Structure of PDB 2qu5 Chain A Binding Site BS01

Receptor Information
>2qu5 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]
HAERLPYDASKWEFPRDRLKLGKPLGRGAFGQVIEADAFGIDKTATCRTV
AVKMLKEGATHSEHRALMSELKILIHIGHHLNVVNLLGACTKPGGPLMVI
TEFCKFGNLSTYLRSKRNEFVPYKVAPEDLYKDFLTLEHLICYSFQVAKG
MEFLASRKCIHRDLAARNILLSEKNVVKICDFGLADARLPLKWMAPETIF
DRVYTIQSDVWSFGVLLWEIFSLGASPYPGVKIDEEFCRRLKEGTRMRAP
DYTTPEMYQTMLDCWHGEPSQRPTFSELVEHLGNLLQANAQQ
Ligand information
Ligand ID276
InChIInChI=1S/C21H15ClF3N5O2/c1-26-19(31)18-10-13(6-7-27-18)32-12-3-5-16-17(9-12)30-20(29-16)28-11-2-4-15(22)14(8-11)21(23,24)25/h2-10H,1H3,(H,26,31)(H2,28,29,30)
InChIKeyZJLSMLDOCGOURY-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04FC(F)(F)c1cc(ccc1Cl)Nc4nc3ccc(Oc2ccnc(C(=O)NC)c2)cc3n4
CACTVS 3.341CNC(=O)c1cc(Oc2ccc3nc(Nc4ccc(Cl)c(c4)C(F)(F)F)[nH]c3c2)ccn1
OpenEye OEToolkits 1.5.0CNC(=O)c1cc(ccn1)Oc2ccc3c(c2)[nH]c(n3)Nc4ccc(c(c4)C(F)(F)F)Cl
FormulaC21 H15 Cl F3 N5 O2
Name4-[[2-[[4-chloro-3-(trifluoromethyl)phenyl]amino]-3H-benzimidazol-5-yl]oxy]-N-methyl-pyridine-2-carboxamide
ChEMBLCHEMBL394826
DrugBankDB06938
ZINCZINC000016052883
PDB chain2qu5 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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PDB2qu5 Design, Synthesis, and Evaluation of Orally Active Benzimidazoles and Benzoxazoles as Vascular Endothelial Growth Factor-2 Receptor Tyrosine Kinase Inhibitors.
Resolution2.95 Å
Binding residue
(original residue number in PDB)		L840 V848 A866 K868 E885 L889 T916 E917 F918 C919 G922 L1019 L1035 C1045 D1046 F1047
Binding residue
(residue number reindexed from 1)		L25 V33 A51 K53 E70 L74 T101 E102 F103 C104 G107 L154 L170 C180 D181 F182
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=8.06,Ki=8.7nM
BindingDB: Ki=9nM
Enzymatic activity
Catalytic site (original residue number in PDB) D1028 A1030 R1032 N1033 D1046 D1064
Catalytic site (residue number reindexed from 1) D163 A165 R167 N168 D181 D186
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:2qu5, PDBe:2qu5, PDBj:2qu5
PDBsum2qu5
PubMed17696416
UniProtP35968|VGFR2_HUMAN Vascular endothelial growth factor receptor 2 (Gene Name=KDR)

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