Structure of PDB 2w3i Chain A Binding Site BS02

Receptor Information
>2w3i 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 IDL1C
InChIInChI=1S/C28H22ClF2N5O4/c29-17-4-7-19(8-5-17)33-27(39)36-16-28(40,21-10-6-18(30)13-22(21)31)14-23(36)26(38)34-24-11-9-20(15-32-24)35-12-2-1-3-25(35)37/h1-13,15,23,40H,14,16H2,(H,33,39)(H,32,34,38)/t23-,28-/m1/s1
InChIKeyBGECSWGTDIXGJY-QDPGVEIFSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.6.1c1cc(ccc1NC(=O)N2CC(CC2C(=O)Nc3ccc(cn3)N4C=CC=CC4=O)(c5ccc(cc5F)F)O)Cl
ACDLabs 10.04Clc1ccc(cc1)NC(=O)N3CC(O)(c2ccc(F)cc2F)CC3C(=O)Nc4ncc(cc4)N5C=CC=CC5=O
CACTVS 3.352O[C@@]1(C[C@@H](N(C1)C(=O)Nc2ccc(Cl)cc2)C(=O)Nc3ccc(cn3)N4C=CC=CC4=O)c5ccc(F)cc5F
CACTVS 3.352O[C]1(C[CH](N(C1)C(=O)Nc2ccc(Cl)cc2)C(=O)Nc3ccc(cn3)N4C=CC=CC4=O)c5ccc(F)cc5F
OpenEye OEToolkits 1.6.1c1cc(ccc1NC(=O)N2C[C@](C[C@@H]2C(=O)Nc3ccc(cn3)N4C=CC=CC4=O)(c5ccc(cc5F)F)O)Cl
FormulaC28 H22 Cl F2 N5 O4
Name(2R,4S)-N^1^-(4-chlorophenyl)-4-(2,4-difluorophenyl)-4-hydroxy-N^2^-(2-oxo-2H-1,3'-bipyridin-6'-yl)pyrrolidine-1,2-dicarboxamide
ChEMBLCHEMBL474678
DrugBank
ZINCZINC000038995989
PDB chain2w3i Chain A Residue 1246 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB2w3i Exploration of 4,4-Disubstituted Pyrrolidine-1,2-Dicarboxamides as Potent, Orally Active Factor Xa Inhibitors with Extended Duration of Action.
Resolution1.9 Å
Binding residue
(original residue number in PDB)		E97 T98 Y99 E147 F174 A190 Q192 V213 W215 G216 G219 G226 Y228
Binding residue
(residue number reindexed from 1)		E83 T84 Y85 E135 F162 A180 Q182 V203 W205 G206 G208 G216 Y218
Annotation score1
Binding affinityMOAD: ic50=0.1nM
PDBbind-CN: -logKd/Ki=10.00,IC50=0.1nM
BindingDB: IC50=0.1nM
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:2w3i, PDBe:2w3i, PDBj:2w3i
PDBsum2w3i
PubMed19231206
UniProtP00742|FA10_HUMAN Coagulation factor X (Gene Name=F10)

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