3B8R

Crystal structure of the VEGFR2 kinase domain in complex with a naphthamide inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.259
  • R-Value Work: 0.204

Literature

Macromolecules
Sequence Display for 3B8R

Classification: TRANSFERASE

Total Structure Weight: 73460.15

Macromolecule Entities
Molecule Chains Length Organism Details
Vascular endothelial growth factor receptor 2 A, B 314 Homo sapiens EC#: 2.7.10.1 IUBMB
Fragment: kinase domain; UNP residues 815-939, 990-1171
Mutation: C817A, V916T, E990V
Gene Name(s): KDR Gene View FLK1 VEGFR2
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 2 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
887
Query on 887

A, B N-cyclopropyl-6-[(6,7-dimethoxyquinolin-4- yl)oxy]naphthalene-1-carboxamide
C25 H22 N2 O4
ZATGFXTWDKIEKC-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
EDO
Query on EDO

A 1,2-ETHANEDIOL
ETHYLENE GLYCOL (Synonym)
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
887 IC50: 0.6 - 0.603 nM (85) BindingDB

N/A in BindingMoad
IC50: 0.6 nM  PDBbind
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
PTR
Query on PTR
A, B L-PEPTIDE LINKING C9 H12 N O6 P TYR

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.259
  • R-Value Work: 0.204
  • Space Group: P 1 21 1

Unit Cell:

Length (Å) Angle (°)
a = 55.44 α = 90.00
b = 67.97 β = 91.36
c = 87.69 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2007-11-01
  • Released Date: 2008-04-01
  • Deposition author(s): Whittington, D.A., Long, A.M., Gu, Y., Zhao, H.

Revision History

  • Version 1_0: 2008-04-01

    Type: Initial release

  • Version 1_1: 2011-07-13

    Type: Version format compliance

  • Version 1_2: 2017-08-23

    Type: Source and taxonomy