› 3u6j

X-ray diffraction
2.15Å resolution

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

Released:
DOI: 10.2210/pdb3u6j/pdb
PDB entry 3u6j coloured by chain, front view.
PDB entry 3u6j coloured by chain, side view.
PDB entry 3u6j coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structure-based design of novel class II c-Met inhibitors: 1. Identification of pyrazolone-based derivatives.
Norman MH, Liu L, Lee M, Xi N, Fellows I, D'Angelo ND, Dominguez C, Rex K, Bellon SF, Kim TS, Dussault I
J Med Chem 55 1858-67 (2012)
PMID: 22320343

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: 36.16 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

1 bound ligand:
Ligand 03X 1 x 03X
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU FR-E SUPERBRIGHT
Spacegroup: P21
Unit cell:
a: 56.194Å b: 65.268Å c: 57.323Å
α: 90° β: 117.94° γ: 90°
R-values:
R R work R free
0.196 0.193 0.23
Expression system: Trichoplusia ni

Quick links

Citations

2 review citations

αC helix displacement as a general approach for allosteric modulation of protein kinases.
Palmieri et al. (2013)
1 more

16 mentions without citation

Pyrazolone structural motif in medicinal chemistry: Retrospect and prospect.
Zhao et al. (2020)
15 more