Crystal Structure of Human PPAR-gamma Ligand Binding Domain Complexed with a Potent and Selective Agonist

Experimental Data Snapshot

  • Resolution: 2.30 Å
  • R-Value Free: 0.298 
  • R-Value Work: 0.230 
  • R-Value Observed: 0.234 

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Ligand Structure Quality Assessment 

This is version 1.2 of the entry. See complete history


Design and structural analysis of novel pharmacophores for potent and selective peroxisome proliferator-activated receptor gamma agonists

Lin, C.-H.Peng, Y.-H.Coumar, M.S.Chittimalla, S.K.Liao, C.-C.Lyn, P.-C.Huang, C.-C.Lien, T.-W.Lin, W.-H.Hsu, J.T.-A.Cheng, J.-H.Chen, X.Wu, J.-S.Chao, Y.-S.Lee, H.-J.Juo, C.-G.Wu, S.-Y.Hsieh, H.-P.

(2009) J Med Chem 52: 2618-2622

  • DOI: https://doi.org/10.1021/jm801594x
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Utilizing medicinal chemistry design strategies such as benzo splitting and ring expansion, we converted PPARalpha/gamma dual agonist 1 to selective PPARgamma agonists 19 and 20. Compounds 19 and 20 were 2- to 4-fold better than rosiglitazone at PPARgamma receptor, with 80- to 100-fold PPARgamma selectivity over PPARalpha receptor. X-ray cocrystal studies in PPARgamma and modeling studies in PPARalpha give molecular insights for the improved PPARgamma potency and selectivity for 19 when compared to 1.

  • Organizational Affiliation

    Division of Biotechnology and Pharmaceutical Research, National Health Research Institutes, 35 Keyan Road, Zhunan Town, Miaoli County 350, Taiwan, ROC.

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: PPAR gamma
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 2PQ

Download Ideal Coordinates CCD File 
C [auth A]2-[(1-{3-[4-(biphenyl-4-ylcarbonyl)-2-propylphenoxy]propyl}-1,2,3,4-tetrahydroquinolin-5-yl)oxy]-2-methylpropanoic acid
C38 H41 N O5
Binding Affinity Annotations 
IDSourceBinding Affinity
2PQ BindingDB:  3GBK EC50: 50 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.30 Å
  • R-Value Free: 0.298 
  • R-Value Work: 0.230 
  • R-Value Observed: 0.234 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.502α = 90
b = 88.892β = 91.06
c = 58.371γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-12-29
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2023-11-01
    Changes: Data collection, Database references, Derived calculations, Refinement description