Structure of PDB 2w3k Chain A Binding Site BS01

Receptor Information
>2w3k 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
RMNVAPACLPERDWAESTLMTQKTGIVSGFGRTHEKGRQSTRLKMLEVPY
VDRNSCKLSSSFIITQNMFCAGYDTKQEDACQGDSGGPHVTRFKDTYFVT
GIVSWGEGCARKGKYGIYTKVTAFLKWIDRSMKT
Ligand information
Ligand IDL1D
InChIInChI=1S/C29H24ClFN4O4/c30-20-9-11-21(12-10-20)32-28(38)35-18-29(39,19-6-2-1-3-7-19)17-25(35)27(37)33-24-14-13-22(16-23(24)31)34-15-5-4-8-26(34)36/h1-16,25,39H,17-18H2,(H,32,38)(H,33,37)/t25-,29-/m1/s1
InChIKeyZFOBYPBSJINJKI-VAVYLYDRSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.6.1c1ccc(cc1)C2(CC(N(C2)C(=O)Nc3ccc(cc3)Cl)C(=O)Nc4ccc(cc4F)N5C=CC=CC5=O)O
OpenEye OEToolkits 1.6.1c1ccc(cc1)[C@]2(C[C@@H](N(C2)C(=O)Nc3ccc(cc3)Cl)C(=O)Nc4ccc(cc4F)N5C=CC=CC5=O)O
CACTVS 3.352O[C]1(C[CH](N(C1)C(=O)Nc2ccc(Cl)cc2)C(=O)Nc3ccc(cc3F)N4C=CC=CC4=O)c5ccccc5
ACDLabs 10.04Clc1ccc(cc1)NC(=O)N3CC(O)(c2ccccc2)CC3C(=O)Nc4c(F)cc(cc4)N5C=CC=CC5=O
CACTVS 3.352O[C@@]1(C[C@@H](N(C1)C(=O)Nc2ccc(Cl)cc2)C(=O)Nc3ccc(cc3F)N4C=CC=CC4=O)c5ccccc5
FormulaC29 H24 Cl F N4 O4
Name(2R,4S)-N^1^-(4-chlorophenyl)-N^2^-[2-fluoro-4-(2-oxopyridin-1(2H)-yl)phenyl]-4-hydroxy-4-phenylpyrrolidine-1,2-dicarboxamide
ChEMBLCHEMBL515107
DrugBank
ZINCZINC000038995990
PDB chain2w3k Chain A Residue 1245 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB2w3k Exploration of 4,4-Disubstituted Pyrrolidine-1,2-Dicarboxamides as Potent, Orally Active Factor Xa Inhibitors with Extended Duration of Action.
Resolution2.05 Å
Binding residue
(original residue number in PDB)		E97 T98 Y99 R143 E147 F174 A190 V213 W215 G216 G219 G226 Y228
Binding residue
(residue number reindexed from 1)		E83 T84 Y85 R132 E135 F162 A180 V203 W205 G206 G208 G216 Y218
Annotation score1
Binding affinityMOAD: ic50=0.08nM
PDBbind-CN: -logKd/Ki=10.10,IC50=0.08nM
BindingDB: IC50=0.08nM
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

View graph for
Molecular Function
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Biological Process
External links
PDB RCSB:2w3k, PDBe:2w3k, PDBj:2w3k
PDBsum2w3k
PubMed19231206
UniProtP00742|FA10_HUMAN Coagulation factor X (Gene Name=F10)

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