7A7H

Crystal structure of PPARgamma in complex with compound TK90


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.231 
  • R-Value Observed: 0.232 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Combined Cardioprotective and Adipocyte Browning Effects Promoted by the Eutomer of Dual sEH/PPAR gamma Modulator.

Hartmann, M.Bibli, S.I.Tews, D.Ni, X.Kircher, T.Kramer, J.S.Kilu, W.Heering, J.Hernandez-Olmos, V.Weizel, L.Scriba, G.K.E.Krait, S.Knapp, S.Chaikuad, A.Merk, D.Fleming, I.Fischer-Posovszky, P.Proschak, E.

(2021) J Med Chem 64: 2815-2828

  • DOI: https://doi.org/10.1021/acs.jmedchem.0c02063
  • Primary Citation of Related Structures:  
    7A7G, 7A7H

  • PubMed Abstract: 

    The metabolic syndrome (MetS) is a constellation of cardiovascular and metabolic symptoms involving insulin resistance, steatohepatitis, obesity, hypertension, and heart disease, and patients suffering from MetS often require polypharmaceutical treatment. PPARγ agonists are highly effective oral antidiabetics with great potential in MetS, which promote adipocyte browning and insulin sensitization. However, the application of PPARγ agonists in clinics is restricted by potential cardiovascular adverse events. We have previously demonstrated that the racemic dual sEH/PPARγ modulator RB394 ( 3 ) simultaneously improves all risk factors of MetS in vivo. In this study, we identify and characterize the eutomer of 3 . We provide structural rationale for molecular recognition of the eutomer. Furthermore, we could show that the dual sEH/PPARγ modulator is able to promote adipocyte browning and simultaneously exhibits cardioprotective activity which underlines its exciting potential in treatment of MetS.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Peroxisome proliferator-activated receptor gamma277Homo sapiensMutation(s): 0 
Gene Names: PPARGNR1C3
UniProt & NIH Common Fund Data Resources
Find proteins for P37231 (Homo sapiens)
Explore P37231 
Go to UniProtKB:  P37231
PHAROS:  P37231
GTEx:  ENSG00000132170 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP37231
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
TK9 (Subject of Investigation/LOI)
Query on TK9

Download Ideal Coordinates CCD File 
B [auth A](2~{R})-2-[[4-[[4-methoxy-2-(trifluoromethyl)phenyl]methylcarbamoyl]phenyl]methyl]butanoic acid
C21 H22 F3 N O4
VPAHYLNIDWFBPW-CQSZACIVSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
C [auth A]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
TK9 BindingDB:  7A7H EC50: min: 300, max: 390 (nM) from 2 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.231 
  • R-Value Observed: 0.232 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.325α = 90
b = 62.325β = 90
c = 167.629γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-08-04
    Type: Initial release
  • Version 1.1: 2024-01-31
    Changes: Data collection, Database references, Refinement description