Crystal structure of human soluble epoxide hydrolase complexed with 1-(1-isobutyrylpiperidin-4-yl)-3-(4-(trifluoromethyl)phenyl)urea

Experimental Data Snapshot

  • Resolution: 2.94 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.191 

wwPDB Validation   3D Report Full Report

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Optimized inhibitors of soluble epoxide hydrolase improve in vitro target residence time and in vivo efficacy.

Lee, K.S.Liu, J.Y.Wagner, K.M.Pakhomova, S.Dong, H.Morisseau, C.Fu, S.H.Yang, J.Wang, P.Ulu, A.Mate, C.A.Nguyen, L.V.Hwang, S.H.Edin, M.L.Mara, A.A.Wulff, H.Newcomer, M.E.Zeldin, D.C.Hammock, B.D.

(2014) J Med Chem 57: 7016-7030

  • DOI: https://doi.org/10.1021/jm500694p
  • Primary Citation of Related Structures:  
    4OCZ, 4OD0

  • PubMed Abstract: 

    Diabetes is affecting the life of millions of people. A large proportion of diabetic patients suffer from severe complications such as neuropathic pain, and current treatments for these complications have deleterious side effects. Thus, alternate therapeutic strategies are needed. Recently, the elevation of epoxy-fatty acids through inhibition of soluble epoxide hydrolase (sEH) was shown to reduce diabetic neuropathic pain in rodents. In this report, we describe a series of newly synthesized sEH inhibitors with at least 5-fold higher potency and doubled residence time inside both the human and rodent sEH enzyme than previously reported inhibitors. These inhibitors also have better physical properties and optimized pharmacokinetic profiles. The optimized inhibitor selected from this new series displayed improved efficacy of almost 10-fold in relieving pain perception in diabetic neuropathic rats as compared to the approved drug, gabapentin, and previously published sEH inhibitors. Therefore, these new sEH inhibitors could be an attractive alternative to treat diabetic neuropathy in humans.

  • Organizational Affiliation

    Department of Entomology and Nematology, UCD Comprehensive Cancer Center, University of California Davis , One Shields Avenue, Davis, California 95616, United States.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Bifunctional epoxide hydrolase 2555Homo sapiensMutation(s): 0 
Gene Names: EPHX2
EC: (PDB Primary Data), (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P34913 (Homo sapiens)
Explore P34913 
Go to UniProtKB:  P34913
PHAROS:  P34913
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP34913
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 2RU

Download Ideal Coordinates CCD File 
D [auth A]1-[1-(2-methylpropanoyl)piperidin-4-yl]-3-[4-(trifluoromethyl)phenyl]urea
C17 H22 F3 N3 O2
Query on PO4

Download Ideal Coordinates CCD File 
O4 P
Query on MG

Download Ideal Coordinates CCD File 
Binding Affinity Annotations 
IDSourceBinding Affinity
2RU BindingDB:  4OCZ Ki: 0.66 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.94 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.191 
  • Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 92.229α = 90
b = 92.229β = 90
c = 243.373γ = 120
Software Package:
Software NamePurpose
xia2data reduction
SCALAdata scaling

Structure Validation

View Full Validation Report

Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2014-09-24
    Type: Initial release
  • Version 1.1: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description