› 4x6x

X-ray diffraction
1.8Å resolution

Human soluble epoxide hydrolase in complex with a three substituted cyclopropane derivative

Released:
DOI: 10.2210/pdb4x6x/pdb
PDB entry 4x6x coloured by chain, front view.
PDB entry 4x6x coloured by chain, side view.
PDB entry 4x6x coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Three-dimensional rational approach to the discovery of potent substituted cyclopropyl urea soluble epoxide hydrolase inhibitors.
Takai K, Chiyo N, Nakajima T, Nariai T, Ishikawa C, Nakatani S, Ikeno A, Yamamoto S, Sone T
Bioorg Med Chem Lett 25 1705-1708 (2015)
PMID: 25800114

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: 336 amino acids
Theoretical weight: 38.65 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P34913 (Residues: 230-555; Coverage: 59%)
Gene name: EPHX2
Sequence domains: alpha/beta hydrolase fold
Structure domains: alpha/beta hydrolase

Ligands and Environments

1 bound ligand:
Ligand S74 2 x S74
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL41XU
Spacegroup: C2
Unit cell:
a: 129.406Å b: 80.544Å c: 88.253Å
α: 90° β: 125.7° γ: 90°
R-values:
R R work R free
0.2 0.199 0.222
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

4 citation in other articles

Enantiopure Sulfinyl Aniline as a Removable and Recyclable Chiral Auxiliary for Asymmetric C(sp3 )-H Bond Activation.
Jerhaoui et al. (2016)
3 more

1 mention without citation

In Silico Modeling and Structural Analysis of Soluble Epoxide Hydrolase Inhibitors for Enhanced Therapeutic Design.
Sar et al. (2023)