Binding Site Information of Target
| Target General Information | Top | ||||
|---|---|---|---|---|---|
| Target ID | T19244 | Target Info | |||
| Target Name | S-mephenytoin 4-hydroxylase (CYP2C9) | ||||
| Synonyms | Cytochrome P450 PB-1; Cytochrome P450 MP-8; Cytochrome P450 MP-4; Cytochrome P450 2C9; Cytochrome P-450MP; Cholesterol 25-hydroxylase; CYPIIC9; CYP2C10; (S)-limonene 7-monooxygenase; (S)-limonene 6-monooxygenase; (R)-limonene 6-monooxygenase | ||||
| Target Type | Successful Target | ||||
| Gene Name | CYP2C9 | ||||
| Biochemical Class | Paired donor oxygen oxidoreductase | ||||
| UniProt ID | |||||
| Drug Binding Sites of Target | Top | |||||
|---|---|---|---|---|---|---|
| Ligand Name: Flurbiprofen | Ligand Info | |||||
| Structure Description | Crystal Structure of P4502C9 with Flurbiprofen bound | PDB:1R9O | ||||
| Method | X-ray diffraction | Resolution | 2.00 Å | Mutation | Yes | [1] |
| PDB Sequence |
RGKLPPGPTP
35 LPLQIGIKDI50 SKSLTNLSKV60 YGPVFTLYFG70 LKPIVVLHGY80 EAVKEALIDL 90 GEEFSGRGIF100 PLAERANRGF110 GIVFSNGKKW120 KEIRRFSLMT130 LRNFGMGKRS 140 IEDRVQEEAR150 CLVEELRKTK160 ASPCDPTFIL170 GCAPCNVICS180 IIFHKRFDYK 190 DQQFLNLMEK200 LNENIKILSS210 PWIPIIDYFP227 GTHNKLLKNV237 AFMKSYILEK 247 VKEHQESMDM257 NNPQDFIDCF267 LMKMEKEKHN277 QPSEFTIESL287 ENTAVDLFGA 297 GTETTSTTLR307 YALLLLLKHP317 EVTAKVQEEI327 ERVIGRNRSP337 CMQDRSHMPY 347 TDAVVHEVQR357 YIDLLPTSLP367 HAVTCDIKFR377 NYLIPKGTTI387 LISLTSVLHD 397 NKEFPNPEMF407 DPHHFLDEGG417 NFKKSKYFMP427 FSAGKRICVG437 EALAGMELFL 447 FLTSILQNFN457 LKSLVDPKNL467 DTTPVVNGFA477 SVPPFYQLCF487 IPIHH |
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| Ligand Name: Losartan | Ligand Info | |||||
| Structure Description | Crystal structure of CYP2C9 genetic variant A477T (*30) in complex with multiple losartan molecules | PDB:5X23 | ||||
| Method | X-ray diffraction | Resolution | 2.00 Å | Mutation | Yes | [2] |
| PDB Sequence |
KLPPGPTPLP
37 VIGNILQIGI47 KDISKSLTNL57 SKVYGPVFTL67 YFGLKPIVVL77 HGYEAVKEAL 87 IDLGEEFSGR97 GIFPLAERAN107 RGFGIVFSNG117 KKWKEIRRFS127 LMTLRNFGMG 137 KRSIEDRVQE147 EARCLVEELR157 KTKASPCDPT167 FILGCAPCNV177 ICSIIFHKRF 187 DYKDQQFLNL197 MEKLNENIKI207 LSSPWIQICN217 NFSPIIDYFP227 GTHNKLLKNV 237 AFMKSYILEK247 VKEHQESMDM257 NNPQDFIDCF267 LMKMEKEKHN277 QPSEFTIESL 287 ENTAVDLFGA297 GTETTSTTLR307 YALLLLLKHP317 EVTAKVQEEI327 ERVIGRNRSP 337 CMQDRSHMPY347 TDAVVHEVQR357 YIDLLPTSLP367 HAVTCDIKFR377 NYLIPKGTTI 387 LISLTSVLHD397 NKEFPNPEMF407 DPHHFLDEGG417 NFKKSKYFMP427 FSAGKRICVG 437 EALAGMELFL447 FLTSILQNFN457 LKSLVDPKNL467 DTTPVVNGFT477 SVPPFYQLCF 487 IPI
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PHE69
3.824
ILE74
4.556
GLY98
4.833
ILE99
4.940
PHE100
3.539
LEU102
4.151
ALA103
3.842
ALA106
3.591
ASN107
4.640
ARG108
2.147
VAL113
3.843
PHE114
3.982
LYS200
4.301
LEU201
2.739
ASN204
3.174
ILE205
4.170
LEU208
3.668
ILE213
4.795
GLN214
2.791
ILE215
4.861
ASN218
2.371
TYR225
4.225
PHE226
3.368
PRO227
3.410
GLY228
3.012
THR229
3.079
ASN231
3.436
LYS232
3.188
LEU233
4.046
LYS235
4.554
ASN236
3.530
VAL237
3.614
MET240
2.957
VAL292
3.689
ASP293
3.180
GLY296
3.580
ALA297
3.412
THR301
4.717
LEU361
4.658
LEU362
3.774
PRO363
3.078
THR364
2.867
SER365
2.214
LEU366
3.840
PRO367
3.324
LEU388
4.091
PHE476
2.286
THR477
4.255
|
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| Click to View More Binding Site Information of This Target and Ligand Pair | ||||||
| Ligand Name: Warfarin | Ligand Info | |||||
| Structure Description | Structure of human cytochrome P450 CYP2C9 | PDB:1OG5 | ||||
| Method | X-ray diffraction | Resolution | 2.55 Å | Mutation | Yes | [3] |
| PDB Sequence |
PPGPTPLPVI
39 GNILQIGIKD49 ISKSLTNLSK59 VYGPVFTLYF69 GLKPIVVLHG79 YEAVKEALID 89 LGEEFSGRGI99 FPLAERANRG109 FGIVFSNGKK119 WKEIRRFSLM129 TLRNFGMGKR 139 SIEDRVQEEA149 RCLVEELRKT159 KASPCDPTFI169 LGCAPCNVIC179 SIIFHKRFDY 189 KDQQFLNLME199 KLNENIEILS209 SPWIQVYNNF219 PALLDYFPGT229 HNKLLKNVAF 239 MKSYILEKVK249 EHQESMDMNN259 PQDFIDCFLM269 KMEKEKHNQP279 SEFTIESLEN 289 TAVDLFGAGT299 ETTSTTLRYA309 LLLLLKHPEV319 TAKVQEEIER329 VIGRNRSPCM 339 QDRSHMPYTD349 AVVHEVQRYI359 DLLPTSLPHA369 VTCDIKFRNY379 LIPKGTTILI 389 SLTSVLHDNK399 EFPNPEMFDP409 HHFLDEGGNF419 KKSKYFMPFS429 AGKRICVGEA 439 LAGMELFLFL449 TSILQNFNLK459 SLVDPKNLDT469 TPVVNGFASV479 PPFYQLCFIP 489 V
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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 .SWF or .SWF2 or .SWF3 or :3SWF;style chemicals stick;color identity;select .A:97 or .A:98 or .A:99 or .A:100 or .A:102 or .A:103 or .A:113 or .A:114 or .A:208 or .A:213 or .A:217 or .A:364 or .A:365 or .A:366 or .A:367 or .A:388 or .A:476; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: Ethyl {2-[([1,3]thiazolo[4,5-C]pyridine-2-Carbonyl)amino]thiophene-3-Carbonyl}carbamate | Ligand Info | |||||
| Structure Description | Cytochrome P450 (CYP) 2C9 TCA007 Inhibitor Complex | PDB:5W0C | ||||
| Method | X-ray diffraction | Resolution | 2.00 Å | Mutation | No | [4] |
| PDB Sequence |
GKLPPGPTPL
36 PVIGNILQIG46 IKDISKSLTN56 LSKVYGPVFT66 LYFGLKPIVV76 LHGYEAVKEA 86 LIDLGEEFSG96 RGIFPLAERA106 NRGFGIVFSN116 GKKWKEIRRF126 SLMTLRNFGM 136 GKRSIEDRVQ146 EEARCLVEEL156 RKTKASPCDP166 TFILGCAPCN176 VICSIIFHKR 186 FDYKDQQFLN196 LMEKLNENIK206 ILSSPWIQIC216 NNFSPIIDYF226 PGTHNKLLKN 236 VAFMKSYILE246 KVKEHQESMD256 MNNPQDFIDC266 FLMKMEKEKH276 NQPSEFTIES 286 LENTAVDLFG296 AGTETTSTTL306 RYALLLLLKH316 PEVTAKVQEE326 IERVIGRNRS 336 PCMQDRSHMP346 YTDAVVHEVQ356 RYIDLLPTSL366 PHAVTCDIKF376 RNYLIPKGTT 386 ILISLTSVLH396 DNKEFPNPEM406 FDPHHFLDEG416 GNFKKSKYFM426 PFSAGKRICV 436 GEALAGMELF446 LFLTSILQNF456 NLKSLVDPKN466 LDTTPVVNGF476 ASVPPFYQLC 486 FIPI
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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 .9W6 or .9W62 or .9W63 or :39W6;style chemicals stick;color identity;select .A:100 or .A:102 or .A:103 or .A:106 or .A:108 or .A:113 or .A:114 or .A:208 or .A:233 or .A:234 or .A:237 or .A:292 or .A:293 or .A:296 or .A:297 or .A:366 or .A:367 or .A:476; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: N-[4-(3-Chloranyl-4-Cyano-Phenoxy)cyclohexyl]-1,1,1-Tris(Fluoranyl)methanesulfonamide | Ligand Info | |||||
| Structure Description | Cytochrome 2C9 P450 inhibitor complex | PDB:5A5I | ||||
| Method | X-ray diffraction | Resolution | 2.00 Å | Mutation | No | [5] |
| PDB Sequence |
RGKLPPGPTP
35 LPLQIGIKDI50 SKSLTNLSKV60 YGPVFTLYFG70 LKPIVVLHGY80 EAVKEALIDL 90 GEEFSGRGIL102 AERANRGFGI112 VFSNGKKWKE122 IRRFSLMTLR132 NFGMGKRSIE 142 DRVQEEARCL152 VEELRKTKAS162 PCDPTFILGC172 APCNVICSII182 FHKRFDYKDQ 192 QFLNLMEKLN202 ENIKILSSPW212 IPIIDYFPGT229 HNKLLKNVAF239 MKSYILEKVK 249 EHQESMDMNN259 PQDFIDCFLM269 KMEKEKHNQP279 SEFTIESLEN289 TAVDLFGAGT 299 ETTSTTLRYA309 LLLLLKHPEV319 TAKVQEEIER329 VIGRNRSPCM339 QDRSHMPYTD 349 AVVHEVQRYI359 DLLPTSLPHA369 VTCDIKFRNY379 LIPKGTTILI389 SLTSVLHDNK 399 EFPNPEMFDP409 HHFLDEGGNF419 KKSKYFMPFS429 AGKRICVGEA439 LAGMELFLFL 449 TSILQNFNLK459 SLVDPKNLDT469 TPVVNGFASV479 PPFYQLCFIP489 IHH |
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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 .XI1 or .XI12 or .XI13 or :3XI1;style chemicals stick;color identity;select .A:108 or .A:113 or .A:114 or .A:201 or .A:204 or .A:205 or .A:208 or .A:233 or .A:237 or .A:240 or .A:292 or .A:293 or .A:296 or .A:297 or .A:301 or .A:362 or .A:366; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: 4-[4-Chloro-2-(1H-pyrazol-4-yl)phenoxy]-3-cyano-N-1,3-thiazol-2-ylbenzenesulfonamide | Ligand Info | |||||
| Structure Description | Design and Optimization of Biaryl Ether Aryl Sulfonamides as Selective Inhibitors of NaV1.7: Discovery of Clinical Candidate PF-05089771 | PDB:5K7K | ||||
| Method | X-ray diffraction | Resolution | 2.30 Å | Mutation | No | [6] |
| PDB Sequence |
RGKLPPGPTP
35 LPLQIGIKDI50 SKSLTNLSKV60 YGPVFTLYFG70 LKPIVVLHGY80 EAVKEALIDL 90 GEEFSGRGIF100 PLAERANRGF110 GIVFSNGKKW120 KEIRRFSLMT130 LRNFGMGKRS 140 IEDRVQEEAR150 CLVEELRKTK160 ASPCDPTFIL170 GCAPCNVICS180 IIFHKRFDYK 190 DQQFLNLMEK200 LNENIKILSS210 PWIPIIDYFP227 GTHNKLLKNV237 AFMKSYILEK 247 VKEHQESMDM257 NNPQDFIDCF267 LMKMEKEKHN277 QPSEFTIESL287 ENTAVDLFGA 297 GTETTSTTLR307 YALLLLLKHP317 EVTAKVQEEI327 ERVIGRNRSP337 CMQDRSHMPY 347 TDAVVHEVQR357 YIDLLPTSLP367 HAVTCDIKFR377 NYLIPKGTTI387 LISLTSVLHD 397 NKEFPNPEMF407 DPHHFLDEGG417 NFKKSKYFMP427 FSAGKRICVG437 EALAGMELFL 447 FLTSILQNFN457 LKSLVDPKNL467 DTTPVVNGFA477 SVPPFYQLCF487 IPIHH |
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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 .6RJ or .6RJ2 or .6RJ3 or :36RJ;style chemicals stick;color identity;select .A:100 or .A:108 or .A:113 or .A:114 or .A:201 or .A:204 or .A:205 or .A:208 or .A:237 or .A:240 or .A:292 or .A:293 or .A:295 or .A:296 or .A:297 or .A:298 or .A:300 or .A:301 or .A:362 or .A:365 or .A:366 or .A:435 or .A:476; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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PHE100
3.858
ARG108
3.338
VAL113
4.094
PHE114
3.633
LEU201
3.309
ASN204
3.730
ILE205
3.256
LEU208
3.299
VAL237
4.001
MET240
3.541
VAL292
2.919
ASP293
4.739
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| Ligand Name: N-[4-(3-Chloranyl-4-Cyano-Phenoxy)-3,5-Dimethoxy-Phenyl]-1,1,1-Tris(Fluoranyl)methanesulfonamide | Ligand Info | |||||
| Structure Description | Cytochrome 2C9 P450 inhibitor complex | PDB:5A5J | ||||
| Method | X-ray diffraction | Resolution | 2.90 Å | Mutation | No | [7] |
| PDB Sequence |
RGKLPPGPTP
35 LPLQIGIKDI50 SKSLTNLSKV60 YGPVFTLYFG70 LKPIVVLHGY80 EAVKEALIDL 90 GEEFSGRGIF100 PLAERANRGF110 GIVFSNGKKW120 KEIRRFSLMT130 LRNFGMGKRS 140 IEDRVQEEAR150 CLVEELRKTK160 ASPCDPTFIL170 GCAPCNVICS180 IIFHKRFDYK 190 DQQFLNLMEK200 LNENIKILSS210 PWIPIIDYFP227 GTHNKLLKNV237 AFMKSYILEK 247 VKEHQESMDM257 NNPQDFIDCF267 LMKMEKEKHN277 QPSEFTIESL287 ENTAVDLFGA 297 GTETTSTTLR307 YALLLLLKHP317 EVTAKVQEEI327 ERVIGRNRSP337 CMQDRSHMPY 347 TDAVVHEVQR357 YIDLLPTSLP367 HAVTCDIKFR377 NYLIPKGTTI387 LISLTSVLHD 397 NKEFPNPEMF407 DPHHFLDEGG417 NFKKSKYFMP427 FSAGKRICVG437 EALAGMELFL 447 FLTSILQNFN457 LKSLVDPKNL467 DTTPVVNGFA477 SVPPFYQLCF487 IPIHH |
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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 .6YF or .6YF2 or .6YF3 or :36YF;style chemicals stick;color identity;select .A:108 or .A:114 or .A:201 or .A:204 or .A:205 or .A:208 or .A:209 or .A:233 or .A:237 or .A:292 or .A:295 or .A:296 or .A:297 or .A:300 or .A:301 or .A:304 or .A:361 or .A:366 or .A:474 or .A:476 or .A:477 or .A:479; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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ARG108
2.595
PHE114
3.474
LEU201
3.370
ASN204
3.938
ILE205
3.107
LEU208
3.210
SER209
3.226
LEU233
4.461
VAL237
3.737
VAL292
4.409
PHE295
4.428
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| Ligand Name: (2r)-N-{4-[(3-Bromophenyl)sulfonyl]-2-Chlorophenyl}-3,3,3-Trifluoro-2-Hydroxy-2-Methylpropanamide | Ligand Info | |||||
| Structure Description | Crystal structure of CYP2C9 in complex with an inhibitor | PDB:4NZ2 | ||||
| Method | X-ray diffraction | Resolution | 2.45 Å | Mutation | Yes | [8] |
| PDB Sequence |
KGRPPGPTPL
36 PVIGNILQIG46 IKDISKSLTN56 LSKVYGPVFT66 LYFGLKPIVV76 LHGYEAVKEA 86 LIDLGEEFSG96 RGIFPLAERA106 NRGFGIVFSN116 GKKWKEIRRF126 SLMTLRNFGM 136 GKRSIEDRVQ146 EEARCLVEEL156 RKTKASPCDP166 TFILGCAPCN176 VICSIIFHKR 186 FDYKDQQFLN196 LMEKLNENIE206 ILSSPWIQVY216 NNFPALLDYF226 PGTHNKLLKN 236 VAFMKSYILE246 KVKEHQESMD256 MNNPQDFIDC266 FLMKMEKEKH276 NQPSEFTIES 286 LENTAVDLFG296 AGTETTSTTL306 RYALLLLLKH316 PEVTAKVQEE326 IERVIGRNRS 336 PCMQDRSHMP346 YTDAVVHEVQ356 RYIDLLPTSL366 PHAVTCDIKF376 RNYLIPKGTT 386 ILISLTSVLH396 DNKEFPNPEM406 FDPHHFLDEG416 GNFKKSKYFM426 PFSAGKRICV 436 GEALAGMELF446 LFLTSILQNF456 NLKSLVDPKN466 LDTTPVVNGF476 ASVPPFYQLC 486 FIPV
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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 .2QJ or .2QJ2 or .2QJ3 or :32QJ;style chemicals stick;color identity;select .A:106 or .A:107 or .A:113 or .A:114 or .A:204 or .A:205 or .A:208 or .A:209 or .A:233 or .A:237 or .A:292 or .A:293 or .A:296 or .A:297 or .A:300 or .A:301 or .A:304 or .A:361 or .A:362 or .A:366 or .A:477 or .A:479; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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ALA106
3.648
ASN107
2.853
VAL113
4.893
PHE114
3.451
ASN204
3.734
ILE205
3.750
LEU208
3.808
SER209
4.893
LEU233
3.581
VAL237
3.741
VAL292
4.895
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| Ligand Name: Ferroheme c(2-) | Ligand Info | |||||
| Structure Description | Structure of human cytochrome P450 CYP2C9 | PDB:1OG5 | ||||
| Method | X-ray diffraction | Resolution | 2.55 Å | Mutation | Yes | [3] |
| PDB Sequence |
PPGPTPLPVI
39 GNILQIGIKD49 ISKSLTNLSK59 VYGPVFTLYF69 GLKPIVVLHG79 YEAVKEALID 89 LGEEFSGRGI99 FPLAERANRG109 FGIVFSNGKK119 WKEIRRFSLM129 TLRNFGMGKR 139 SIEDRVQEEA149 RCLVEELRKT159 KASPCDPTFI169 LGCAPCNVIC179 SIIFHKRFDY 189 KDQQFLNLME199 KLNENIEILS209 SPWIQVYNNF219 PALLDYFPGT229 HNKLLKNVAF 239 MKSYILEKVK249 EHQESMDMNN259 PQDFIDCFLM269 KMEKEKHNQP279 SEFTIESLEN 289 TAVDLFGAGT299 ETTSTTLRYA309 LLLLLKHPEV319 TAKVQEEIER329 VIGRNRSPCM 339 QDRSHMPYTD349 AVVHEVQRYI359 DLLPTSLPHA369 VTCDIKFRNY379 LIPKGTTILI 389 SLTSVLHDNK399 EFPNPEMFDP409 HHFLDEGGNF419 KKSKYFMPFS429 AGKRICVGEA 439 LAGMELFLFL449 TSILQNFNLK459 SLVDPKNLDT469 TPVVNGFASV479 PPFYQLCFIP 489 V
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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 .HEC or .HEC2 or .HEC3 or :3HEC;style chemicals stick;color identity;select .A:97 or .A:112 or .A:113 or .A:120 or .A:124 or .A:131 or .A:178 or .A:294 or .A:297 or .A:298 or .A:301 or .A:302 or .A:305 or .A:356 or .A:361 or .A:362 or .A:365 or .A:366 or .A:368 or .A:391 or .A:427 or .A:428 or .A:429 or .A:433 or .A:434 or .A:435 or .A:436 or .A:437 or .A:440 or .A:441 or .A:444 or .A:445; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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ARG97
2.526
ILE112
3.851
VAL113
3.678
TRP120
3.154
ARG124
2.759
LEU131
4.199
ILE178
4.722
LEU294
3.538
ALA297
3.223
GLY298
3.337
THR301
3.351
THR302
3.356
THR305
3.123
GLN356
3.596
LEU361
4.968
LEU362
3.473
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| Click to View More Binding Site Information of This Target and Ligand Pair | ||||||
| References | Top | ||||
|---|---|---|---|---|---|
| REF 1 | The structure of human cytochrome P450 2C9 complexed with flurbiprofen at 2.0-A resolution. J Biol Chem. 2004 Aug 20;279(34):35630-7. | ||||
| REF 2 | Structural Basis of Single-Nucleotide Polymorphisms in Cytochrome P450 2C9. Biochemistry. 2017 Oct 17;56(41):5476-5480. | ||||
| REF 3 | Crystal structure of human cytochrome P450 2C9 with bound warfarin. Nature. 2003 Jul 24;424(6947):464-8. | ||||
| REF 4 | Determinants of the Inhibition of DprE1 and CYP2C9 by Antitubercular Thiophenes. Angew Chem Int Ed Engl. 2017 Oct 9;56(42):13011-13015. | ||||
| REF 5 | Discovery of a Novel Binding Pocket for Cyp 2C9 Inhibitors: Crystallography, Pharmacophore Modelling and Inhibitor Sar.. doi:10.1039/C6MD00011H. | ||||
| REF 6 | Discovery of Clinical Candidate 4-[2-(5-Amino-1H-pyrazol-4-yl)-4-chlorophenoxy]-5-chloro-2-fluoro-N-1,3-thiazol-4-ylbenzenesulfonamide (PF-05089771): Design and Optimization of Diaryl Ether Aryl Sulfonamides as Selective Inhibitors of Na(V)1.7. J Med Chem. 2017 Aug 24;60(16):7029-7042. | ||||
| REF 7 | Discovery of a Novel Binding Pocket for Cyp 2C9 Inhibitors: Crystallography, Pharmacophore Modelling and Inhibitor Sar. | ||||
| REF 8 | Structure-based ligand design to overcome CYP inhibition in drug discovery projects. Drug Discov Today. 2014 Jul;19(7):905-11. | ||||
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