› 2rl5

X-ray diffraction
2.65Å resolution

Crystal structure of the VEGFR2 kinase domain in complex with a 2,3-dihydro-1,4-benzoxazine inhibitor

Released:
DOI: 10.2210/pdb2rl5/pdb
PDB entry 2rl5 coloured by chain, front view.
PDB entry 2rl5 coloured by chain, side view.
PDB entry 2rl5 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Novel 2,3-dihydro-1,4-benzoxazines as potent and orally bioavailable inhibitors of tumor-driven angiogenesis.
La DS, Belzile J, Bready JV, Coxon A, DeMelfi T, Doerr N, Estrada J, Flynn JC, Flynn SR, Graceffa RF, Harriman SP, Larrow JF, Long AM, Martin MW, Morrison MJ, Patel VF, Roveto PM, Wang L, Weiss MM, Whittington DA, Teffera Y, Zhao Z, Polverino AJ, Harmange JC
J Med Chem 51 1695-705 (2008)
PMID: 18311900

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: 36.28 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 2RL 1 x 2RL
1 modified residue:
Ligand PTR 2 x PTR

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 5.0.2
Spacegroup: P21212
Unit cell:
a: 66.76Å b: 139.774Å c: 57.55Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.199 0.199 0.233
Expression system: Trichoplusia ni

Quick links

Citations

2 review citations

Protein kinase inhibitors: contributions from structure to clinical compounds.
Johnson LN. (2009)
1 more

5 mentions without citation

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