Structure of PDB 3cpb Chain A Binding Site BS01

Receptor Information
>3cpb Chain A (length=285) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
RLPYDASKWEFPRDRLKLGKPLQVIEADAFGIDKTATCRTVAVKMLKEGA
THSEHRALMSELKILIHIGHHLNVVNLLGACTKPGGPLMVITEFCKFGNL
STYLRSKRNEFVPYKVAPEDLYKDFLTLEHLICYSFQVAKGMEFLASRKC
IHRDLAARNILLSEKNVVKICDFLPLKWMAPETIFDRVYTIQSDVWSFGV
LLWEIFSLGASPYPGVKIDEEFCRRLKEGTRMRAPDYTTPEMYQTMLDCW
HGEPSQRPTFSELVEHLGNLLQANAQQDRHHHHHH
Ligand information
Ligand IDC92
InChIInChI=1S/C21H26N4O2/c1-14-6-7-16(20(26)23-11-10-15-4-2-3-5-15)12-18(14)21(27)25-17-8-9-19(22)24-13-17/h6-9,12-13,15H,2-5,10-11H2,1H3,(H2,22,24)(H,23,26)(H,25,27)
InChIKeyCLEGTVIMOPPIBR-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04O=C(NCCC1CCCC1)c3cc(C(=O)Nc2cnc(N)cc2)c(cc3)C
OpenEye OEToolkits 1.5.0Cc1ccc(cc1C(=O)Nc2ccc(nc2)N)C(=O)NCCC3CCCC3
CACTVS 3.341Cc1ccc(cc1C(=O)Nc2ccc(N)nc2)C(=O)NCCC3CCCC3
FormulaC21 H26 N4 O2
NameN'-(6-aminopyridin-3-yl)-N-(2-cyclopentylethyl)-4-methyl-benzene-1,3-dicarboxamide
ChEMBLCHEMBL487431
DrugBankDB07537
ZINC
PDB chain3cpb Chain A Residue 1 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3cpb Discovery of Aryl Aminoquinazoline Pyridones as Potent, Selective, and Orally Efficacious Inhibitors of Receptor Tyrosine Kinase c-Kit.
Resolution2.7 Å
Binding residue
(original residue number in PDB)		A866 K868 E885 V914 T916 F918 C919 L1035 C1045 D1046 F1047
Binding residue
(residue number reindexed from 1)		A42 K44 E61 V90 T92 F94 C95 L161 C171 D172 F173
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=4.60,IC50=25uM
BindingDB: IC50=>25000nM
Enzymatic activity
Catalytic site (original residue number in PDB) D1028 A1030 R1032 N1033 D1046
Catalytic site (residue number reindexed from 1) D154 A156 R158 N159 D172
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

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Molecular Function
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Biological Process
External links
PDB RCSB:3cpb, PDBe:3cpb, PDBj:3cpb
PDBsum3cpb
PubMed18447379
UniProtP35968|VGFR2_HUMAN Vascular endothelial growth factor receptor 2 (Gene Name=KDR)

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