Structure of PDB 2vwl Chain A Binding Site BS01

Receptor Information
>2vwl Chain A (length=234) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
IVGGQECKDGECPWQALLINEENEGFCGGTILSEFYILTAAHCLYQAKRF
KVRVGDRNTEQEEGGEAVHEVEVVIKHNRFTKETYDFDIAVLRLKTPITF
RMNVAPACLPERDWAESTLMTQKTGIVSGFGRTHEKGEQSTRLKMLEVPY
VDRNSCKLSSSFIITQNMFCAGYDTKQEDACQGDSGGPHVTRFKDTYFVT
GIVSWGEGCARKGKYGIYTKVTAFLKWIDRSMKT
Ligand information
Ligand IDLZH
InChIInChI=1S/C23H22ClFN4O4S/c24-20-7-6-19(34-20)23(33)26-14-9-16(13-30)28(11-14)12-21(31)27-18-5-4-15(10-17(18)25)29-8-2-1-3-22(29)32/h1-8,10,14,16,30H,9,11-13H2,(H,26,33)(H,27,31)/t14-,16+/m1/s1
InChIKeyFMLMGXAAZAZCMG-ZBFHGGJFSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04O=C(NC3CC(N(CC(=O)Nc2ccc(N1C=CC=CC1=O)cc2F)C3)CO)c4sc(Cl)cc4
OpenEye OEToolkits 1.5.0c1cc(c(cc1N2C=CC=CC2=O)F)NC(=O)C[N@]3C[C@@H](C[C@H]3CO)NC(=O)c4ccc(s4)Cl
CACTVS 3.341OC[C@@H]1C[C@H](CN1CC(=O)Nc2ccc(cc2F)N3C=CC=CC3=O)NC(=O)c4sc(Cl)cc4
CACTVS 3.341OC[CH]1C[CH](CN1CC(=O)Nc2ccc(cc2F)N3C=CC=CC3=O)NC(=O)c4sc(Cl)cc4
OpenEye OEToolkits 1.5.0c1cc(c(cc1N2C=CC=CC2=O)F)NC(=O)CN3CC(CC3CO)NC(=O)c4ccc(s4)Cl
FormulaC23 H22 Cl F N4 O4 S
Name5-CHLORO-THIOPHENE-2-CARBOXYLIC ACID ((3R,5S)-1-{[2-FLUORO-4-(2-OXO-PYRIDIN-1-YL)-PHENYLCARBAMOYL]-METHYL}-5-HYDROXYMETHYL-PYRROLIDIN-3-YL)-AMIDE
ChEMBLCHEMBL550102
DrugBank
ZINCZINC000038994596
PDB chain2vwl Chain A Residue 1246 [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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PDB2vwl Design of Novel Aminopyrrolidine Factor Xa Inhibitors from a Screening Hit.
Resolution1.8 Å
Binding residue
(original residue number in PDB)		E97 T98 Y99 F174 D189 A190 C191 Q192 V213 W215 G216 G218 C220 G226 I227 Y228
Binding residue
(residue number reindexed from 1)		E83 T84 Y85 F162 D179 A180 C181 Q182 V203 W205 G206 G208 C209 G216 I217 Y218
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=7.02,Ki=95nM
BindingDB: Ki=95nM
Enzymatic activity
Catalytic site (original residue number in PDB) H57 D102 Q192 G193 D194 S195 G196
Catalytic site (residue number reindexed from 1) H42 D88 Q182 G183 D184 S185 G186
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:2vwl, PDBe:2vwl, PDBj:2vwl
PDBsum2vwl
PubMed19200624
UniProtP00742|FA10_HUMAN Coagulation factor X (Gene Name=F10)

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