2OH4

Crystal structure of Vegfr2 with a benzimidazole-urea inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.231
  • R-Value Work: 0.187

Literature

Macromolecules
Sequence Display for 2OH4

Classification: TRANSFERASE

Total Structure Weight: 37104.21

Macromolecule Entities
Molecule Chains Length Organism Details
Vascular endothelial growth factor receptor 2 A 316 Homo sapiens EC#: 2.7.10.1 IUBMB
Fragment: kinase domain
Mutation: K833N
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
GIG
Query on GIG

A METHYL (5-{4-[({[2-FLUORO-5-(TRIFLUOROMETHYL)PHENYL]AMINO}CARBONYL)AMINO]PHENOXY}- 1H-BENZIMIDAZOL-2-YL)CARBAMATE
C23 H17 F4 N5 O4
KADQEUOYNAPXRD-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SO4
Query on SO4

A SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
GIG N/A in BindingDB
IC50: 3.5 nM  BindingMOAD
IC50: 3.5 nM  PDBbind
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
PTR
Query on PTR
A L-PEPTIDE LINKING C9 H12 N O6 P TYR

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.231
  • R-Value Work: 0.187
  • Space Group: P 21 21 21

Unit Cell:

Length (Å) Angle (°)
a = 38.37 α = 90.00
b = 94.25 β = 90.00
c = 95.75 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2007-01-09
  • Released Date: 2007-09-18
  • Deposition author(s): Nolte, R.T., Wang, L.

Revision History

  • Version 1_0: 2007-09-18

    Type: Initial release

  • Version 1_1: 2011-07-13

    Type: Advisory, Version format compliance

  • Version 1_2: 2017-06-14

    Type: Advisory, Database references, Source and taxonomy, Structure summary

  • Version 1_3: 2017-10-18

    Type: Refinement description