Crystal structure of PPAR gamma (PPARG) in complex with WY-14643

Experimental Data Snapshot

  • Resolution: 2.10 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.225 

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Targeting the Alternative Vitamin E Metabolite Binding Site Enables Noncanonical PPAR gamma Modulation.

Arifi, S.Marschner, J.A.Pollinger, J.Isigkeit, L.Heitel, P.Kaiser, A.Obeser, L.Hofner, G.Proschak, E.Knapp, S.Chaikuad, A.Heering, J.Merk, D.

(2023) J Am Chem Soc 145: 14802-14810

  • DOI: https://doi.org/10.1021/jacs.3c03417
  • Primary Citation of Related Structures:  
    8ATY, 8ATZ, 8CPH, 8CPI, 8CPJ

  • PubMed Abstract: 

    The lipid-sensing transcription factor PPARγ is the target of antidiabetic thiazolidinediones (TZD). At two sites within its ligand binding domain, it also binds oxidized vitamin E metabolites and the vitamin E mimetic garcinoic acid. While the canonical interaction within the TZD binding site mediates classical PPARγ activation, the effects of the second binding on PPARγ activity remain elusive. Here, we identified an agonist mimicking dual binding of vitamin E metabolites and developed a selective ligand of the second site, unveiling potential noncanonical regulation of PPARγ activities. We found that this alternative binding event can simultaneously occur with orthosteric ligands and it exerted different effects on PPARγ-cofactor interactions compared to both orthosteric PPARγ agonists and antagonists, indicating the diverse roles of the two binding sites. Alternative site binding lacked the pro-adipogenic effect of TZD and mediated no classical PPAR signaling in differential gene expression analysis but markedly diminished FOXO signaling, suggesting potential therapeutic applications.

  • Organizational Affiliation

    Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, D-60438 Frankfurt, Germany.

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
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
WY1 (Subject of Investigation/LOI)
Query on WY1

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A]
C14 H14 Cl N3 O2 S
Experimental Data & Validation

Experimental Data

  • Resolution: 2.10 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.225 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.595α = 90
b = 65.595β = 90
c = 157.264γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
XDSdata reduction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2023-07-12
    Type: Initial release
  • Version 1.1: 2023-07-19
    Changes: Database references
  • Version 1.2: 2024-06-19
    Changes: Data collection