3WKD: Crystal Structure Of Soluble Epoxide Hydrolase In Complex With Fragment Inhibitor

Soluble epoxide hydrolase (sEH) is a component of the arachidonic acid cascade and is a candidate target for therapies for hypertension or inflammation. Although many sEH inhibitors are available, their scaffolds are not structurally diverse, and knowledge of their specific interactions with sEH is limited. To obtain detailed structural information about protein-ligand interactions, we conducted fragment screening of sEH, analyzed the fragments using high-throughput X-ray crystallography, and determined 126 fragment-bound structures at high resolution. Aminothiazole and benzimidazole derivatives were identified as novel scaffolds that bind to the catalytic triad of sEH with good ligand efficiency. We further identified fragment hits that bound to subpockets of sEH called the short and long branches. The water molecule conserved in the structure plays an important role in binding to the long branch, whereas Asp496 and the main chain of Phe497 form hydrogen bonds with fragment hits in the short branch. Fragment hits and their crystal structures provide structural insights into ligand binding to sEH that will facilitate the discovery of novel and potent inhibitors of sEH.
PDB ID: 3WKDDownload
MMDB ID: 119137
PDB Deposition Date: 2013/10/18
Updated in MMDB: 2014/05
Experimental Method:
x-ray diffraction
Resolution: 2.48  Å
Source Organism:
Similar Structures:
Biological Unit for 3WKD: dimeric; determined by author and by software (PISA)
Molecular Components in 3WKD
Label Count Molecule
Proteins (2 molecules)
Bifunctional Epoxide Hydrolase 2(Gene symbol: EPHX2)
Molecule annotation
Chemicals (6 molecules)
* Click molecule labels to explore molecular sequence information.

Citing MMDB