› 3vhk

X-ray diffraction
2.49Å resolution

Crystal structure of the VEGFR2 kinase domain in complex with a back pocket binder

Released:
DOI: 10.2210/pdb3vhk/pdb
PDB entry 3vhk coloured by chain, front view.
PDB entry 3vhk coloured by chain, side view.
PDB entry 3vhk coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
A Back-to-Front Fragment-Based Drug Design Search Strategy Targeting the DFG-Out Pocket of Protein Tyrosine Kinases.
Iwata H, Oki H, Okada K, Takagi T, Tawada M, Miyazaki Y, Imamura S, Hori A, Lawson JD, Hixon MS, Kimura H, Miki H
ACS Med Chem Lett 3 342-6 (2012)
PMID: 24900475

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: 368 amino acids
Theoretical weight: 41.8 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: P35968 (Residues: 806-1171; Coverage: 27%)
Gene names: FLK1, KDR, VEGFR2
Sequence domains: Protein tyrosine and serine/threonine kinase
Structure domains:

Ligands and Environments

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

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL32B2
Spacegroup: C2
Unit cell:
a: 135.719Å b: 56.354Å c: 51.875Å
α: 90° β: 95.61° γ: 90°
R-values:
R R work R free
0.21 0.207 0.262
Expression system: Spodoptera frugiperda

Quick links

Citations

6 citation in other articles

Novel approaches for targeting kinases: allosteric inhibition, allosteric activation and pseudokinases.
Cowan-Jacob et al. (2014)
5 more

6 mentions without citation

Transformer neural network for protein-specific de novo drug generation as a machine translation problem.
Grechishnikova D. (2021)
5 more