› 3wk4

X-ray diffraction
2.11Å resolution

Crystal structure of soluble epoxide hydrolase in complex with fragment inhibitor

Released:
DOI: 10.2210/pdb3wk4/pdb
PDB entry 3wk4 coloured by chain, front view.
PDB entry 3wk4 coloured by chain, side view.
PDB entry 3wk4 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structural insights into binding of inhibitors to soluble epoxide hydrolase gained by fragment screening and X-ray crystallography.
Amano Y, Yamaguchi T, Tanabe E
Bioorg Med Chem 22 2427-34 (2014)
PMID: 24656800

Function and Biology Details

Reactions catalysed: 
(9S,10S)-10-hydroxy-9-(phosphonooxy)octadecanoate + H(2)O = (9S,10S)-9,10-dihydroxyoctadecanoate + phosphate
An epoxide + H(2)O = a glycol
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-152745 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Bifunctional epoxide hydrolase 2 Chain: A
Molecule details ›
Chain: A
Length: 561 amino acids
Theoretical weight: 63.51 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P34913 (Residues: 1-555; Coverage: 100%)
Gene name: EPHX2
Sequence domains:
Structure domains:

Ligands and Environments

3 bound ligands:
Ligand MG 1 x MG
Ligand PO4 1 x PO4
Ligand S0A 1 x S0A
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PHOTON FACTORY BEAMLINE AR-NE3A
Spacegroup: P6522
Unit cell:
a: 93.104Å b: 93.104Å c: 244.315Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.211 0.208 0.257
Expression system: Escherichia coli

Quick links

Citations

2 review citations

Successful generation of structural information for fragment-based drug discovery.
Öster et al. (2015)
1 more

3 mentions without citation

A thiol redox sensor in soluble epoxide hydrolase enables oxidative activation by intra-protein disulfide bond formation.
Charles et al. (2021)
2 more