Structure of PDB 2vvc Chain B Binding Site BS01

Receptor Information
>2vvc Chain B (length=225) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
IVGGQECKDGECPWQALLINEENEGFCGGTILSEFYILTAAHCLYQAKRF
KVRVGGGEAVHEVEVVIKHNRFTKETYDFDIAVLRLKTPITFRMNVAPAC
LPERDWAESTLMTQKTGIVSGFGRTHEKGEQSTRLKMLEVPYVDRNSCKL
SSSFIITQNMFCAGYDTKQEDACQGDSGGPHVTRFKDTYFVTGIVSWGEG
CARKGKYGIYTKVTAFLKWIDRSMK
Ligand information
Ligand IDLZF
InChIInChI=1S/C23H22ClFN4O4S/c1-33-18-12-28(11-17(18)27-23(32)19-7-8-20(24)34-19)13-21(30)26-16-6-5-14(10-15(16)25)29-9-3-2-4-22(29)31/h2-10,17-18H,11-13H2,1H3,(H,26,30)(H,27,32)/t17-,18-/m0/s1
InChIKeyBOCLXHFYRGMFSC-ROUUACIJSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0COC1CN(CC1NC(=O)c2ccc(s2)Cl)CC(=O)Nc3ccc(cc3F)N4C=CC=CC4=O
OpenEye OEToolkits 1.5.0CO[C@H]1C[N@](C[C@@H]1NC(=O)c2ccc(s2)Cl)CC(=O)Nc3ccc(cc3F)N4C=CC=CC4=O
CACTVS 3.341CO[CH]1CN(C[CH]1NC(=O)c2sc(Cl)cc2)CC(=O)Nc3ccc(cc3F)N4C=CC=CC4=O
ACDLabs 10.04O=C(NC3C(OC)CN(CC(=O)Nc2ccc(N1C=CC=CC1=O)cc2F)C3)c4sc(Cl)cc4
CACTVS 3.341CO[C@H]1CN(C[C@@H]1NC(=O)c2sc(Cl)cc2)CC(=O)Nc3ccc(cc3F)N4C=CC=CC4=O
FormulaC23 H22 Cl F N4 O4 S
Name5-chloro-N-[(3S,4S)-1-(2-{[2-fluoro-4-(2-oxopyridin-1(2H)-yl)phenyl]amino}-2-oxoethyl)-4-methoxypyrrolidin-3-yl]thiophene-2-carboxamide
ChEMBLCHEMBL551393
DrugBank
ZINCZINC000038994189
PDB chain2vvc Chain B Residue 1244 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB2vvc Design of Novel Aminopyrrolidine Factor Xa Inhibitors from a Screening Hit.
Resolution1.95 Å
Binding residue
(original residue number in PDB)		T98 Y99 E147 F174 D189 A190 C191 Q192 W215 G216 G218 C220 G226 I227 Y228
Binding residue
(residue number reindexed from 1)		T76 Y77 E127 F154 D171 A172 C173 Q174 W197 G198 G200 C201 G208 I209 Y210
Annotation score1
Binding affinityBindingDB: Ki=3nM
Enzymatic activity
Catalytic site (original residue number in PDB) H57 D102 Q192 G193 D194 S195 G196
Catalytic site (residue number reindexed from 1) H42 D80 Q174 G175 D176 S177 G178
Enzyme Commision number 3.4.21.6: coagulation factor Xa.
Gene Ontology
Molecular Function
GO:0004252 serine-type endopeptidase activity
Biological Process
GO:0006508 proteolysis

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Molecular Function
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Biological Process
External links
PDB RCSB:2vvc, PDBe:2vvc, PDBj:2vvc
PDBsum2vvc
PubMed19200624
UniProtP00742|FA10_HUMAN Coagulation factor X (Gene Name=F10)

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