Structure of PDB 2qu6 Chain A Binding Site BS01

Receptor Information
>2qu6 Chain A (length=283) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
AERLPYDASKWEFPRDRLKLGKPLGQVIEADAFGIDKTCRTVAVKMLKTH
SEHRALMSELKILIHIGHHLNVVNLLGACTKPGGPLMVITEFCKFGNLST
YLRSKRNEFVPYKVAPEDLYKDFLTLEHLICYSFQVAKGMEFLASRKCIH
RDLAARNILLSEKNVVKICDFGPLKWMAPETIFDRVYTIQSDVWSFGVLL
WEIFSLGASPYPGVKIDEEFCRRLKEGTRMRAPDYTTPEMYQTMLDCWHG
EPSQRPTFSELVEHLGNLLQANAQQDRHHHHHH
Ligand information
Ligand ID857
InChIInChI=1S/C26H26ClN5O4/c1-28-25(33)22-14-19(9-10-29-22)35-18-6-8-23-21(13-18)31-26(36-23)30-16-5-7-20(27)24(12-16)34-15-17-4-3-11-32(17)2/h5-10,12-14,17H,3-4,11,15H2,1-2H3,(H,28,33)(H,30,31)/t17-/m0/s1
InChIKeyKMNCFOUKJYOZIF-KRWDZBQOSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0CNC(=O)c1cc(ccn1)Oc2ccc3c(c2)nc(o3)Nc4ccc(c(c4)OCC5CCCN5C)Cl
OpenEye OEToolkits 1.5.0CNC(=O)c1cc(ccn1)Oc2ccc3c(c2)nc(o3)Nc4ccc(c(c4)OC[C@@H]5CCC[N@]5C)Cl
ACDLabs 10.04O=C(NC)c5nccc(Oc1cc2nc(oc2cc1)Nc4ccc(Cl)c(OCC3N(C)CCC3)c4)c5
CACTVS 3.341CNC(=O)c1cc(Oc2ccc3oc(Nc4ccc(Cl)c(OC[CH]5CCCN5C)c4)nc3c2)ccn1
CACTVS 3.341CNC(=O)c1cc(Oc2ccc3oc(Nc4ccc(Cl)c(OC[C@@H]5CCCN5C)c4)nc3c2)ccn1
FormulaC26 H26 Cl N5 O4
Name4-({2-[(4-chloro-3-{[(2S)-1-methylpyrrolidin-2-yl]methoxy}phenyl)amino]-1,3-benzoxazol-5-yl}oxy)-N-methylpyridine-2-carboxamide
ChEMBLCHEMBL231568
DrugBank
ZINCZINC000014965294
PDB chain2qu6 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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PDB2qu6 Design, Synthesis, and Evaluation of Orally Active Benzimidazoles and Benzoxazoles as Vascular Endothelial Growth Factor-2 Receptor Tyrosine Kinase Inhibitors.
Resolution2.1 Å
Binding residue
(original residue number in PDB)		V848 A866 E885 T916 E917 F918 C919 I1025 L1035 C1045 D1046 F1047
Binding residue
(residue number reindexed from 1)		V27 A43 E59 T90 E91 F92 C93 I149 L159 C169 D170 F171
Annotation score1
Binding affinityMOAD: Ki=3nM
PDBbind-CN: -logKd/Ki=8.52,Ki=3nM
BindingDB: IC50=4.6nM,Ki=2.8nM
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

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Molecular Function
View graph for
Biological Process
External links
PDB RCSB:2qu6, PDBe:2qu6, PDBj:2qu6
PDBsum2qu6
PubMed17696416
UniProtP35968|VGFR2_HUMAN Vascular endothelial growth factor receptor 2 (Gene Name=KDR)

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