Human PPAR gamma ligand binding domain in complex with a gamma selective agonist MO3S

Experimental Data Snapshot

  • Resolution: 2.30 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.227 

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Design, Synthesis, and Structural Analysis of Phenylpropanoic Acid-Type PPAR gamma-Selective Agonists: Discovery of Reversed Stereochemistry-Activity Relationship

Ohashi, M.Oyama, T.Nakagome, I.Satoh, M.Nishio, Y.Nobusada, H.Hirono, S.Morikawa, K.Hashimoto, Y.Miyachi, H.

(2011) J Med Chem 54: 331-341

  • DOI: https://doi.org/10.1021/jm101233f
  • Primary Citation of Related Structures:  
    3AN3, 3AN4

  • PubMed Abstract: 

    Peroxisome proliferator-activated receptor gamma (PPARγ) is a ligand-mediated transcription factor with roles in glucose, lipid, and lipoprotein homeostasis, and PPARγ ligands are expected have therapeutic potential in these as well as other areas. We report here the design, synthesis, crystallographic analysis, and computational studies of α-benzylphenylpropanoic acid PPARγ agonists. Interestingly, these compounds show a reversal of the stereochemistry-transactivation activity relationship observed with other phenylpropanoic acid ligands.

  • Organizational Affiliation

    Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Kita-ku, Okayama, Japan.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Peroxisome proliferator-activated receptor gamma
A, B
286Homo 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 M7S

Download Ideal Coordinates CCD File 
C [auth A](2S)-2-benzyl-3-(4-propoxy-3-{[({4-[(3S,5S,7S)-tricyclo[,7~]dec-1-yl]phenyl}carbonyl)amino]methyl}phenyl)propanoic acid
C37 H43 N O4
Binding Affinity Annotations 
IDSourceBinding Affinity
M7S BindingDB:  3AN3 EC50: min: 3.6, max: 22 (nM) from 2 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.30 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.227 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 93.192α = 90
b = 61.061β = 102.82
c = 118.618γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data reduction
HKL-2000data 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: 2011-07-27
    Type: Initial release
  • Version 1.1: 2023-11-01
    Changes: Data collection, Database references, Derived calculations, Refinement description