Structure of PDB 3vhe Chain A Binding Site BS01

Receptor Information
>3vhe Chain A (length=303) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
LPLDEHCERLPYDASKWEFPRDRLKLGKPLGRGAFGQVIEADAFGIDKTA
TCRTVAVKMLKEGATHSEHRALMSELKILIHIGHHLNVVNLLGACTKPGG
PLMVIVEFCKFGNLSTYLRSKRNEFVPYKDLYKDFLTLEHLICYSFQVAK
GMEFLASRKCIHRDLAARNILLSEKNVVKICDFGLARDIYKDPDYVRKAR
LPLKWMAPETIFDRVYTIQSDVWSFGVLLWEIFSLGASPYPGVKIDEEFC
RRLKEGTRMRAPDYTTPEMYQTMLDCWHGEPSQRPTFSELVEHLGNLLQA
NAQ
Ligand information
Ligand ID42Q
InChIInChI=1S/C21H15F4N5O2/c1-30-8-7-17-18(30)19(27-11-26-17)32-14-5-6-16(15(22)10-14)29-20(31)28-13-4-2-3-12(9-13)21(23,24)25/h2-11H,1H3,(H2,28,29,31)
InChIKeyTWOLOZGQZKJZKJ-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.370Cn1ccc2ncnc(Oc3ccc(NC(=O)Nc4cccc(c4)C(F)(F)F)c(F)c3)c12
ACDLabs 12.01FC(F)(F)c1cc(ccc1)NC(=O)Nc4ccc(Oc2ncnc3c2n(cc3)C)cc4F
OpenEye OEToolkits 1.7.2Cn1ccc2c1c(ncn2)Oc3ccc(c(c3)F)NC(=O)Nc4cccc(c4)C(F)(F)F
FormulaC21 H15 F4 N5 O2
Name1-{2-fluoro-4-[(5-methyl-5H-pyrrolo[3,2-d]pyrimidin-4-yl)oxy]phenyl}-3-[3-(trifluoromethyl)phenyl]urea
ChEMBLCHEMBL1254007
DrugBank
ZINC
PDB chain3vhe Chain A Residue 1170 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB3vhe Design, synthesis, and evaluation of 5-methyl-4-phenoxy-5H-pyrrolo[3,2-d]pyrimidine derivatives: novel VEGFR2 kinase inhibitors binding to inactive kinase conformation.
Resolution1.55 Å
Binding residue
(original residue number in PDB)		L840 V848 A866 K868 E885 L889 V916 F918 C919 L1035 C1045 D1046 F1047
Binding residue
(residue number reindexed from 1)		L30 V38 A56 K58 E75 L79 V106 F108 C109 L171 C181 D182 F183
Annotation score1
Binding affinityMOAD: ic50=6.2nM
PDBbind-CN: -logKd/Ki=8.21,IC50=6.2nM
BindingDB: Ki=4.6nM,Kd=19nM,IC50=4.7nM
Enzymatic activity
Catalytic site (original residue number in PDB) D1028 R1032 N1033 D1046 K1055
Catalytic site (residue number reindexed from 1) D164 R168 N169 D182 K191
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:3vhe, PDBe:3vhe, PDBj:3vhe
PDBsum3vhe
PubMed20833055
UniProtP35968|VGFR2_HUMAN Vascular endothelial growth factor receptor 2 (Gene Name=KDR)

[Back to BioLiP]