Target Binding Site Detail
| Target General Information | Top | ||||
|---|---|---|---|---|---|
| Target ID | T11843 | Target Info | |||
| Target Name | Vitamin K epoxide reductase complex 1 (VKORC1) | ||||
| Synonyms | Vitamin K1 2,3-epoxide reductase subunit 1; VKORC1; VKOR; UNQ308/PRO351; MSTP576; MSTP134 | ||||
| Target Type | Successful Target | ||||
| Gene Name | VKORC1 | ||||
| Biochemical Class | Short-chain dehydrogenases reductase | ||||
| UniProt ID | |||||
| Ligand General Information | Top | ||||
|---|---|---|---|---|---|
| Ligand Name | 2-[(4Z)-2-[(1R,2R)-1-amino-2-hydroxypropyl]-4-[(4-hydroxyphenyl)methylidene]-5-oxoimidazol-1-yl]acetic acid | Ligand Info | |||
| Canonical SMILES | CC(C(C1=NC(=CC2=CC=C(C=C2)O)C(=O)N1CC(=O)O)N)O | ||||
| InChI | 1S/C15H17N3O5/c1-8(19)13(16)14-17-11(15(23)18(14)7-12(21)22)6-9-2-4-10(20)5-3-9/h2-6,8,13,19-20H,7,16H2,1H3,(H,21,22)/b11-6-/t8-,13+/m1/s1 | ||||
| InChIKey | UZCDFHUXSDKGEZ-NGDPAIJVSA-N | ||||
| PubChem Compound ID | 49866829 | ||||
| Drug Binding Sites of Target | Top | |||||
|---|---|---|---|---|---|---|
| PDB ID: 6WVH Human VKOR with Brodifacoum | ||||||
| Method | X-ray diffraction | Resolution | 1.99 Å | Mutation | Yes | [1] |
| PDB Sequence |
SKGEELFTGV
11 VPILVELDGD21 VNGHKFSVRG31 EGEGDATNGK41 LTLKFICTTG51 KLPVPWPTLV 61 TTLVQCFSRY74 PDHMKRHDFF84 KSAMPEGYVQ94 ERTISFKDDG104 TYKTRAEVKF 114 EGDTLVNRIE124 LKGIDFKEDG134 NILGHKLEYN144 STWGSPGWVR154 LALCLTGLVL 164 SLYALHVKAA174 RARDRDYRAL184 CDVGTAISCS194 RVFSSRWGRG204 FGLVEHVLGQ 214 DSILNQSNSI224 FGCIFYTLQL234 LLGCLRTRWA244 SVLMLLSSLV254 SLAGSVYLAW 264 ILFFVLYDFC274 IVCITTYAIN284 VSLMWLSFRK294 VQENSHNVYI304 TADKQKNGIK 314 ANFKIRHNVE324 DGSVQLADHY334 QQNTPIGDGP344 VLLPDNHYLS354 TQSVLSKDPN 364 EKRDHMVLLE374 FVTAAGITHH384
|
|||||
|
|
LEU42
4.089
LEU44
3.790
PHE46
3.621
LEU60
4.706
VAL61
2.807
THR62
2.967
THR63
3.408
LEU64
1.428
VAL68
1.431
GLN69
3.438
TYR92
4.280
GLN94
2.868
|
|||||
| PDB ID: 6WV3 Human VKOR with warfarin | ||||||
| Method | X-ray diffraction | Resolution | 2.20 Å | Mutation | Yes | [1] |
| PDB Sequence |
KGEELFTGVV
12 PILVELDGDV22 NGHKFSVRGE32 GEGDATNGKL42 TLKFICTTGK52 LPVPWPTLVT 62 TLVQCFSRYP75 DHMKRHDFFK85 SAMPEGYVQE95 RTISFKDDGT105 YKTRAEVKFE 115 GDTLVNRIEL125 KGIDFKEDGN135 ILGHKLEYNS145 TWGSPGWVRL155 ALCLTGLVLS 165 LYALHVKAAR175 ARDRDYRALC185 DVGTAISCSR195 VFSSRWGRGF205 GLVEHVLGQD 215 SILNQSNSIF225 GCIFYTLQLL235 LGCLRTRWAS245 VLMLLSSLVS255 LAGSVYLAWI 265 LFFVLYDFCI275 VCITTYAINV285 SLMWLSFRKV295 QENSHNVYIT305 ADKQKNGIKA 315 NFKIRHNVED325 GSVQLADHYQ335 QNTPIGDGPV345 LLPDNHYLST355 QSVLSKDPNE 365 KRDHMVLLEF375 VTAAGITHHH385
|
|||||
|
|
LEU42
4.332
LEU44
3.608
PHE46
3.835
LEU60
4.726
VAL61
2.818
THR62
3.043
THR63
3.501
LEU64
1.409
VAL68
1.421
GLN69
3.283
TYR92
4.361
GLN94
2.897
|
|||||
| PDB ID: 6WV7 Human VKOR with Chlorophacinone | ||||||
| Method | X-ray diffraction | Resolution | 2.48 Å | Mutation | Yes | [1] |
| PDB Sequence |
SKGEELFTGV
11 VPILVELDGD21 VNGHKFSVRG31 EGEGDATNGK41 LTLKFICTTG51 KLPVPWPTLV 61 TTLVQCFSRY74 PDHMKRHDFF84 KSAMPEGYVQ94 ERTISFKDDG104 TYKTRAEVKF 114 EGDTLVNRIE124 LKGIDFKEDG134 NILGHKLEYN144 STWGSPGWVR154 LALCLTGLVL 164 SLYALHVKAA174 RARDRDYRAL184 CDVGTAISCS194 RVFSSRWGRG204 FGLVEHVLGQ 214 DSILNQSNSI224 FGCIFYTLQL234 LLGCLRTRWA244 SVLMLLSSLV254 SLAGSVYLAW 264 ILFFVLYDFC274 IVCITTYAIN284 VSLMWLSFRK294 VQENSHNVYI304 TADKQKNGIK 314 ANFKIRHNVE324 DGSVQLADHY334 QQNTPIGDGP344 VLLPDNHYLS354 TQSVLSKDPN 364 EKRDHMVLLE374 FVTAAGITHH384
|
|||||
|
|
LEU42
4.083
LEU44
3.584
PHE46
4.052
LEU60
4.895
VAL61
3.070
THR62
2.968
THR63
3.287
LEU64
1.339
VAL68
1.451
GLN69
3.446
TYR92
4.107
GLN94
2.933
|
|||||
| PDB ID: 6WV6 Human VKOR with phenindione | ||||||
| Method | X-ray diffraction | Resolution | 2.70 Å | Mutation | Yes | [1] |
| PDB Sequence |
SKGEELFTGV
11 VPILVELDGD21 VNGHKFSVRG31 EGEGDATNGK41 LTLKFICTTG51 KLPVPWPTLV 61 TTLVQCFSRY74 PDHMKRHDFF84 KSAMPEGYVQ94 ERTISFKDDG104 TYKTRAEVKF 114 EGDTLVNRIE124 LKGIDFKEDG134 NILGHKLEYN144 STWGSPGWVR154 LALCLTGLVL 164 SLYALHVKAA174 RARDRDYRAL184 CDVGTAISCS194 RVFSSRWGRG204 FGLVEHVLGQ 214 DSILNQSNSI224 FGCIFYTLQL234 LLGCLRTRWA244 SVLMLLSSLV254 SLAGSVYLAW 264 ILFFVLYDFC274 IVCITTYAIN284 VSLMWLSFRK294 VQENSHNVYI304 TADKQKNGIK 314 ANFKIRHNVE324 DGSVQLADHY334 QQNTPIGDGP344 VLLPDNHYLS354 TQSVLSKDPN 364 EKRDHMVLLE374 FVTAAGITHH384 H
|
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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 .CRO or .CRO2 or .CRO3 or :3CRO;style chemicals stick;color identity;select .A:42 or .A:44 or .A:46 or .A:60 or .A:61 or .A:62 or .A:63 or .A:64 or .A:68 or .A:69 or .A:92 or .A:94 or .A:96 or .A:112 or .A:121 or .A:300 or .A:302 or .A:317 or .A:319 or .A:335 or .A:355 or .A:357 or .A:372 or .A:374; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
LEU42
3.790
LEU44
3.646
PHE46
3.683
LEU60
4.707
VAL61
2.754
THR62
2.894
THR63
3.691
LEU64
1.329
VAL68
1.347
GLN69
3.662
TYR92
3.988
GLN94
3.085
|
|||||
| PDB ID: 6WV5 Human VKOR C43S mutant with vitamin K1 epoxide | ||||||
| Method | X-ray diffraction | Resolution | 2.80 Å | Mutation | Yes | [1] |
| PDB Sequence |
KGEELFTGVV
12 PILVELDGDV22 NGHKFSVRGE32 GEGDATNGKL42 TLKFICTTGK52 LPVPWPTLVT 62 TLVQCFSRYP75 DHMKRHDFFK85 SAMPEGYVQE95 RTISFKDDGT105 YKTRAEVKFE 115 GDTLVNRIEL125 KGIDFKEDGN135 ILGHKLEYNS145 TWGSPGWVRL155 ALCLTGLVLS 165 LYALHVKAAR175 ARDRDYRSCS194 RVFSSRWGRG204 FGLVEHVLGQ214 DSILNQSNSI 224 FGCIFYTLQL234 LLGCLRTRWA244 SVLMLLSSLV254 SLAGSVYLAW264 ILFFVLYDFC 274 IVCITTYAIN284 VSLMWLSFRK294 VQENSHNVYI304 TADKQKNGIK314 ANFKIRHNVE 324 DGSVQLADHY334 QQNTPIGDGP344 VLLPDNHYLS354 TQSVLSKDPN364 EKRDHMVLLE 374 FVTAAGITHH384
|
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .CRO or .CRO2 or .CRO3 or :3CRO;style chemicals stick;color identity;select .A:42 or .A:44 or .A:46 or .A:60 or .A:61 or .A:62 or .A:63 or .A:64 or .A:68 or .A:69 or .A:92 or .A:94 or .A:96 or .A:112 or .A:121 or .A:300 or .A:302 or .A:317 or .A:319 or .A:335 or .A:355 or .A:357 or .A:372 or .A:374; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
LEU42
3.439
LEU44
3.968
PHE46
4.193
LEU60
4.458
VAL61
2.400
THR62
2.839
THR63
3.470
LEU64
1.515
VAL68
1.330
GLN69
3.185
TYR92
4.323
GLN94
3.101
|
|||||
| PDB ID: 6WV4 Human VKOR C43S with warfarin | ||||||
| Method | X-ray diffraction | Resolution | 3.01 Å | Mutation | Yes | [1] |
| PDB Sequence |
SKGEELFTGV
11 VPILVELDGD21 VNGHKFSVRG31 EGEGDATNGK41 LTLKFICTGK52 LPVPWPTLVT 62 TLVQCFSRYP75 DHMKRHDFFK85 SAMPEGYVQE95 RTISFKDDGT105 YKTRAEVKFE 115 GDTLVNRIEL125 KGIDFKEDGN135 ILGHKLEYNS145 TWGSPGWVRL155 ALCLTGLVLS 165 LYALHVKAAG188 TAISCSRVFS198 SRWGRGFGLV208 EHVLGQDSIL218 NQSNSIFGCI 228 FYTLQLLLGC238 LRTRWASVLM248 LLSSLVSLAG258 SVYLAWILFF268 VLYDFCIVCI 278 TTYAINVSLM288 WLSFRKVQEN298 SHNVYITADK308 QKNGIKANFK318 IRHNVEDGSV 328 QLADHYQQNT338 PIGDGPVLLP348 DNHYLSTQSV358 LSKDPNEKRD368 HMVLLEFVTA 378 AGI
|
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .CRO or .CRO2 or .CRO3 or :3CRO;style chemicals stick;color identity;select .A:42 or .A:44 or .A:46 or .A:60 or .A:61 or .A:62 or .A:63 or .A:64 or .A:68 or .A:69 or .A:92 or .A:94 or .A:96 or .A:112 or .A:121 or .A:300 or .A:302 or .A:317 or .A:319 or .A:335 or .A:355 or .A:357 or .A:372 or .A:374; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
LEU42
4.036
LEU44
3.668
PHE46
4.003
LEU60
4.674
VAL61
2.670
THR62
2.950
THR63
3.405
LEU64
1.476
VAL68
1.414
GLN69
3.488
TYR92
3.944
GLN94
2.931
|
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| References | Top | ||||
|---|---|---|---|---|---|
| REF 1 | Structural basis of antagonizing the vitamin K catalytic cycle for anticoagulation. Science. 2021 Jan 1;371(6524):eabc5667. | ||||
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