Structure of PDB 3be2 Chain A Binding Site BS01

Receptor Information
>3be2 Chain A (length=290) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
EHAERLPYDASKWEFPRDRLKLGKPLGRGAFGQVIEADAFGIDTCRTVAV
KMLKEGATHSEHRALMSELKILIHIGHHLNVVNLLGACTKPGGPLMVITE
FCKFGNLSTYLRSKRNEFVPYKVAPEDLYKDFLTLEHLICYSFQVAKGME
FLASRKCIHRDLAARNILLSEKNVVKICDFGPLKWMAPETIFDRVYTIQS
DVWSFGVLLWEIFSLGASPYPGVKIDEEFCRRLKEGTRMRAPDYTTPEMY
QTMLDCWHGEPSQRPTFSELVEHLGNLLQANAQQDRHHHH
Ligand information
Ligand IDRAJ
InChIInChI=1S/C29H29F3N6O/c1-19-8-9-21(16-26(19)37-27-24(7-4-11-34-27)25-10-12-33-18-35-25)28(39)36-23-15-20(6-5-13-38(2)3)14-22(17-23)29(30,31)32/h4,7-12,14-18H,5-6,13H2,1-3H3,(H,34,37)(H,36,39)
InChIKeyOHHGYJBFPVJURR-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04FC(F)(F)c1cc(cc(c1)NC(=O)c2cc(c(cc2)C)Nc3ncccc3c4ncncc4)CCCN(C)C
OpenEye OEToolkits 1.5.0Cc1ccc(cc1Nc2c(cccn2)c3ccncn3)C(=O)Nc4cc(cc(c4)C(F)(F)F)CCCN(C)C
CACTVS 3.341CN(C)CCCc1cc(NC(=O)c2ccc(C)c(Nc3ncccc3c4ccncn4)c2)cc(c1)C(F)(F)F
FormulaC29 H29 F3 N6 O
NameN-{3-[3-(DIMETHYLAMINO)PROPYL]-5-(TRIFLUOROMETHYL)PHENYL}-4-METHYL-3-[(3-PYRIMIDIN-4-YLPYRIDIN-2-YL)AMINO]BENZAMIDE
ChEMBLCHEMBL221484
DrugBank
ZINCZINC000008582033
PDB chain3be2 Chain A Residue 501 [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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PDB3be2 Naphthamides as novel and potent vascular endothelial growth factor receptor tyrosine kinase inhibitors: design, synthesis, and evaluation.
Resolution1.75 Å
Binding residue
(original residue number in PDB)		V848 A866 E885 T916 F918 C919 H1026 L1035 I1044 C1045 D1046 F1047
Binding residue
(residue number reindexed from 1)		V34 A49 E68 T99 F101 C102 H159 L168 I177 C178 D179 F180
Annotation score1
Binding affinityMOAD: ic50=2nM
PDBbind-CN: -logKd/Ki=8.70,IC50=2nM
BindingDB: IC50=2nM
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
View graph for
Biological Process
External links
PDB RCSB:3be2, PDBe:3be2, PDBj:3be2
PDBsum3be2
PubMed18324761
UniProtP35968|VGFR2_HUMAN Vascular endothelial growth factor receptor 2 (Gene Name=KDR)

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