Crystal structure of the ligand binding domain of human PPAR-gamma im complex with an agonist

Experimental Data Snapshot

  • Resolution: 2.28 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.216 

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This is version 1.3 of the entry. See complete history


Novel indole-based peroxisome proliferator-activated receptor agonists: design, SAR, structural biology, and biological activities

Mahindroo, N.Huang, C.-F.Peng, Y.-H.Wang, C.-C.Liao, C.-C.Lien, T.-W.Chittimalla, S.K.Huang, W.-J.Chai, C.-H.Prakash, E.Chen, C.-P.Hsu, T.-A.Peng, C.-H.Lu, I.-L.Lee, L.-H.Chang, Y.-W.Chen, W.-C.Chou, Y.-C.Chen, C.-T.Goparaju, C.M.V.Chen, Y.-S.Lan, S.-J.Yu, M.-C.Chen, X.Chao, Y.-S.Wu, S.-Y.Hsieh, H.-P.

(2005) J Med Chem 48: 8194-8208

  • DOI: https://doi.org/10.1021/jm0506930
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    The synthesis and structure-activity relationship studies of novel indole derivatives as peroxisome proliferator-activated receptor (PPAR) agonists are reported. Indole, a drug-like scaffold, was studied as a core skeleton for the acidic head part of PPAR agonists. The structural features (acidic head, substitution on indole, and linker) were optimized first, by keeping benzisoxazole as the tail part, based on binding and functional activity at PPARgamma protein. The variations in the tail part, by introducing various heteroaromatic ring systems, were then studied. In vitro evaluation led to identification of a novel series of indole compounds with a benzisoxazole tail as potent PPAR agonists with the lead compound 14 (BPR1H036) displaying an excellent pharmacokinetic profile in BALB/c mice and an efficacious glucose lowering activity in KKA(y) mice. Structural biology studies of 14 showed that the indole ring contributes strong hydrophobic interactions with PPARgamma and could be an important moiety for the binding to the protein.

  • Organizational Affiliation

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

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 
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 3EA

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
C24 H23 F3 N2 O5
Binding Affinity Annotations 
IDSourceBinding Affinity
3EA PDBBind:  2ATH IC50: 152 (nM) from 1 assay(s)
BindingDB:  2ATH IC50: min: 152, max: 152.05 (nM) from 2 assay(s)
EC50: 230 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.28 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.216 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.78α = 90
b = 88.523β = 90.43
c = 57.565γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
SCALEPACKdata scaling
HKL-2000data reduction

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-08-25
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2024-03-13
    Changes: Data collection, Database references, Derived calculations