTURE OF SMYD3 in complex with benzodiazepine-type inhibitor 6 | PDB:7O2B | ||||
| Method | X-ray diffraction | Resolution | 2.03 Å | Mutation | Yes | [5] |
| 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
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|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .UZQ or .UZQ2 or .UZQ3 or :3UZQ;style chemicals stick;color identity;select .A:180 or .A:181 or .A:182 or .A:183 or .A:184 or .A:185 or .A:186 or .A:190 or .A:192 or .A:214 or .A:215 or .A:216 or .A:237 or .A:238 or .A:239 or .A:240 or .A:241 or .A:257 or .A:366 or .A:367 or .A:368; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
CYS180
3.941
ASN181
3.810
SER182
3.742
PHE183
3.175
THR184
2.850
ILE185
4.510
CYS186
3.113
MET190
4.047
GLU192
3.555
ILE214
3.534
VAL215
4.852
|
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| Ligand Name: propyl (2R)-4-[2-[4-(1-aminocyclopropyl)phenyl]quinoline-7-carbonyl]-2-methylpiperazine-1-carboxylate | Ligand Info | |||||
| Structure Description | Crystal structure of SmyD3 in complex with covalent inhibitor 5 | PDB:6IJL | ||||
| Method | X-ray diffraction | Resolution | 2.35 Å | Mutation | Yes | [6] |
| 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
|
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .A8U or .A8U2 or .A8U3 or :3A8U;style chemicals stick;color identity;select .A:180 or .A:181 or .A:182 or .A:183 or .A:184 or .A:185 or .A:186 or .A:190 or .A:191 or .A:192 or .A:201 or .A:202 or .A:214 or .A:216 or .A:237 or .A:238 or .A:239 or .A:241 or .A:243 or .A:257 or .A:297 or .A:329 or .A:332 or .A:358 or .A:362 or .A:368; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
CYS180
4.172
ASN181
4.023
SER182
3.424
PHE183
3.383
THR184
3.189
ILE185
4.817
CYS186
1.758
MET190
2.913
GLN191
4.681
GLU192
4.775
ILE201
4.769
SER202
4.046
ILE214
3.410
|
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| Ligand Name: Selenomethionine | Ligand Info | |||||
| Structure Description | Crystal Structure of Human Histone-Lysine N-methyltransferase SMYD3 in Complex with S-adenosyl-L-methionine | PDB:3MEK | ||||
| Method | X-ray diffraction | Resolution | 2.10 Å | Mutation | No | [7] |
| 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 |
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|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .MSE or .MSE2 or .MSE3 or :3MSE;style chemicals stick;color identity;select .A:58 or .A:59 or .A:61 or .A:62 or .A:68 or .A:69 or .A:70 or .A:71 or .A:72 or .A:73 or .A:76 or .A:85 or .A:89 or .A:106 or .A:108 or .A:109 or .A:110 or .A:111 or .A:112 or .A:114 or .A:115 or .A:145 or .A:146 or .A:147 or .A:148 or .A:150 or .A:151 or .A:152 or .A:153 or .A:154 or .A:156 or .A:157 or .A:158 or .A:159 or .A:164 or .A:165 or .A:166 or .A:167 or .A:186 or .A:187 or .A:188 or .A:189 or .A:191 or .A:192 or .A:208 or .A:215 or .A:238 or .A:240 or .A:241 or .A:243 or .A:245 or .A:246 or .A:248 or .A:249 or .A:252 or .A:265 or .A:271 or .A:272 or .A:273 or .A:274 or .A:276 or .A:277 or .A:289 or .A:292 or .A:293 or .A:296 or .A:297 or .A:304 or .A:305 or .A:306 or .A:307 or .A:309 or .A:310 or .A:311 or .A:312 or .A:323 or .A:324 or .A:325 or .A:326 or .A:329 or .A:330 or .A:331 or .A:332 or .A:333 or .A:334 or .A:336 or .A:337 or .A:338 or .A:339 or .A:347 or .A:348 or .A:350 or .A:351 or .A:352 or .A:353 or .A:354 or .A:356 or .A:357 or .A:358 or .A:359 or .A:361 or .A:362 or .A:363 or .A:366 or .A:367 or .A:368 or .A:369 or .A:370 or .A:371 or .A:372 or .A:373 or .A:375 or .A:376 or .A:377 or .A:378 or .A:379 or .A:380 or .A:381 or .A:383 or .A:384 or .A:386 or .A:387 or .A:388 or .A:389 or .A:391 or .A:392 or .A:393 or .A:394 or .A:395 or .A:396 or .A:397 or .A:398 or .A:399 or .A:401 or .A:402 or .A:403 or .A:404 or .A:405 or .A:410 or .A:411 or .A:413 or .A:414 or .A:417 or .A:418 or .A:421 or .A:422 or .A:425; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
LYS58
4.394
LEU59
1.334
ARG61
1.320
CYS62
4.277
ALA68
4.197
LYS69
3.188
TYR70
2.687
CYS71
4.423
SER72
3.704
ALA73
3.590
GLN76
3.494
ARG85
4.393
CYS89
3.684
GLY106
3.889
VAL108
4.846
VAL109
2.907
PHE110
3.233
LYS111
3.303
LEU112
1.324
ASP114
1.331
GLY115
3.719
ARG145
3.083
GLN146
3.351
LEU147
3.295
VAL148
1.332
THR150
1.339
PHE151
2.850
GLN152
3.364
HIS153
3.082
PHE154
1.333
ARG156
1.336
GLU157
3.002
GLU158
2.868
ILE159
2.829
GLN164
3.506
LEU165
3.592
PRO166
3.432
PRO167
4.728
CYS186
4.016
ASN187
2.832
ALA188
3.193
GLU189
1.333
GLN191
1.329
GLU192
3.823
CYS208
3.913
VAL215
4.440
CYS238
3.810
LEU240
3.406
ASP241
1.333
LEU243
1.326
THR245
1.327
SER246
4.073
GLU248
3.344
ARG249
3.079
GLN252
3.433
ARG265
3.805
LYS271
3.035
ASP272
3.268
ALA273
3.304
ASP274
1.332
LEU276
1.337
THR277
3.564
SER289
3.666
LYS292
3.808
ILE293
3.675
LEU296
3.702
LYS297
4.818
GLN304
3.253
VAL305
3.258
LEU306
3.219
ALA307
1.333
CYS309
1.339
GLN310
3.424
ALA311
3.656
ILE312
3.635
ILE323
3.885
ASN324
3.291
ILE325
2.958
TYR326
4.951
LYS329
4.994
VAL330
4.910
LEU331
2.874
ASP332
3.293
CYS333
3.322
ALA334
1.324
ASP336
1.331
ALA337
3.375
CYS338
3.333
ILE339
2.890
ALA347
3.512
LEU348
3.721
TYR350
3.948
GLY351
3.566
THR352
3.235
ARG353
3.342
THR354
1.338
GLU356
1.324
PRO357
3.493
TYR358
3.420
ARG359
2.959
PHE361
3.694
PHE362
3.429
PRO363
4.891
HIS366
3.393
PRO367
3.913
VAL368
4.370
ARG369
4.743
GLY370
2.936
VAL371
3.220
GLN372
3.283
VAL373
1.333
LYS375
1.334
VAL376
3.312
GLY377
3.435
LYS378
2.859
LEU379
4.738
GLN380
2.930
LEU381
4.660
GLN383
3.399
GLY384
1.331
PHE386
1.334
PRO387
3.268
GLN388
3.227
ALA389
1.336
LYS391
1.332
ASN392
3.315
LEU393
3.657
ARG394
2.969
LEU395
4.894
ALA396
2.743
PHE397
3.382
ASP398
3.542
ILE399
1.331
ARG401
1.325
VAL402
3.086
THR403
3.329
HIS404
2.705
GLY405
2.971
LEU410
3.648
ILE411
3.866
ASP413
4.048
LEU414
3.757
LEU417
3.940
LEU418
3.595
CYS421
3.666
ASP422
3.831
ILE425
3.817
|
|||||
| Ligand Name: N-(1-(2-chloroacetyl)piperidin-4-yl)-5-cyclopropylisoxazole-3-carboxamide | Ligand Info | |||||
| Structure Description | Crystal structure of SMYD3 conjugate with piperidine-based covalent inhibitor EM127 | PDB:6ZRB | ||||
| Method | X-ray diffraction | Resolution | 1.55 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 ANIRA
|
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .QON or .QON2 or .QON3 or :3QON;style chemicals stick;color identity;select .A:180 or .A:181 or .A:182 or .A:183 or .A:184 or .A:186 or .A:190 or .A:192 or .A:202 or .A:214 or .A:216 or .A:237 or .A:238 or .A:239 or .A:257; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
||||||
| Ligand Name: Diperodon anhydrous, (S)- | Ligand Info | |||||
| Structure Description | Crystal structure of SMYD3 with diperodon S enantiomer bound to allosteric site | PDB:7BJ1 | ||||
| Method | X-ray diffraction | Resolution | 1.61 Å | Mutation | Yes | [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 ANIRAS
|
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .QKT or .QKT2 or .QKT3 or :3QKT;style chemicals stick;color identity;select .A:188 or .A:189 or .A:339 or .A:340 or .A:344 or .A:371 or .A:374 or .A:375 or .A:378 or .A:379 or .A:382 or .A:410; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
||||||
| Ligand Name: Diperodon | Ligand Info | |||||
| Structure Description | Crystal structure of SMYD3 with diperodon R enantiomer bound to allosteric site | PDB:6YUH | ||||
| Method | X-ray diffraction | Resolution | 1.93 Å | Mutation | No | [10] |
| 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 .POW or .POW2 or .POW3 or :3POW;style chemicals stick;color identity;select .A:188 or .A:189 or .A:339 or .A:344 or .A:371 or .A:374 or .A:375 or .A:378 or .A:379 or .A:382 or .A:410 or .A:413; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
||||||
| Ligand Name: 5-cyclopropyl-N-[1-(methylsulfonyl)piperidin-4-yl]-1,2-oxazole-3-carboxamide | Ligand Info | |||||
| Structure Description | Co-crystal Structure of human SMYD3 with Isoxazole Amides Inhibitors | PDB:6P7Z | ||||
| Method | X-ray diffraction | Resolution | 1.19 Å | Mutation | No | [1] |
| 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 .O41 or .O412 or .O413 or :3O41;style chemicals stick;color identity;select .A:180 or .A:181 or .A:182 or .A:183 or .A:184 or .A:186 or .A:190 or .A:202 or .A:214 or .A:216 or .A:237 or .A:238 or .A:239 or .A:240 or .A:241 or .A:257 or .A:366 or .A:367 or .A:368; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
||||||
| Ligand Name: N-(1-{[4-(aminomethyl)phenyl]sulfonyl}piperidin-4-yl)-5-cyclopropyl-1,2-oxazole-3-carboxamide | Ligand Info | |||||
| Structure Description | Co-crystal Structure of human SMYD3 with Isoxazole Amides Inhibitors | PDB:6PAF | ||||
| Method | X-ray diffraction | Resolution | 1.24 Å | Mutation | No | [1] |
| 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 .O6A or .O6A2 or .O6A3 or :3O6A;style chemicals stick;color identity;select .A:180 or .A:181 or .A:182 or .A:183 or .A:184 or .A:186 or .A:190 or .A:192 or .A:202 or .A:214 or .A:216 or .A:237 or .A:238 or .A:239 or .A:240 or .A:241 or .A:257 or .A:294 or .A:297 or .A:366 or .A:367 or .A:368; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
CYS180
3.481
ASN181
3.521
SER182
3.280
PHE183
3.361
THR184
2.859
CYS186
3.595
MET190
3.187
GLU192
3.931
SER202
4.267
ILE214
4.048
PHE216
4.602
|
|||||
| Ligand Name: 2-Oxidanylidene-N-Piperidin-4-Yl-1,3-Dihydroindole-5-Carboxamide | Ligand Info | |||||
| Structure Description | Crystal structure of SMYD3 with SAM and oxindole compound | PDB:5CCL | ||||
| Method | X-ray diffraction | Resolution | 1.50 Å | Mutation | No | [11] |
| 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 .4ZW or .4ZW2 or .4ZW3 or :34ZW;style chemicals stick;color identity;select .A:7 or .A:19 or .A:21 or .A:180 or .A:181 or .A:182 or .A:183 or .A:184 or .A:186 or .A:192 or .A:201 or .A:202 or .A:214 or .A:231 or .A:232 or .A:237 or .A:238 or .A:239 or .A:240 or .A:241 or .A:257; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
GLU7
3.794
ARG19
3.140
VAL21
3.504
CYS180
3.880
ASN181
3.475
SER182
3.148
PHE183
3.261
THR184
2.764
CYS186
4.148
GLU192
3.488
ILE201
4.960
|
|||||
| Ligand Name: N-{1-[(2-aminoethyl)sulfonyl]piperidin-4-yl}-5-cyclopropyl-1,2-oxazole-3-carboxamide | Ligand Info | |||||
| Structure Description | Co-crystal Structure of human SMYD3 with Isoxazole Amides Inhibitors | PDB:6P6K | ||||
| Method | X-ray diffraction | Resolution | 1.55 Å | Mutation | No | [1] |
| 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 .L0J or .L0J2 or .L0J3 or :3L0J;style chemicals stick;color identity;select .A:180 or .A:181 or .A:182 or .A:183 or .A:184 or .A:186 or .A:190 or .A:192 or .A:202 or .A:214 or .A:216 or .A:237 or .A:238 or .A:239 or .A:240 or .A:241 or .A:257 or .A:366 or .A:367 or .A:368; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
CYS180
3.542
ASN181
3.441
SER182
3.350
PHE183
3.365
THR184
2.833
CYS186
3.659
MET190
2.837
GLU192
4.997
SER202
4.266
ILE214
3.984
|
|||||
| Ligand Name: 5-cyclopropyl-N-{1-[({trans-4-[(4,4,4-trifluorobutyl)amino]cyclohexyl}methyl)sulfonyl]piperidin-4-yl}-1,2-oxazole-3-carboxamide | Ligand Info | |||||
| Structure Description | Crystal Structure of SMYD3 with Potent and Selective Isoxazole Amide Inhibitor 1 | PDB:6O9O | ||||
| Method | X-ray diffraction | Resolution | 1.59 Å | Mutation | No | [12] |
| 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 ANIRAS
|
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .LUP or .LUP2 or .LUP3 or :3LUP;style chemicals stick;color identity;select .A:180 or .A:181 or .A:182 or .A:183 or .A:184 or .A:186 or .A:190 or .A:192 or .A:202 or .A:204 or .A:214 or .A:216 or .A:237 or .A:238 or .A:239 or .A:240 or .A:241 or .A:257 or .A:290 or .A:293 or .A:294 or .A:297 or .A:329 or .A:333 or .A:366 or .A:367 or .A:368; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
CYS180
3.606
ASN181
4.568
SER182
3.342
PHE183
3.520
THR184
2.896
CYS186
3.567
MET190
3.734
GLU192
3.142
SER202
4.546
LEU204
4.304
ILE214
4.363
PHE216
4.579
ILE237
3.491
CYS238
4.232
|
|||||
| Click to View More Binding Site Information of This Target and Ligand Pair | ||||||
| Ligand Name: propyl (2R)-4-[4-chloro-2-[4-(2-hydroxypropan-2-yl)phenyl]quinoline-7-carbonyl]-2-methylpiperazine-1-carboxylate | Ligand Info | |||||
| Structure Description | Crystal structure of SmyD3 in complex with covalent inhibitor 3 | PDB:5XXJ | ||||
| Method | X-ray diffraction | Resolution | 1.69 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 .8HF or .8HF2 or .8HF3 or :38HF;style chemicals stick;color identity;select .A:180 or .A:181 or .A:182 or .A:183 or .A:184 or .A:185 or .A:186 or .A:190 or .A:192 or .A:202 or .A:214 or .A:216 or .A:237 or .A:238 or .A:239 or .A:240 or .A:241 or .A:243 or .A:257 or .A:329 or .A:332 or .A:358 or .A:362 or .A:368; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
CYS180
3.748
ASN181
3.897
SER182
3.467
PHE183
3.272
THR184
3.237
ILE185
4.598
CYS186
1.765
MET190
3.380
GLU192
4.874
SER202
4.051
ILE214
2.876
PHE216
3.573
|
|||||
| Ligand Name: propyl (3S)-4-[(6R)-6-(aminomethyl)-5,6,7,8-tetrahydroacridine-3-carbonyl]-3-methylpiperazine-1-carboxylate | Ligand Info | |||||
| Structure Description | Crystal structure of SmyD3 in complex with covalent inhibitor 4 | PDB:5YJO | ||||
| Method | X-ray diffraction | Resolution | 2.13 Å | Mutation | Yes | [6] |
| 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 .8W0 or .8W02 or .8W03 or :38W0;style chemicals stick;color identity;select .A:180 or .A:181 or .A:182 or .A:183 or .A:184 or .A:185 or .A:186 or .A:190 or .A:191 or .A:192 or .A:202 or .A:214 or .A:216 or .A:237 or .A:238 or .A:239 or .A:240 or .A:241 or .A:257 or .A:297 or .A:332 or .A:368; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
CYS180
3.905
ASN181
3.684
SER182
3.352
PHE183
3.482
THR184
3.272
ILE185
4.534
CYS186
1.766
MET190
3.192
GLN191
4.566
GLU192
4.568
SER202
4.464
|
|||||
| Ligand Name: Propyl 4-(4-chloro-2-phenylquinoline-7-carbonyl)piperazine-1-carboxylate | Ligand Info | |||||
| Structure Description | Crystal structure of SmyD3 in complex with covalent inhibitor 2 | PDB:5XXG | ||||
| Method | X-ray diffraction | Resolution | 2.14 Å | Mutation | No | [14] |
| 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 .8HR or .8HR2 or .8HR3 or :38HR;style chemicals stick;color identity;select .A:180 or .A:181 or .A:182 or .A:183 or .A:184 or .A:185 or .A:186 or .A:190 or .A:191 or .A:192 or .A:202 or .A:214 or .A:216 or .A:237 or .A:238 or .A:239 or .A:241 or .A:257 or .A:332 or .A:358 or .A:362 or .A:368; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
CYS180
4.085
ASN181
3.461
SER182
3.520
PHE183
3.349
THR184
3.255
ILE185
4.325
CYS186
1.754
MET190
3.025
GLN191
4.684
GLU192
4.124
SER202
3.631
|
|||||
| Ligand Name: Ethyl 4-(5,6,7,8-tetrahydroacridine-3-carbonyl)piperazine-1-carboxylate | Ligand Info | |||||
| Structure Description | Crystal structure of SmyD3 in complex with covalent inhibitor 1 | PDB:5XXD | ||||
| Method | X-ray diffraction | Resolution | 2.31 Å | Mutation | No | [15] |
| 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
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set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .8NR or .8NR2 or .8NR3 or :38NR;style chemicals stick;color identity;select .A:180 or .A:181 or .A:182 or .A:183 or .A:184 or .A:185 or .A:186 or .A:190 or .A:191 or .A:192 or .A:202 or .A:214 or .A:216 or .A:237 or .A:238 or .A:239 or .A:257 or .A:368; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: 6-chloranyl-2-oxidanylidene-N-[(1S,5R)-8-[4-[(phenylmethyl)amino]piperidin-1-yl]sulfonyl-8-azabicyclo[3.2.1]octan-3-yl]-1,3-dihydroindole-5-carboxamide | Ligand Info | |||||
| Structure Description | Crystal structure of SMYD3 with SAM and EPZ030456 | PDB:5CCM | ||||
| Method | X-ray diffraction | Resolution | 2.30 Å | Mutation | No | [11] |
| 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
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .4ZX or .4ZX2 or .4ZX3 or :34ZX;style chemicals stick;color identity;select .A:180 or .A:181 or .A:182 or .A:183 or .A:184 or .A:186 or .A:190 or .A:192 or .A:201 or .A:202 or .A:214 or .A:237 or .A:238 or .A:239 or .A:240 or .A:241 or .A:242 or .A:257 or .A:294 or .A:297 or .A:329 or .A:332 or .A:333 or .A:358 or .A:366 or .A:368; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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CYS180
3.652
ASN181
3.477
SER182
3.173
PHE183
3.258
THR184
2.844
CYS186
3.689
MET190
3.504
GLU192
3.341
ILE201
4.938
SER202
3.017
ILE214
3.653
ILE237
3.625
CYS238
3.129
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| References | Top | ||||
|---|---|---|---|---|---|
| REF 1 | Discovery of Isoxazole Amides as Potent and Selective SMYD3 Inhibitors. ACS Med Chem Lett. 2019 Dec 27;11(2):133-140. | ||||
| REF 2 | Structure-Based Design of a Novel SMYD3 Inhibitor that Bridges the SAM-and MEKK2-Binding Pockets. Structure. 2016 May 3;24(5):774-781. | ||||
| REF 3 | Structural insights into the autoinhibition and posttranslational activation of histone methyltransferase SmyD3. J Mol Biol. 2011 Feb 11;406(1):149-59. | ||||
| REF 4 | 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 5 | 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 6 | Discovery of Irreversible Inhibitors Targeting Histone Methyltransferase, SMYD3. ACS Med Chem Lett. 2019 May 23;10(6):978-984. | ||||
| REF 7 | Crystal Structure of Human Histone-Lysine N-methyltransferase SMYD3 in Complex with S-adenosyl-L-methionine | ||||
| REF 8 | Discovery of the 4-aminopiperidine-based compound EM127 for the site-specific covalent inhibition of SMYD3. doi:10.1016/j.ejmech.2022.114683. | ||||
| REF 9 | Discovery of an Allosteric Ligand Binding Site in SMYD3 Lysine Methyltransferase. doi:10.1002/cbic.202000736. | ||||
| REF 10 | Discovery of an Allosteric Ligand Binding Site in SMYD3 Lysine Methyltransferase. Chembiochem. 2021 May 4;22(9):1597-1608. | ||||
| REF 11 | 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 12 | Discovery of Isoxazole Amides as Potent and Selective SMYD3 Inhibitors | ||||
| REF 13 | Crystal structure of SmyD3 in complex with covalent inhibitor 3 | ||||
| REF 14 | Crystal structure of SmyD3 in complex with covalent inhibitor 2 | ||||
| REF 15 | Crystal structure of SmyD3 in complex with covalent inhibitor 1 | ||||
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