X-ray Crystal structure of the nuclear hormone receptor PPAR-gamma in a complex with a PPAR gamma/alpha dual agonist

Experimental Data Snapshot

  • Resolution: 2.31 Å
  • R-Value Free: 0.297 
  • R-Value Work: 0.238 
  • R-Value Observed: 0.241 

Starting Model: experimental
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Synthesis and evaluation of novel alpha-heteroaryl-phenylpropanoic acid derivatives as PPARalpha/gamma dual agonists.

Casimiro-Garcia, A.Bigge, C.F.Davis, J.A.Padalino, T.Pulaski, J.Ohren, J.F.McConnell, P.Kane, C.D.Royer, L.J.Stevens, K.A.Auerbach, B.Collard, W.McGregor, C.Song, K.

(2009) Bioorg Med Chem 17: 7113-7125

  • DOI: https://doi.org/10.1016/j.bmc.2009.09.001
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    The synthesis of a new series of phenylpropanoic acid derivatives incorporating an heteroaryl group at the alpha-position and their evaluation for binding and activation of PPARalpha and PPARgamma are presented in this report. Among the new compounds, (S)-3-{4-[3-(5-methyl-2-phenyl-oxazol-4-yl)-propyl]-phenyl}-2-1,2,3-triazol-2-yl-propionic acid (17j), was identified as a potent human PPARalpha/gamma dual agonist (EC(50)=0.013 and 0.061 microM, respectively) with demonstrated oral bioavailability in rat and dog. 17j was shown to decrease insulin levels, plasma glucose, and triglycerides in the ZDF female rat model. In the human apolipoprotein A-1/CETP transgenic mouse model 17j produced increases in hApoA1 and HDL-C and decreases in plasma triglycerides. The increased potency for binding and activation of both PPAR subtypes observed with 17j when compared to previous analogs in this series was explained based on results derived from crystallographic and modeling studies.

  • Organizational Affiliation

    Department of Chemistry, Pfizer Global Research and Development, Michigan Laboratories, 2800 Plymouth Rd, Ann Arbor, MI 48105, USA. agustin.casimiro-garcia@pfizer.com

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Peroxisome proliferator-activated receptor gamma
A, B
271Homo sapiensMutation(s): 0 
Gene Names: PPARGNR1C3
UniProt & NIH Common Fund Data Resources
Find proteins for P37231 (Homo sapiens)
Explore P37231 
Go to UniProtKB:  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 UNT

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
(2S)-3-{4-[3-(5-methyl-2-phenyl-1,3-oxazol-4-yl)propyl]phenyl}-2-(2H-1,2,3-triazol-2-yl)propanoic acid
C24 H24 N4 O3
Binding Affinity Annotations 
IDSourceBinding Affinity
UNT BindingDB:  3IA6 IC50: min: 3, max: 5 (nM) from 2 assay(s)
EC50: min: 13, max: 15 (nM) from 2 assay(s)
PDBBind:  3IA6 IC50: 3 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.31 Å
  • R-Value Free: 0.297 
  • R-Value Work: 0.238 
  • R-Value Observed: 0.241 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 93.041α = 90
b = 62.187β = 102.66
c = 118.547γ = 90
Software Package:
Software NamePurpose

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

  • Released Date: 2009-10-13 
  • Deposition Author(s): Ohren, J.F.

Revision History  (Full details and data files)

  • Version 1.0: 2009-10-13
    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