Structure of PDB 3lc3 Chain A Binding Site BS01

Receptor Information
>3lc3 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 IDIYX
InChIInChI=1S/C17H18N2O2S/c1-20-13-5-3-11(8-14(13)21-2)10-4-6-15-12(7-10)9-16(22-15)17(18)19/h3-9,17H,18-19H2,1-2H3
InChIKeyXZOIHOQTJVDJCE-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.352COc1ccc(cc1OC)c2ccc3sc(cc3c2)C(N)N
OpenEye OEToolkits 1.7.0COc1ccc(cc1OC)c2ccc3c(c2)cc(s3)C(N)N
FormulaC17 H18 N2 O2 S
Name1-[5-(3,4-dimethoxyphenyl)-1-benzothiophen-2-yl]methanediamine
ChEMBL
DrugBank
ZINCZINC000058639142
PDB chain3lc3 Chain A Residue 1 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB3lc3 Studies of Benzothiophene Template as Potent Factor IXa (FIXa) Inhibitors in Thrombosis.
Resolution1.9 Å
Binding residue
(original residue number in PDB)		D189 S190 C191 Q192 S195 W215 G216 E217 C220
Binding residue
(residue number reindexed from 1)		D179 S180 C181 Q182 S185 W205 G206 E207 C209
Annotation score1
Binding affinityMOAD: Ki=5.9uM
PDBbind-CN: -logKd/Ki=5.23,Ki=5.9uM
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
View graph for
Biological Process
External links
PDB RCSB:3lc3, PDBe:3lc3, PDBj:3lc3
PDBsum3lc3
PubMed20121198
UniProtP00740|FA9_HUMAN Coagulation factor IX (Gene Name=F9)

[Back to BioLiP]