Structure of PDB 5ew3 Chain A Binding Site BS01

Receptor Information
>5ew3 Chain A (length=274) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PYDASKWEFPRDRLKLGKPLGRGAFGQVIEADAFGIDKTATCRTVAVKML
KEGATHSEHRALMSELKILIHIGHHLNVVNLLGACTKPGGPLMVIVEFCK
FGNLSTYLRSKRNEFVPYKVKDFLTLEHLICYSFQVAKGMEFLASRKCIH
RDLAARNILLSEKNVVKICDFGLPLKWMAPETIFDRVYTIQSDVWSFGVL
LWEIFSLGASPYPGVKIDEEFCRRLKEGTRMRAPDYTTPEMYQTMLDCWH
GEPSQRPTFSELVEHLGNLLQANA
Ligand information
Ligand ID5T2
InChIInChI=1S/C20H16F3N3O/c21-20(22,23)15-4-3-5-16(12-15)26-19(27)17-6-1-2-7-18(17)25-13-14-8-10-24-11-9-14/h1-12,25H,13H2,(H,26,27)
InChIKeyBLAFVGLBBOPRLP-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.4c1ccc(c(c1)C(=O)Nc2cccc(c2)C(F)(F)F)NCc3ccncc3
CACTVS 3.385FC(F)(F)c1cccc(NC(=O)c2ccccc2NCc3ccncc3)c1
FormulaC20 H16 F3 N3 O
Name2-(pyridin-4-ylmethylamino)-~{N}-[3-(trifluoromethyl)phenyl]benzamide
ChEMBLCHEMBL153843
DrugBank
ZINCZINC000001912572
PDB chain5ew3 Chain A Residue 1201 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5ew3 A Novel Potent Oral Series of VEGFR2 Inhibitors Abrogate Tumor Growth by Inhibiting Angiogenesis.
Resolution2.5 Å
Binding residue
(original residue number in PDB)		A866 K868 E885 V916 C919 H1026 L1035 I1044 C1045 D1046 F1047
Binding residue
(residue number reindexed from 1)		A46 K48 E65 V96 C99 H150 L159 I168 C169 D170 F171
Annotation score1
Binding affinityMOAD: ic50=0.0012uM
PDBbind-CN: -logKd/Ki=8.92,IC50=0.0012uM
BindingDB: IC50=23nM
Enzymatic activity
Catalytic site (original residue number in PDB) D1028 A1030 R1032 N1033 D1046
Catalytic site (residue number reindexed from 1) D152 A154 R156 N157 D170
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
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Biological Process
External links
PDB RCSB:5ew3, PDBe:5ew3, PDBj:5ew3
PDBsum5ew3
PubMed26629594
UniProtP35968|VGFR2_HUMAN Vascular endothelial growth factor receptor 2 (Gene Name=KDR)

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