Structure of PDB 3cpc Chain A Binding Site BS01

Receptor Information
>3cpc Chain A (length=284) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
LPYDASKWEFPRDRLKLGKPLQVIEADAFGIDKTATCRTVAVKMLKEGAT
HSEHRALMSELKILIHIGHHLNVVNLLGACTKPGGPLMVITEFCKFGNLS
TYLRSKRNEFVPYKVAPEDLYKDFLTLEHLICYSFQVAKGMEFLASRKCI
HRDLAARNILLSEKNVVKICDFLPLKWMAPETIFDRVYTIQSDVWSFGVL
LWEIFSLGASPYPGVKIDEEFCRRLKEGTRMRAPDYTTPEMYQTMLDCWH
GEPSQRPTFSELVEHLGNLLQANAQQDRHHHHHH
Ligand information
Ligand IDC52
InChIInChI=1S/C21H15F3N4O/c1-12-7-8-28(16-4-2-3-15(10-16)21(22,23)24)19(29)18(12)13-5-6-17-14(9-13)11-26-20(25)27-17/h2-11H,1H3,(H2,25,26,27)
InChIKeyHXUZQEYFKAZBPX-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0CC1=C(C(=O)N(C=C1)c2cccc(c2)C(F)(F)F)c3ccc4c(c3)cnc(n4)N
CACTVS 3.341CC1=C(C(=O)N(C=C1)c2cccc(c2)C(F)(F)F)c3ccc4nc(N)ncc4c3
ACDLabs 10.04FC(F)(F)c1cc(ccc1)N2C=CC(=C(C2=O)c4cc3cnc(nc3cc4)N)C
FormulaC21 H15 F3 N4 O
Name3-(2-aminoquinazolin-6-yl)-4-methyl-1-[3-(trifluoromethyl)phenyl]pyridin-2(1H)-one
ChEMBLCHEMBL504805
DrugBankDB07528
ZINCZINC000016052721
PDB chain3cpc 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]
PDB3cpc Discovery of Aryl Aminoquinazoline Pyridones as Potent, Selective, and Orally Efficacious Inhibitors of Receptor Tyrosine Kinase c-Kit.
Resolution2.4 Å
Binding residue
(original residue number in PDB)		V848 A866 K868 E885 L889 V899 T916 C919 L1035 C1045 D1046 F1047
Binding residue
(residue number reindexed from 1)		V23 A41 K43 E60 L64 V74 T91 C94 L160 C170 D171 F172
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=5.30,IC50=5uM
BindingDB: IC50=>5000nM
Enzymatic activity
Catalytic site (original residue number in PDB) D1028 A1030 R1032 N1033 D1046
Catalytic site (residue number reindexed from 1) D153 A155 R157 N158 D171
Enzyme Commision number 2.7.10.1: receptor protein-tyrosine kinase.
Gene Ontology
Molecular Function
GO:0004672 protein kinase activity
GO:0004713 protein tyrosine kinase activity
GO:0004714 transmembrane receptor protein tyrosine kinase activity
GO:0005524 ATP binding
Biological Process
GO:0006468 protein phosphorylation
GO:0007169 cell surface receptor protein tyrosine kinase signaling pathway

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:3cpc, PDBe:3cpc, PDBj:3cpc
PDBsum3cpc
PubMed18447379
UniProtP35968|VGFR2_HUMAN Vascular endothelial growth factor receptor 2 (Gene Name=KDR)

[Back to BioLiP]