Structure of PDB 3lc5 Chain A Binding Site BS02

Receptor Information
>3lc5 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
LNSYVTPICIADKEYTNIFLKFGSGYVSGWGRVFHKGRSALVLQYLRVPL
VDRATCLRSTKFTIYNNMFCAGFHEGGRDSCQGDSGGPHVTEVEGTSFLT
GIISWGEECAMKGKYGIYTKVSRYVNWIKEKTKLT
Ligand information
Ligand IDIZX
InChIInChI=1S/C24H20N4O2S/c25-22(26)20-14-17-18(12-7-13-19(17)31-20)29-21(15-8-3-1-4-9-15)24-27-23(28-30-24)16-10-5-2-6-11-16/h1-14,21-22H,25-26H2/t21-/m1/s1
InChIKeyVBSNODZWDZSFEZ-OAQYLSRUSA-N
SMILES
SoftwareSMILES
CACTVS 3.352NC(N)c1sc2cccc(O[CH](c3onc(n3)c4ccccc4)c5ccccc5)c2c1
OpenEye OEToolkits 1.7.0c1ccc(cc1)c2nc(on2)[C@@H](c3ccccc3)Oc4cccc5c4cc(s5)C(N)N
OpenEye OEToolkits 1.7.0c1ccc(cc1)c2nc(on2)C(c3ccccc3)Oc4cccc5c4cc(s5)C(N)N
CACTVS 3.352NC(N)c1sc2cccc(O[C@@H](c3onc(n3)c4ccccc4)c5ccccc5)c2c1
FormulaC24 H20 N4 O2 S
Name1-{4-[(R)-phenyl(3-phenyl-1,2,4-oxadiazol-5-yl)methoxy]-1-benzothiophen-2-yl}methanediamine
ChEMBL
DrugBank
ZINCZINC000058661034
PDB chain3lc5 Chain A Residue 1 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3lc5 Structure Based Drug Design: Development of Potent and Selective Factor IXa (FIXa) Inhibitors.
Resolution2.62 Å
Binding residue
(original residue number in PDB)		R143 H147 F174 D189 S190 Q192 S195 W215 G216 E219 C220
Binding residue
(residue number reindexed from 1)		R132 H135 F162 D179 S180 Q182 S185 W205 G206 E208 C209
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=6.57,Ki=0.27uM
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

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Molecular Function
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Biological Process
External links
PDB RCSB:3lc5, PDBe:3lc5, PDBj:3lc5
PDBsum3lc5
PubMed20121197
UniProtP00740|FA9_HUMAN Coagulation factor IX (Gene Name=F9)

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