› 3ewh

X-ray diffraction
1.6Å resolution

Crystal structure of the VEGFR2 kinase domain in complex with a pyridyl-pyrimidine benzimidazole inhibitor

Released:
DOI: 10.2210/pdb3ewh/pdb
PDB entry 3ewh coloured by chain, front view.
PDB entry 3ewh coloured by chain, side view.
PDB entry 3ewh coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Pyridyl-pyrimidine benzimidazole derivatives as potent, selective, and orally bioavailable inhibitors of Tie-2 kinase.
Cee VJ, Cheng AC, Romero K, Bellon S, Mohr C, Whittington DA, Bak A, Bready J, Caenepeel S, Coxon A, Deak HL, Fretland J, Gu Y, Hodous BL, Huang X, Kim JL, Lin J, Long AM, Nguyen H, Olivieri PR, Patel VF, Wang L, Zhou Y, Hughes P, Geuns-Meyer S
Bioorg Med Chem Lett 19 424-7 (2009)
PMID: 19062275

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: 314 amino acids
Theoretical weight: 36.12 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: P35968 (Residues: 815-1171; Coverage: 23%)
Gene names: FLK1, KDR, VEGFR2
Sequence domains: Protein tyrosine and serine/threonine kinase
Structure domains:

Ligands and Environments

2 bound ligands:
Ligand K11 1 x K11
Ligand EDO 1 x EDO
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU FR-E SUPERBRIGHT
Spacegroup: P21
Unit cell:
a: 41.319Å b: 84.38Å c: 47.404Å
α: 90° β: 99.33° γ: 90°
R-values:
R R work R free
0.208 0.206 0.234
Expression system: Trichoplusia ni

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Citations

2 review citations

The therapeutic journey of benzimidazoles: a review.
Bansal et al. (2012)
1 more

20 mentions without citation

Recent progress on vascular endothelial growth factor receptor inhibitors with dual targeting capabilities for tumor therapy.
Liu et al. (2022)
19 more