Structure of PDB 2bqw Chain B Binding Site BS02

Receptor Information
>2bqw Chain B (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 IDIIE
InChIInChI=1S/C25H29ClN4O2/c1-17(2)29-13-11-21(12-14-29)28-25(32)23-15-18-5-3-4-6-22(18)30(23)16-24(31)27-20-9-7-19(26)8-10-20/h3-10,15,17,21H,11-14,16H2,1-2H3,(H,27,31)(H,28,32)
InChIKeyBDLMBQRBNPDCSS-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0CC(C)N1CCC(CC1)NC(=O)c2cc3ccccc3n2CC(=O)Nc4ccc(cc4)Cl
ACDLabs 10.04Clc1ccc(cc1)NC(=O)Cn2c4ccccc4cc2C(=O)NC3CCN(C(C)C)CC3
CACTVS 3.341CC(C)N1CCC(CC1)NC(=O)c2cc3ccccc3n2CC(=O)Nc4ccc(Cl)cc4
FormulaC25 H29 Cl N4 O2
Name1-{2-[(4-CHLOROPHENYL)AMINO]-2-OXOETHYL}-N-(1-ISOPROPYLPIPERIDIN-4-YL)-1H-INDOLE-2-CARBOXAMIDE
ChEMBLCHEMBL368238
DrugBankDB07974
ZINCZINC000013646547
PDB chain2bqw Chain B 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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PDB2bqw Probing the Subpockets of Factor Xa Reveals Two Binding Modes for Inhibitors Based on a 2-Carboxyindole Scaffold: A Study Combining Structure-Activity Relationship and X-Ray Crystallography.
Resolution2.95 Å
Binding residue
(original residue number in PDB)		E97 Y99 R143 F174 D189 A190 Q192 V213 W215 G216 G219 C220 G226 I227 Y228
Binding residue
(residue number reindexed from 1)		E83 Y85 R132 F162 D179 A180 Q182 V203 W205 G206 G208 C209 G216 I217 Y218
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=8.52,Ki=3nM
BindingDB: 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 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:2bqw, PDBe:2bqw, PDBj:2bqw
PDBsum2bqw
PubMed15999990
UniProtP00742|FA10_HUMAN Coagulation factor X (Gene Name=F10)

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