Structure of PDB 3ewh Chain A Binding Site BS01

Receptor Information
>3ewh Chain A (length=300) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
EHAERLPYDASKWEFPRDRLKLGKPLGRGAFGQVIEADAFGIDTCRTVAV
KMLKEGATHSEHRALMSELKILIHIGHHLNVVNLLGACTKPGGPLMVITE
FCKFGNLSTYLRSKRNEFVPYKVAPEDLYKDFLTLEHLICYSFQVAKGME
FLASRKCIHRDLAARNILLSEKNVVKICDFGLARDPDYVRLPLKWMAPET
IFDRVYTIQSDVWSFGVLLWEIFSLGASPYPGVKIDEEFCRRLKEGTRMR
APDYTTPEMYQTMLDCWHGEPSQRPTFSELVEHLGNLLQANAQQDRHHHH
Ligand information
Ligand IDK11
InChIInChI=1S/C28H20F3N7O/c1-32-26-34-14-12-21(35-26)19-7-4-13-33-25(19)39-24-11-10-20(17-5-2-3-6-18(17)24)36-27-37-22-9-8-16(28(29,30)31)15-23(22)38-27/h2-15H,1H3,(H,32,34,35)(H2,36,37,38)
InChIKeyVIHXUAKPZPXVSW-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0CNc1nccc(n1)c2cccnc2Oc3ccc(c4c3cccc4)Nc5[nH]c6cc(ccc6n5)C(F)(F)F
ACDLabs 10.04FC(F)(F)c6cc1c(nc(n1)Nc5c2ccccc2c(Oc4ncccc4c3nc(ncc3)NC)cc5)cc6
CACTVS 3.341CNc1nccc(n1)c2cccnc2Oc3ccc(Nc4[nH]c5cc(ccc5n4)C(F)(F)F)c6ccccc36
FormulaC28 H20 F3 N7 O
NameN-[4-({3-[2-(methylamino)pyrimidin-4-yl]pyridin-2-yl}oxy)naphthalen-1-yl]-6-(trifluoromethyl)-1H-benzimidazol-2-amine
ChEMBLCHEMBL463323
DrugBank
ZINCZINC000039205007
PDB chain3ewh Chain A Residue 1 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB3ewh Pyridyl-pyrimidine benzimidazole derivatives as potent, selective, and orally bioavailable inhibitors of Tie-2 kinase.
Resolution1.6 Å
Binding residue
(original residue number in PDB)		L840 V848 A866 K868 E885 T916 F918 C919 L1019 L1035 C1045 D1046 F1047
Binding residue
(residue number reindexed from 1)		L26 V34 A49 K51 E68 T99 F101 C102 L152 L168 C178 D179 F180
Annotation score1
Binding affinityMOAD: ic50=69nM
PDBbind-CN: -logKd/Ki=7.16,IC50=69nM
BindingDB: IC50=70nM
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
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Biological Process
External links
PDB RCSB:3ewh, PDBe:3ewh, PDBj:3ewh
PDBsum3ewh
PubMed19062275
UniProtP35968|VGFR2_HUMAN Vascular endothelial growth factor receptor 2 (Gene Name=KDR)

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