Structure of PDB 3b8q Chain A Binding Site BS01

Receptor Information
>3b8q Chain A (length=292) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ERLPYDASKWEFPRDRLKLGKPLGRGAFGQVIEADAFGIDKTATCRTVAV
KMLKEGATHSEHRALMSELKILIHIGHHLNVVNLLGACTKPGGPLMVITE
FCKFGNLSTYLRSKRNEFVPYKVAPEDLYKDFLTLEHLICYSFQVAKGME
FLASRKCIHRDLAARNILLSEKNVVKICDFLPLKWMAPETIFDRVYTIQS
DVWSFGVLLWEIFSLGASPYPGVKIDEEFCRRLKEGTRMRAPDYTTPEMY
QTMLDCWHGEPSQRPTFSELVEHLGNLLQANAQQDRHHHHHH
Ligand information
Ligand ID900
InChIInChI=1S/C28H21ClN2O4/c1-33-26-15-23-24(16-27(26)34-2)30-13-12-25(23)35-20-10-11-21-17(14-20)4-3-5-22(21)28(32)31-19-8-6-18(29)7-9-19/h3-16H,1-2H3,(H,31,32)
InChIKeyWUBFAXNVDMCVIO-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.341COc1cc2nccc(Oc3ccc4c(cccc4C(=O)Nc5ccc(Cl)cc5)c3)c2cc1OC
OpenEye OEToolkits 1.5.0COc1cc2c(ccnc2cc1OC)Oc3ccc4c(c3)cccc4C(=O)Nc5ccc(cc5)Cl
ACDLabs 10.04Clc1ccc(cc1)NC(=O)c5cccc4cc(Oc2c3cc(OC)c(OC)cc3ncc2)ccc45
FormulaC28 H21 Cl N2 O4
NameN-(4-chlorophenyl)-6-[(6,7-dimethoxyquinolin-4-yl)oxy]naphthalene-1-carboxamide
ChEMBLCHEMBL429743
DrugBank
ZINCZINC000016052730
PDB chain3b8q Chain A Residue 501 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3b8q Naphthamides as Novel and Potent Vascular Endothelial Growth Factor Receptor Tyrosine Kinase Inhibitors: Design, Synthesis and Evaluation
Resolution2.75 Å
Binding residue
(original residue number in PDB)		L840 V848 A866 K868 E885 L889 T916 C919 L1035 C1045 D1046 F1047
Binding residue
(residue number reindexed from 1)		L23 V31 A49 K51 E68 L72 T99 C102 L168 C178 D179 F180
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=9.30,IC50=0.5nM
BindingDB: IC50=0.480000nM
Enzymatic activity
Catalytic site (original residue number in PDB) D1028 A1030 R1032 N1033 D1046
Catalytic site (residue number reindexed from 1) D161 A163 R165 N166 D179
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:3b8q, PDBe:3b8q, PDBj:3b8q
PDBsum3b8q
PubMed18324761
UniProtP35968|VGFR2_HUMAN Vascular endothelial growth factor receptor 2 (Gene Name=KDR)

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