Structure of PDB 3cp9 Chain A Binding Site BS01

Receptor Information
>3cp9 Chain A (length=288) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
AERLPYDASKWEFPRDRLKLGKPLQVIEADAFGIDKTATCRTVAVKMLKE
GATHSEHRALMSELKILIHIGHHLNVVNLLGACTKPGGPLMVITEFCKFG
NLSTYLRSKRNEFVPYKVAPEDLYKDFLTLEHLICYSFQVAKGMEFLASR
KCIHRDLAARNILLSEKNVVKICDFGLPLKWMAPETIFDRVYTIQSDVWS
FGVLLWEIFSLGASPYPGVKIDEEFCRRLKEGTRMRAPDYTTPEMYQTML
DCWHGEPSQRPTFSELVEHLGNLLQANAQQDRHHHHHH
Ligand information
Ligand IDC19
InChIInChI=1S/C24H23N5O/c1-14-8-9-29(17-5-6-18-20(11-17)27-13-24(18,2)3)22(30)21(14)15-4-7-19-16(10-15)12-26-23(25)28-19/h4-12,27H,13H2,1-3H3,(H2,25,26,28)
InChIKeyLHLGUOHREUTYTO-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0CC1=C(C(=O)N(C=C1)c2ccc3c(c2)NCC3(C)C)c4ccc5c(c4)cnc(n5)N
ACDLabs 10.04O=C5C(c2cc1cnc(nc1cc2)N)=C(C=CN5c3ccc4c(c3)NCC4(C)C)C
CACTVS 3.341CC1=C(C(=O)N(C=C1)c2ccc3c(NCC3(C)C)c2)c4ccc5nc(N)ncc5c4
FormulaC24 H23 N5 O
Name3-(2-aminoquinazolin-6-yl)-1-(3,3-dimethylindolin-6-yl)-4-methylpyridin-2(1H)-one
ChEMBLCHEMBL493986
DrugBankDB07514
ZINCZINC000016052723
PDB chain3cp9 Chain A Residue 501 [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]
PDB3cp9 Discovery of Aryl Aminoquinazoline Pyridones as Potent, Selective, and Orally Efficacious Inhibitors of Receptor Tyrosine Kinase c-Kit.
Resolution2.5 Å
Binding residue
(original residue number in PDB)		L840 V848 A866 K868 E885 L889 V898 T916 C919 L1035 C1045 D1046 F1047
Binding residue
(residue number reindexed from 1)		L24 V26 A44 K46 E63 L67 V76 T94 C97 L163 C173 D174 F175
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=7.32,IC50=0.048uM
BindingDB: IC50=48nM
Enzymatic activity
Catalytic site (original residue number in PDB) D1028 A1030 R1032 N1033 D1046
Catalytic site (residue number reindexed from 1) D156 A158 R160 N161 D174
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:3cp9, PDBe:3cp9, PDBj:3cp9
PDBsum3cp9
PubMed18447379
UniProtP35968|VGFR2_HUMAN Vascular endothelial growth factor receptor 2 (Gene Name=KDR)

[Back to BioLiP]