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

Experimental Data Snapshot

  • Resolution: 2.07 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.222 

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This is version 1.3 of the entry. See complete history


Indol-1-yl Acetic Acids as Peroxisome Proliferator-Activated Receptor Agonists: Design, Synthesis, Structural Biology, and Molecular Docking Studies

Mahindroo, N.Wang, C.C.Liao, C.C.Huang, C.F.Lu, I.L.Lien, T.W.Peng, Y.H.Huang, W.J.Lin, Y.T.Hsu, M.C.Lin, C.H.Tsai, C.H.Hsu, J.T.Chen, X.Lyu, P.C.Chao, Y.S.Wu, S.Y.Hsieh, H.P.

(2006) J Med Chem 49: 1212-1216

  • DOI: https://doi.org/10.1021/jm0510373
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    A series of novel indole-based PPAR agonists is described leading to discovery of 10k, a highly potent PPAR pan-agonist. The structural biology and molecular docking studies revealed that the distances between the acidic group and the linker, when a ligand was complexed with PPARgamma protein, were important for the potent activity. The hydrophobic tail part of 10k makes intensive hydrophobic interaction with the PPARgamma protein resulting in potent activity.

  • 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 EHA

Download Ideal Coordinates CCD File 
C33 H31 N O5
Binding Affinity Annotations 
IDSourceBinding Affinity
EHA PDBBind:  2F4B IC50: 50 (nM) from 1 assay(s)
BindingDB:  2F4B IC50: 50 (nM) from 1 assay(s)
EC50: 70 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.07 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.222 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.967α = 90
b = 88.642β = 90.01
c = 57.878γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
SCALEPACKdata scaling
HKL-2000data reduction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-02-14
    Type: Initial release
  • Version 1.1: 2008-05-01
    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