Structure of PDB 4yzu Chain A Binding Site BS01

Receptor Information
>4yzu Chain A (length=235) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VVGGEDAKPGQFPWQVVLNGKVDAFCGGSIVNEKWIVTAAHCVETGVKIT
VVAGEHNIEETEHTEQKRNVIRIIPHHNYNAAINKYNHDIALLELDEPLV
LNSYVTPICIADKEYTNIFLKFGSGYVSGWGRVFHKGASALVLQYLRVPL
VDRATCLRSTKFTIYNNMFCAGFHEGGRDSCQGDSGGPHVTEVEGTSFLT
GIISWGEECAMKGKYGIYTKVSRYVNWIKEKTKLT
Ligand information
Ligand ID4K6
InChIInChI=1S/C20H20N6O/c1-13-9-17-18(10-14(13)2)25-19(24-17)7-8-21-20(27)15-3-5-16(6-4-15)26-11-22-23-12-26/h3-6,9-12H,7-8H2,1-2H3,(H,21,27)(H,24,25)
InChIKeyQNOXZLGNUKPKFJ-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01O=C(c1ccc(cc1)n2cnnc2)NCCc3nc4c(n3)cc(c(c4)C)C
OpenEye OEToolkits 1.9.2Cc1cc2c(cc1C)nc([nH]2)CCNC(=O)c3ccc(cc3)n4cnnc4
CACTVS 3.385Cc1cc2[nH]c(CCNC(=O)c3ccc(cc3)n4cnnc4)nc2cc1C
FormulaC20 H20 N6 O
NameN-[2-(5,6-dimethyl-1H-benzimidazol-2-yl)ethyl]-4-(4H-1,2,4-triazol-4-yl)benzamide
ChEMBLCHEMBL3423033
DrugBank
ZINC
PDB chain4yzu Chain A Residue 301 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4yzu Rapid development of two factor IXa inhibitors from hit to lead.
Resolution1.41 Å
Binding residue
(original residue number in PDB)		Y99 F174 S190 C191 Q192 W215 G216 E217 C220
Binding residue
(residue number reindexed from 1)		Y86 F162 S180 C181 Q182 W205 G206 E207 C209
Annotation score1
Binding affinityMOAD: Ki=9uM
PDBbind-CN: -logKd/Ki=5.05,Ki=9uM
BindingDB: Ki=9000nM
Enzymatic activity
Catalytic site (original residue number in PDB) H57 D102 Q192 G193 D194 S195 G196
Catalytic site (residue number reindexed from 1) H41 D89 Q182 G183 D184 S185 G186
Enzyme Commision number 3.4.21.22: coagulation factor IXa.
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:4yzu, PDBe:4yzu, PDBj:4yzu
PDBsum4yzu
PubMed25937013
UniProtP00740|FA9_HUMAN Coagulation factor IX (Gene Name=F9)

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