› 3vo3

X-ray diffraction
1.52Å resolution

Crystal Structure of the Kinase domain of Human VEGFR2 with imidazo[1,2-b]pyridazine derivative

Released:
DOI: 10.2210/pdb3vo3/pdb
PDB entry 3vo3 coloured by chain, front view.
PDB entry 3vo3 coloured by chain, side view.
PDB entry 3vo3 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Discovery of N-[5-({2-[(cyclopropylcarbonyl)amino]imidazo[1,2-b]pyridazin-6-yl}oxy)-2-methylphenyl]-1,3-dimethyl-1H-pyrazole-5-carboxamide (TAK-593), a highly potent VEGFR2 kinase inhibitor.
Miyamoto N, Sakai N, Hirayama T, Miwa K, Oguro Y, Oki H, Okada K, Takagi T, Iwata H, Awazu Y, Yamasaki S, Takeuchi T, Miki H, Hori A, Imamura S
Bioorg Med Chem 21 2333-2345 (2013)
PMID: 23498918

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: 318 amino acids
Theoretical weight: 36.35 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
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 0KF 1 x 0KF
Ligand EDO 1 x EDO
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 5.0.3
Spacegroup: C2
Unit cell:
a: 134.093Å b: 55.77Å c: 51.572Å
α: 90° β: 94.41° γ: 90°
R-values:
R R work R free
0.162 0.161 0.182
Expression system: Spodoptera frugiperda

Quick links

Citations

7 review citations

Synthesis and Pharmacological Activities of Pyrazole Derivatives: A Review.
Karrouchi et al. (2018)
6 more

21 mentions without citation

Peptide and protein nanoparticle conjugates: versatile platforms for biomedical applications.
Spicer et al. (2018)
20 more