Structure of PDB 5egm Chain A Binding Site BS01

Receptor Information
>5egm 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 ID5NY
InChIInChI=1S/C29H24ClN9O/c1-18-7-10-24-22(13-18)26(27-34-36-37-35-27)25-11-12-29(15-39(24)25,19-5-3-2-4-6-19)33-28(40)21-9-8-20(14-23(21)30)38-16-31-32-17-38/h2-10,13-14,16-17H,11-12,15H2,1H3,(H,33,40)(H,34,35,36,37)/t29-/m1/s1
InChIKeyTUCDMISJVGVBLL-GDLZYMKVSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.4Cc1ccc2c(c1)c(c3n2C[C@](CC3)(c4ccccc4)NC(=O)c5ccc(cc5Cl)n6cnnc6)c7[nH]nnn7
CACTVS 3.385Cc1ccc2n3C[C](CCc3c(c4[nH]nnn4)c2c1)(NC(=O)c5ccc(cc5Cl)n6cnnc6)c7ccccc7
CACTVS 3.385Cc1ccc2n3C[C@@](CCc3c(c4[nH]nnn4)c2c1)(NC(=O)c5ccc(cc5Cl)n6cnnc6)c7ccccc7
OpenEye OEToolkits 2.0.4Cc1ccc2c(c1)c(c3n2CC(CC3)(c4ccccc4)NC(=O)c5ccc(cc5Cl)n6cnnc6)c7[nH]nnn7
FormulaC29 H24 Cl N9 O
Name2-chloranyl-~{N}-[(7~{S})-2-methyl-7-phenyl-10-(1~{H}-1,2,3,4-tetrazol-5-yl)-8,9-dihydro-6~{H}-pyrido[1,2-a]indol-7-yl]-4-(1,2,4-triazol-4-yl)benzamide
ChEMBL
DrugBank
ZINCZINC000263621069
PDB chain5egm Chain A Residue 303 [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]
PDB5egm Development of a novel tricyclic class of potent and selective FIXa inhibitors.
Resolution1.841 Å
Binding residue
(original residue number in PDB)		H57 Y99 H147 F174 C191 Q192 S195 W215 G216 E217
Binding residue
(residue number reindexed from 1)		H41 Y86 H135 F162 C181 Q182 S185 W205 G206 E207
Annotation score1
Binding affinityMOAD: Ki=2.4nM
PDBbind-CN: -logKd/Ki=8.62,Ki=2.4nM
BindingDB: IC50=2.38nM
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:5egm, PDBe:5egm, PDBj:5egm
PDBsum5egm
PubMed26318999
UniProtP00740|FA9_HUMAN Coagulation factor IX (Gene Name=F9)

[Back to BioLiP]