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

Starting Model: experimental
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Effects of modifications of the linker in a series of phenylpropanoic acid derivatives: Synthesis, evaluation as PPARalpha/gamma dual agonists, and X-ray crystallographic studies.

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.J.Collard, W.T.McGregor, C.Fakhoury, S.A.Schaum, R.P.Zhou, H.

(2008) Bioorg Med Chem 16: 4883-4907

  • DOI: https://doi.org/10.1016/j.bmc.2008.03.043
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    A new series of alpha-aryl or alpha-heteroarylphenyl propanoic acid derivatives was synthesized that incorporate acetylene-, ethylene-, propyl-, or nitrogen-derived linkers as a replacement of the commonly used ether moiety that joins the central phenyl ring with the lipophilic tail. The effect of these modifications in the binding and activation of PPARalpha and PPARgamma was first evaluated in vitro. Compounds possessing suitable profiles were then evaluated in the ob/ob mouse model of type 2 diabetes. The propylene derivative 40 and the propyl derivative 53 demonstrated robust plasma glucose lowering activity in this model. Compound 53 was also evaluated in male Zucker diabetic fatty rats and was found to achieve normalization of glucose, triglycerides, and insulin levels. An X-ray crystal structure of the complex of 53 with the PPARgamma-ligand-binding domain was obtained and discussed in this report.

  • Organizational Affiliation

    Department of Chemistry, Pfizer Global Research and Development, Michigan Laboratories, 2800 Plymouth Road, 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 L92

Download Ideal Coordinates CCD File 
C26 H26 N2 O3
Binding Affinity Annotations 
IDSourceBinding Affinity
L92 BindingDB:  2Q8S IC50: 185 (nM) from 1 assay(s)
EC50: 140 (nM) from 1 assay(s)
PDBBind:  2Q8S IC50: 185 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.30 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.225 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 93.455α = 90
b = 62.016β = 102.54
c = 118.66γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

  • Released Date: 2008-10-14 
  • Deposition Author(s): Ohren, J.F.

Revision History  (Full details and data files)

  • Version 1.0: 2008-10-14
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2023-08-30
    Changes: Data collection, Database references, Derived calculations, Refinement description