› 3pdc

X-ray diffraction
2.6Å resolution

Crystal structure of hydrolase domain of human soluble epoxide hydrolase complexed with a benzoxazole inhibitor

Released:
DOI: 10.2210/pdb3pdc/pdb
PDB entry 3pdc coloured by chain, front view.
PDB entry 3pdc coloured by chain, side view.
PDB entry 3pdc coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Discovery of potent inhibitors of soluble epoxide hydrolase by combinatorial library design and structure-based virtual screening.
Xing L, McDonald JJ, Kolodziej SA, Kurumbail RG, Williams JM, Warren CJ, O'Neal JM, Skepner JE, Roberds SL
J Med Chem 54 1211-22 (2011)
PMID: 21302953

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:
  • not assigned
Cellular component:
  • not assigned
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 Chains: A, B
Molecule details ›
Chains: A, B
Length: 344 amino acids
Theoretical weight: 39.31 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: P34913 (Residues: 226-548; Coverage: 58%)
Gene name: EPHX2
Sequence domains: alpha/beta hydrolase fold
Structure domains: alpha/beta hydrolase

Ligands and Environments

1 bound ligand:
Ligand ZYI 2 x ZYI
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU MICROMAX-007
Spacegroup: P21
Unit cell:
a: 46.523Å b: 79.902Å c: 89.318Å
α: 90° β: 90.223° γ: 90°
R-values:
R R work R free
0.288 0.279 0.333
Expression system: Spodoptera frugiperda

Quick links

Citations

5 review citations

Impact of soluble epoxide hydrolase and epoxyeicosanoids on human health.
Morisseau et al. (2013)
4 more

2 mentions without citation

Discovery of Soluble Epoxide Hydrolase Inhibitors from Chemical Synthesis and Natural Products.
Sun et al. (2021)
1 more