Structure of PDB 2bq6 Chain B Binding Site BS02

Receptor Information
>2bq6 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 IDIIB
InChIInChI=1S/C27H28ClN5O2S/c1-16(2)32-11-9-18(10-12-32)30-27(34)26-21(14-29)20-6-4-5-17(3)25(20)33(26)15-19-13-22(35-31-19)23-7-8-24(28)36-23/h4-8,13,16,18H,9-12,15H2,1-3H3,(H,30,34)
InChIKeyMCLVKEPZVPUETD-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.341CC(C)N1CCC(CC1)NC(=O)c2n(Cc3cc(on3)c4sc(Cl)cc4)c5c(C)cccc5c2C#N
OpenEye OEToolkits 1.5.0Cc1cccc2c1n(c(c2C#N)C(=O)NC3CCN(CC3)C(C)C)Cc4cc(on4)c5ccc(s5)Cl
ACDLabs 10.04Clc5sc(c1onc(c1)Cn4c2c(cccc2c(C#N)c4C(=O)NC3CCN(C(C)C)CC3)C)cc5
FormulaC27 H28 Cl N5 O2 S
Name1-{[5-(5-CHLORO-2-THIENYL)ISOXAZOL-3-YL]METHYL}-3-CYANO-N-(1-ISOPROPYLPIPERIDIN-4-YL)-7-METHYL-1H-INDOLE-2-CARBOXAMIDE;
1-[5-(5-CHLORO-THIOPHEN-2-YL)-ISOXAZOL-3-YLMETHYL]-3-CYANO-7-METHYL-1H-INDOLE-2-CARBOXYLIC ACID (1-ISOPROPYL-PIPERIDIN-4-YL)-AMIDE
ChEMBLCHEMBL191394
DrugBank
ZINCZINC000003816191
PDB chain2bq6 Chain B Residue 1246 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB2bq6 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.
Resolution3.0 Å
Binding residue
(original residue number in PDB)		Y99 E147 F174 D189 A190 C191 Q192 W215 G216 E217 G219 G226 Y228
Binding residue
(residue number reindexed from 1)		Y85 E135 F162 D179 A180 C181 Q182 W205 G206 E207 G208 G216 Y218
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=10.15,Ki=0.07nM
BindingDB: Ki=0.07nM
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:2bq6, PDBe:2bq6, PDBj:2bq6
PDBsum2bq6
PubMed15999990
UniProtP00742|FA10_HUMAN Coagulation factor X (Gene Name=F10)

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