2P2I

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.266
  • R-Value Work: 0.222

Literature

Macromolecules
Sequence Display for 2P2I

Classification: TRANSFERASE

Total Structure Weight: 73358.11

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
Mutation: C817A, E990V
Gene Name(s): KDR Gene View FLK1 VEGFR2
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 1 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
608
Query on 608

A, B N-(4-phenoxyphenyl)-2-[(pyridin-4-ylmethyl)amino]nicotinamide
C24 H20 N4 O2
CPVRYQAOUPSUDO-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
608 IC50: 38 nM (85) BindingDB
Ki: 10 nM (85) BindingDB

IC50: 38 nM  BindingMOAD
IC50: 38 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: 2.4 Å
  • R-Value Free: 0.266
  • R-Value Work: 0.222
  • Space Group: P 1 21 1

Unit Cell:

Length (Å) Angle (°)
a = 55.42 α = 90.00
b = 67.06 β = 94.51
c = 88.51 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2007-03-07
  • Released Date: 2007-03-20
  • Deposition author(s): Whittington, D.A., Kim, J.L., Long, A.M., Rose, P., Gu, Y., Zhao, H.

Revision History

  • 2008-05-01
    Type: Version format compliance
  • 2011-07-13
    Type: Version format compliance
  • 2017-08-16
    Type: Refinement description, Source and taxonomy