› 2xyu

X-ray diffraction
2.12Å resolution

Crystal structure of EphA4 kinase domain in complex with VUF 12058

Released:
DOI: 10.2210/pdb2xyu/pdb
PDB entry 2xyu coloured by chain, front view.
PDB entry 2xyu coloured by chain, side view.
PDB entry 2xyu coloured by chain, top view.
Source organism: Mus musculus
Primary publication:
Fragment based lead discovery of small molecule inhibitors for the EPHA4 receptor tyrosine kinase.
van Linden OP, Farenc C, Zoutman WH, Hameetman L, Wijtmans M, Leurs R, Tensen CP, Siegal G, de Esch IJ
Eur J Med Chem 47 493-500 (2012)
PMID: 22137457

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-169846 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Ephrin type-A receptor 4 Chain: A
Molecule details ›
Chain: A
Length: 285 amino acids
Theoretical weight: 32.23 KDa
Source organism: Mus musculus
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q03137 (Residues: 612-896; Coverage: 30%)
Gene names: Epha4, Sek, Sek1
Sequence domains: Protein tyrosine and serine/threonine kinase
Structure domains:

Ligands and Environments

2 bound ligands:
Ligand GOL 6 x GOL
Ligand Q9G 1 x Q9G
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID23-2
Spacegroup: P212121
Unit cell:
a: 32.544Å b: 91.545Å c: 97.959Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.192 0.189 0.23
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

2 review citations

1H-Pyrazolo[3,4-b]pyridines: Synthesis and Biomedical Applications.
Donaire-Arias et al. (2022)
1 more

1 mention without citation

KLIFS: a structural kinase-ligand interaction database.
Kooistra et al. (2016)