6YL4

Soluble epoxide hydrolase in complex with 3-((R)-3-(1-hydroxyureido)but-1-yn-1-yl)-N-((S)-3-phenyl-3-(4-trifluoromethoxy)phenyl)propyl)benzamide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.185 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Design, Synthesis, and Structure-Activity Relationship Studies of Dual Inhibitors of Soluble Epoxide Hydrolase and 5-Lipoxygenase.

Hiesinger, K.Kramer, J.S.Beyer, S.Eckes, T.Brunst, S.Flauaus, C.Wittmann, S.K.Weizel, L.Kaiser, A.Kretschmer, S.B.M.George, S.Angioni, C.Heering, J.Geisslinger, G.Schubert-Zsilavecz, M.Schmidtko, A.Pogoryelov, D.Pfeilschifter, J.Hofmann, B.Steinhilber, D.Schwalm, S.Proschak, E.

(2020) J Med Chem 63: 11498-11521

  • DOI: https://doi.org/10.1021/acs.jmedchem.0c00561
  • Primary Citation of Related Structures:  
    6YL4

  • PubMed Abstract: 

    Inhibition of multiple enzymes of the arachidonic acid cascade leads to synergistic anti-inflammatory effects. Merging of 5-lipoxygenase (5-LOX) and soluble epoxide hydrolase (sEH) pharmacophores led to the discovery of a dual 5-LOX/sEH inhibitor, which was subsequently optimized in terms of potency toward both targets and metabolic stability. The optimized lead structure displayed cellular activity in human polymorphonuclear leukocytes, oral bioavailability, and target engagement in vivo and demonstrated profound anti-inflammatory and anti-fibrotic efficiency in a kidney injury model caused by unilateral ureteral obstruction in mice. These results pave the way for investigating the therapeutic potential of dual 5-LOX/sEH inhibitors in other inflammation- and fibrosis-related disease models.


  • Organizational Affiliation

    Institute of Pharmaceutical Chemistry, Goethe-University of Frankfurt, Max-von-Laue Str. 9 D-60438 Frankfurt a.M., Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Bifunctional epoxide hydrolase 2346Homo 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 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
OWW (Subject of Investigation/LOI)
Query on OWW

Download Ideal Coordinates CCD File 
B [auth A]3-[(3~{R})-3-[aminocarbonyl(oxidanyl)amino]but-1-ynyl]-~{N}-[(3~{S})-3-phenyl-3-[4-(trifluoromethyloxy)phenyl]propyl]benzamide
C28 H26 F3 N3 O4
HQXPQGGUDYBGKG-CLOONOSVSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
OWW Binding MOAD:  6YL4 IC50: 7 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.185 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 79.934α = 90
b = 92.238β = 90
c = 106.646γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)GermanyPR1405/2-2
German Research Foundation (DFG)GermanyPR1405/4-1
German Research Foundation (DFG)GermanySFB1039 TP A07

Revision History  (Full details and data files)

  • Version 1.0: 2020-10-21
    Type: Initial release
  • Version 1.1: 2020-11-04
    Changes: Database references
  • Version 1.2: 2021-02-24
    Changes: Derived calculations