› 2x9f

X-ray diffraction
1.75Å resolution

ephB4 kinase domain inhibitor complex

Released:
DOI: 10.2210/pdb2x9f/pdb
PDB entry 2x9f coloured by chain, front view.
PDB entry 2x9f coloured by chain, side view.
PDB entry 2x9f coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Inhibitors of the tyrosine kinase EphB4. Part 3: identification of non-benzodioxole-based kinase inhibitors.
Bardelle C, Barlaam B, Brooks N, Coleman T, Cross D, Ducray R, Green I, Brempt CL, Olivier A, Read J
Bioorg Med Chem Lett 20 6242-5 (2010)
PMID: 20850301

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-157090 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Ephrin type-B receptor 4 Chain: A
Molecule details ›
Chain: A
Length: 302 amino acids
Theoretical weight: 33.93 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: P54760 (Residues: 598-899; Coverage: 31%)
Gene names: EPHB4, HTK, MYK1, TYRO11
Sequence domains: Protein tyrosine and serine/threonine kinase
Structure domains:

Ligands and Environments

2 bound ligands:
Ligand X9F 1 x X9F
Ligand MG 2 x MG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU FR-E
Spacegroup: P21
Unit cell:
a: 47.12Å b: 52.479Å c: 61.369Å
α: 90° β: 112.05° γ: 90°
R-values:
R R work R free
0.159 0.157 0.194
Expression system: Spodoptera frugiperda

Quick links

Citations

6 review citations

Targeting Eph receptors with peptides and small molecules: progress and challenges.
Noberini et al. (2012)
5 more

2 mentions without citation

Delineation of Polypharmacology across the Human Structural Kinome Using a Functional Site Interaction Fingerprint Approach.
Zhao et al. (2016)
1 more