Structure of PDB 3b8r Chain B Binding Site BS01

Receptor Information
>3b8r Chain B (length=267) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PYDASKWEFPRDRLKLGKPLGRGQVIEADAFGIDKTATCRTVAVKMLATH
SEHRALMSELKILIHIGHHLNVVNLLGACTKPGGPLMVITEFCKFGNLST
YLRSKRNEFVPYKYKDFLTLEHLICYSFQVAKGMEFLASRKCIHRDLAAR
NILLSEKNVVKICDFGLLPLKWMAPETIFDRVYTIQSDVWSFGVLLWEIF
SLGASPYPGVKIDEEFCRRLKEGTRMRAPDYTTPEMYQTMLDCWHGEPSQ
RPTFSELVEHLGNLLQA
Ligand information
Ligand ID887
InChIInChI=1S/C25H22N2O4/c1-29-23-13-20-21(14-24(23)30-2)26-11-10-22(20)31-17-8-9-18-15(12-17)4-3-5-19(18)25(28)27-16-6-7-16/h3-5,8-14,16H,6-7H2,1-2H3,(H,27,28)
InChIKeyZATGFXTWDKIEKC-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04O=C(NC1CC1)c5cccc4cc(Oc2c3cc(OC)c(OC)cc3ncc2)ccc45
OpenEye OEToolkits 1.5.0COc1cc2c(ccnc2cc1OC)Oc3ccc4c(c3)cccc4C(=O)NC5CC5
CACTVS 3.341COc1cc2nccc(Oc3ccc4c(cccc4C(=O)NC5CC5)c3)c2cc1OC
FormulaC25 H22 N2 O4
NameN-cyclopropyl-6-[(6,7-dimethoxyquinolin-4-yl)oxy]naphthalene-1-carboxamide
ChEMBLCHEMBL272198
DrugBankDB07274
ZINCZINC000016052729
PDB chain3b8r Chain B Residue 202 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3b8r Evaluation of a Series of Naphthamides as Potent, Orally Active Vascular Endothelial Growth Factor Receptor-2 Tyrosine Kinase Inhibitors
Resolution2.7 Å
Binding residue
(original residue number in PDB)		L840 A866 K868 E885 L889 T916 C919 L1035 C1045 D1046 F1047
Binding residue
(residue number reindexed from 1)		L20 A43 K45 E59 L63 T90 C93 L153 C163 D164 F165
Annotation score1
Binding affinityBindingDB: IC50=0.600000nM
Enzymatic activity
Catalytic site (original residue number in PDB) D1028 A1030 R1032 N1033 D1046
Catalytic site (residue number reindexed from 1) D146 A148 R150 N151 D164
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:3b8r, PDBe:3b8r, PDBj:3b8r
PDBsum3b8r
PubMed18324759
UniProtP35968|VGFR2_HUMAN Vascular endothelial growth factor receptor 2 (Gene Name=KDR)

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