› 4y2p

X-ray diffraction
2.05Å resolution

Structure of soluble epoxide hydrolase in complex with N-methyl-1-[3-(pyridin-3-yl)phenyl]methanamine

Released:
DOI: 10.2210/pdb4y2p/pdb
PDB entry 4y2p coloured by chain, front view.
PDB entry 4y2p coloured by chain, side view.
PDB entry 4y2p coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Identification of N-ethylmethylamine as a novel scaffold for inhibitors of soluble epoxide hydrolase by crystallographic fragment screening.
Amano Y, Tanabe E, Yamaguchi T
Bioorg Med Chem 23 2310-7 (2015)
PMID: 25862210

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

2 bound ligands:
Ligand MG 1 x MG
Ligand 3C5 1 x 3C5
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PHOTON FACTORY BEAMLINE AR-NW12A
Spacegroup: P6522
Unit cell:
a: 93.059Å b: 93.059Å c: 244.652Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.194 0.192 0.226
Expression system: Escherichia coli

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Citations

8 citation in other articles

Structures of endothiapepsin-fragment complexes from crystallographic fragment screening using a novel, diverse and affordable 96-compound fragment library.
Huschmann et al. (2016)
7 more