› 5aly

X-ray diffraction
1.9Å resolution

ligand complex structure of soluble epoxide hydrolase

Released:
DOI: 10.2210/pdb5aly/pdb
PDB entry 5aly coloured by chain, front view.
PDB entry 5aly coloured by chain, side view.
PDB entry 5aly coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Successful generation of structural information for fragment-based drug discovery.
Öster L, Tapani S, Xue Y, Käck H
Drug Discov Today 20 1104-11 (2015)
PMID: 25931264

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: 549 amino acids
Theoretical weight: 62 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: P34913 (Residues: 1-548; Coverage: 99%)
Gene name: EPHX2
Sequence domains:
Structure domains:

Ligands and Environments

3 bound ligands:
Ligand SO4 2 x SO4
Ligand DMS 5 x DMS
Ligand B7H 1 x B7H
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU FR-E+
Spacegroup: P6522
Unit cell:
a: 92.103Å b: 92.103Å c: 244.045Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.198 0.195 0.246
Expression system: Spodoptera frugiperda

Quick links

Citations

6 review citations

Applications of (19)F-NMR in Fragment-Based Drug Discovery.
Norton et al. (2016)
5 more

1 mention without citation

Combining Machine Learning and Enhanced Sampling Techniques for Efficient and Accurate Calculation of Absolute Binding Free Energies.
Evans et al. (2020)