5MWA

human sEH Phosphatase in complex with 3-4-3,4-dichlorophenyl-5-phenyl-1,3-oxazol-2-yl-benzoic-acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.205 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

Discovery of first in vivo active inhibitors of soluble epoxide hydrolase (sEH) phosphatase domain.

Kramer, J.S.Woltersdorf, S.Duflot, T.Hiesinger, K.Lillich, F.F.Knoll, F.Wittmann, S.K.Klingler, F.M.Brunst, S.Chaikuad, A.Morisseau, C.Hammock, B.D.Buccellati, C.Sala, A.Rovati, G.E.Leuillier, M.Fraineau, S.Rondeaux, J.Hernandez Olmos, V.Heering, J.Merk, D.Pogoryelov, D.Steinhilber, D.Knapp, S.Bellien, J.Proschak, E.

(2019) J Med Chem 

  • DOI: https://doi.org/10.1021/acs.jmedchem.9b00445
  • Primary Citation of Related Structures:  
    5MWA

  • PubMed Abstract: 

    The emerging pharmacological target soluble epoxide hydrolase (sEH) is a bifunctional enzyme exhibiting two different catalytic activities that are located in two distinct domains. Although the physiological role of the C-terminal hydrolase domain is well-investigated, little is known about its phosphatase activity, located in the N-terminal phosphatase domain of sEH (sEH-P). Herein we report the discovery and optimization of the first inhibitor of human and rat sEH-P that is applicable in vivo. X-ray structure analysis of the sEH phosphatase domain complexed with an inhibitor provides insights in the molecular basis of small-molecule sEH-P inhibition and helps to rationalize the structure-activity relationships. 4-(4-(3,4-Dichlorophenyl)-5-phenyloxazol-2-yl)butanoic acid ( 22b , SWE101) has an excellent pharmacokinetic and pharmacodynamic profile in rats and enables the investigation of the physiological and pathophysiological role of sEH-P in vivo.


  • Organizational Affiliation

    Institute of Pharmaceutical Chemistry , Goethe-University Frankfurt , Max-von-Laue-Strasse 9 , 60438 Frankfurt am Main , Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Bifunctional epoxide hydrolase 2245Homo sapiensMutation(s): 0 
Gene Names: EPHX2
EC: 3.3.2.10 (PDB Primary Data), 3.1.3.76 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P34913 (Homo sapiens)
Explore P34913 
Go to UniProtKB:  P34913
PHAROS:  P34913
GTEx:  ENSG00000120915 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP34913
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
8S9
Query on 8S9

Download Ideal Coordinates CCD File 
C [auth A]3-[4-(3,4-dichlorophenyl)-5-phenyl-1,3-oxazol-2-yl]benzoic acid
C22 H13 Cl2 N O3
PQUPXYCKNHJSHO-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
B [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.205 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 52.09α = 90
b = 54.11β = 90
c = 75.44γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
xia2data reduction
SCALAdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research FoundationGermanySFB1039/A07

Revision History  (Full details and data files)

  • Version 1.0: 2018-02-28
    Type: Initial release
  • Version 1.1: 2019-09-04
    Changes: Data collection, Database references
  • Version 1.2: 2021-02-24
    Changes: Derived calculations
  • Version 1.3: 2021-03-31
    Changes: Derived calculations
  • Version 1.4: 2024-01-17
    Changes: Data collection, Database references, Refinement description