Structure of PDB 6x5p Chain A Binding Site BS01

Receptor Information
>6x5p Chain A (length=232) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VVGGEDAKPGQFPWQVVLNGKVDAFCGGSIVNEKWIVTAAHCVEVKITVV
AGEHNIEETEHTEQKRNVIRIIPHHNYNAAINKYNHDIALLELDEPLVLN
SYVTPICIADKEYTNIFLKFGSGYVSGWGRVFHKGASALVLQYLRVPLVD
RATCLRSTKFTIYNNMFCAGFHEGGRDSCQGDSGGPHVTEVEGTSFLTGI
ISWGEECAMKGKYGIYTKVSRYVNWIKEKTKL
Ligand information
Ligand IDUQD
InChIInChI=1S/C18H16ClN5O/c1-10-2-4-11(5-3-10)15-16(25)18(23-9-22-15)24-14-7-6-12(17(20)21)8-13(14)19/h2-9,25H,1H3,(H3,20,21)(H,22,23,24)
InChIKeySNGWZJUYWHIFIM-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.385Cc1ccc(cc1)c2ncnc(Nc3ccc(cc3Cl)C(N)=N)c2O
ACDLabs 12.01n2cnc(c1ccc(C)cc1)c(O)c2Nc3ccc(/C(N)=N)cc3Cl
OpenEye OEToolkits 2.0.7[H]/N=C(\c1ccc(c(c1)Cl)Nc2c(c(ncn2)c3ccc(cc3)C)O)/N
OpenEye OEToolkits 2.0.7Cc1ccc(cc1)c2c(c(ncn2)Nc3ccc(cc3Cl)C(=N)N)O
FormulaC18 H16 Cl N5 O
Name3-chloro-4-{[5-hydroxy-6-(4-methylphenyl)pyrimidin-4-yl]amino}benzene-1-carboximidamide
ChEMBLCHEMBL4643810
DrugBank
ZINC
PDB chain6x5p Chain A Residue 301 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB6x5p Discovery of hydroxy pyrimidine Factor IXa inhibitors.
Resolution1.997 Å
Binding residue
(original residue number in PDB)		H56 D194 S195 C196 Q197 S200 S219 W220 G221 E222 C224
Binding residue
(residue number reindexed from 1)		H41 D177 S178 C179 Q180 S183 S202 W203 G204 E205 C207
Annotation score1
Binding affinityMOAD: ic50=30nM
BindingDB: IC50=30nM
Enzymatic activity
Catalytic site (original residue number in PDB) H56 D104 Q197 G198 D199 S200 G201
Catalytic site (residue number reindexed from 1) H41 D87 Q180 G181 D182 S183 G184
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:6x5p, PDBe:6x5p, PDBj:6x5p
PDBsum6x5p
PubMed32527459
UniProtP00740|FA9_HUMAN Coagulation factor IX (Gene Name=F9)

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