7P4K

Soluble epoxide hydrolase in complex with FL217


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.180 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Structure-Based Design of Dual Partial Peroxisome Proliferator-Activated Receptor gamma Agonists/Soluble Epoxide Hydrolase Inhibitors.

Lillich, F.F.Willems, S.Ni, X.Kilu, W.Borkowsky, C.Brodsky, M.Kramer, J.S.Brunst, S.Hernandez-Olmos, V.Heering, J.Schierle, S.Kestner, R.I.Mayser, F.M.Helmstadter, M.Gobel, T.Weizel, L.Namgaladze, D.Kaiser, A.Steinhilber, D.Pfeilschifter, W.Kahnt, A.S.Proschak, A.Chaikuad, A.Knapp, S.Merk, D.Proschak, E.

(2021) J Med Chem 64: 17259-17276

  • DOI: https://doi.org/10.1021/acs.jmedchem.1c01331
  • Primary Citation of Related Structures:  
    7P4E, 7P4K

  • PubMed Abstract: 

    Polypharmaceutical regimens often impair treatment of patients with metabolic syndrome (MetS), a complex disease cluster, including obesity, hypertension, heart disease, and type II diabetes. Simultaneous targeting of soluble epoxide hydrolase (sEH) and peroxisome proliferator-activated receptor γ (PPARγ) synergistically counteracted MetS in various in vivo models, and dual sEH inhibitors/PPARγ agonists hold great potential to reduce the problems associated with polypharmacy in the context of MetS. However, full activation of PPARγ leads to fluid retention associated with edema and weight gain, while partial PPARγ agonists do not have these drawbacks. In this study, we designed a dual partial PPARγ agonist/sEH inhibitor using a structure-guided approach. Exhaustive structure-activity relationship studies lead to the successful optimization of the designed lead. Crystal structures of one representative compound with both targets revealed potential points for optimization. The optimized compounds exhibited favorable metabolic stability, toxicity, selectivity, and desirable activity in adipocytes and macrophages.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Bifunctional epoxide hydrolase 2
A, B
346Homo 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
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
5IV (Subject of Investigation/LOI)
Query on 5IV

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
~{N}-[[4-(cyclopropylsulfonylamino)-2-(trifluoromethyl)phenyl]methyl]-1-[(3-fluorophenyl)methyl]indole-5-carboxamide
C27 H23 F4 N3 O3 S
NONHTXRHOREFAH-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
5IV BindingDB:  7P4K IC50: 8 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.180 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 127.82α = 90
b = 79.326β = 126.65
c = 88.599γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2022-07-06
    Type: Initial release
  • Version 1.1: 2024-01-31
    Changes: Data collection, Refinement description