› 3vhe

X-ray diffraction
1.55Å resolution

Crystal structure of human VEGFR2 kinase domain with a novel pyrrolopyrimidine inhibitor.

Released:
DOI: 10.2210/pdb3vhe/pdb
PDB entry 3vhe coloured by chain, front view.
PDB entry 3vhe coloured by chain, side view.
PDB entry 3vhe coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Design, synthesis, and evaluation of 5-methyl-4-phenoxy-5H-pyrrolo[3,2-d]pyrimidine derivatives: novel VEGFR2 kinase inhibitors binding to inactive kinase conformation.
Oguro Y, Miyamoto N, Okada K, Takagi T, Iwata H, Awazu Y, Miki H, Hori A, Kamiyama K, Imamura S
Bioorg Med Chem 18 7260-73 (2010)
PMID: 20833055

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: 359 amino acids
Theoretical weight: 40.85 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: P35968 (Residues: 811-1169; Coverage: 27%)
Gene names: FLK1, KDR, VEGFR2
Sequence domains: Protein tyrosine and serine/threonine kinase
Structure domains:

Ligands and Environments

1 bound ligand:
Ligand 42Q 1 x 42Q
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL32B2
Spacegroup: C2
Unit cell:
a: 134.34Å b: 56.27Å c: 52.07Å
α: 90° β: 95.24° γ: 90°
R-values:
R R work R free
0.186 0.186 0.209
Expression system: Spodoptera frugiperda

Quick links

Citations

1 review citation

Development of anti-angiogenic tyrosine kinases inhibitors: molecular structures and binding modes.
Zhang et al. (2016)
24 other articles

47 mentions without citation

Bioactive pyrrole-based compounds with target selectivity.
Li Petri et al. (2020)
46 more