› 2oh4

X-ray diffraction
2.05Å resolution

Crystal structure of Vegfr2 with a benzimidazole-urea inhibitor

Released:
DOI: 10.2210/pdb2oh4/pdb
PDB entry 2oh4 coloured by chain, front view.
PDB entry 2oh4 coloured by chain, side view.
PDB entry 2oh4 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Discovery of novel benzimidazoles as potent inhibitors of TIE-2 and VEGFR-2 tyrosine kinase receptors.
Hasegawa M, Nishigaki N, Washio Y, Kano K, Harris PA, Sato H, Mori I, West RI, Shibahara M, Toyoda H, Wang L, Nolte RT, Veal JM, Cheung M
J Med Chem 50 4453-70 (2007)
PMID: 17676829

Function and Biology Details

Reaction catalysed: 
ATP + a [protein]-L-tyrosine = ADP + a [protein]-L-tyrosine phosphate
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-153084 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Vascular endothelial growth factor receptor 2 Chain: A
Molecule details ›
Chain: A
Length: 316 amino acids
Theoretical weight: 36.41 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P35968 (Residues: 806-1171; Coverage: 24%)
Gene names: FLK1, KDR, VEGFR2
Sequence domains: Protein tyrosine and serine/threonine kinase
Structure domains:

Ligands and Environments

2 bound ligands:
Ligand SO4 2 x SO4
Ligand GIG 1 x GIG
1 modified residue:
Ligand PTR 2 x PTR

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 17-ID
Spacegroup: P212121
Unit cell:
a: 38.37Å b: 94.25Å c: 95.754Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.189 0.187 0.231
Expression system: Escherichia coli

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Citations

6 review citations

Control of vascular morphogenesis and homeostasis through the angiopoietin-Tie system.
Augustin et al. (2009)
5 more

55 mentions without citation

Recent advances in the area of plant-based anti-cancer drug discovery using computational approaches.
Das et al. (2023)
54 more