Crystal Structure of PPARg in complex with T2384

Experimental Data Snapshot

  • Resolution: 2.55 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.226 

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T2384, a novel antidiabetic agent with unique peroxisome proliferator-activated receptor gamma binding properties

Li, Y.Wang, Z.Furukawa, N.Escaron, P.Weiszmann, J.Lee, G.Lindstrom, M.Liu, J.Liu, X.Xu, H.Plotnikova, O.Prasad, V.Walker, N.Learned, R.M.Chen, J.-L.

(2008) J Biol Chem 283: 9168-9176

  • DOI: https://doi.org/10.1074/jbc.M800104200
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    The nuclear hormone receptor peroxisome proliferator-activated receptor gamma (PPARgamma) plays central roles in adipogenesis and glucose homeostasis and is the molecular target for the thiazolidinedione (TZD) class of antidiabetic drugs. Activation of PPARgamma by TZDs improves insulin sensitivity; however, this is accompanied by the induction of several undesirable side effects. We have identified a novel synthetic PPARgamma ligand, T2384, to explore the biological activities associated with occupying different regions of the receptor ligand-binding pocket. X-ray crystallography studies revealed that T2384 can adopt two distinct binding modes, which we have termed "U" and "S", interacting with the ligand-binding pocket of PPARgamma primarily via hydrophobic contacts that are distinct from full agonists. The different binding modes occupied by T2384 induced distinct patterns of coregulatory protein interaction with PPARgamma in vitro and displayed unique receptor function in cell-based activity assays. We speculate that these unique biochemical and cellular activities may be responsible for the novel in vivo profile observed in animals treated systemically with T2384. When administered to diabetic KKAy mice, T2384 rapidly improved insulin sensitivity in the absence of weight gain, hemodilution, and anemia characteristics of treatment with rosiglitazone (a TZD). Moreover, upon coadministration with rosiglitazone, T2384 was able to antagonize the side effects induced by rosiglitazone treatment alone while retaining robust effects on glucose disposal. These results are consistent with the hypothesis that interactions between ligands and specific regions of the receptor ligand-binding pocket might selectively trigger a subset of receptor-mediated biological responses leading to the improvement of insulin sensitivity, without eliciting less desirable responses associated with full activation of the receptor. We suggest that T2384 may represent a prototype for a novel class of PPARgamma ligand and, furthermore, that molecules sharing some of these properties would be useful for treatment of type 2 diabetes.

  • Organizational Affiliation

    Amgen Inc., South San Francisco, CA 94080, USA. yangl@amgen.com

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Peroxisome proliferator-activated receptor gamma
A, B
272Homo 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
Query on Z27

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B],
E [auth B]
C20 H10 Cl3 F3 N2 O2 S3
Experimental Data & Validation

Experimental Data

  • Resolution: 2.55 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.226 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 91.553α = 90
b = 62.396β = 102.63
c = 118.943γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

  • Released Date: 2009-11-03 
  • Deposition Author(s): Wang, Z.

Revision History  (Full details and data files)

  • Version 1.0: 2009-11-03
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2023-09-06
    Changes: Data collection, Database references, Derived calculations, Refinement description