3QT0

Revealing a steroid receptor ligand as a unique PPARgamma agonist


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 
    0.277 (Depositor), 0.280 (DCC) 
  • R-Value Work: 
    0.196 (Depositor), 0.210 (DCC) 
  • R-Value Observed: 
    0.200 (Depositor) 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted 486Click on this verticalbar to view details

This is version 1.2 of the entry. See complete history


Literature

Revealing a steroid receptor ligand as a unique PPAR gamma agonist.

Lin, S.Han, Y.Shi, Y.Rong, H.Zheng, S.Jin, S.Lin, S.Y.Lin, S.C.Li, Y.

(2012) Cell Res 22: 746-756

  • DOI: https://doi.org/10.1038/cr.2011.162
  • Primary Citation of Related Structures:  
    3QT0

  • PubMed Abstract: 

    Peroxisome proliferator-activated receptor gamma (PPARγ) regulates metabolic homeostasis and is a molecular target for anti-diabetic drugs. We report here the identification of a steroid receptor ligand, RU-486, as an unexpected PPARγ agonist, thereby uncovering a novel signaling route for this steroid drug. Similar to rosiglitazone, RU-486 modulates the expression of key PPARγ target genes and promotes adipocyte differentiation, but with a lower adipogenic activity. Structural and functional studies of receptor-ligand interactions reveal the molecular basis for a unique binding mode for RU-486 in the PPARγ ligand-binding pocket with distinctive properties and epitopes, providing the molecular mechanisms for the discrimination of RU-486 from thiazolidinediones (TZDs) drugs. Our findings together indicate that steroid compounds may represent an alternative approach for designing non-TZD PPARγ ligands in the treatment of insulin resistance.


  • Organizational Affiliation

    State Key Laboratory for Cellular Stress Biology, School of Life Sciences, Xiamen University, Fujian, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Peroxisome proliferator-activated receptor gamma271Homo sapiensMutation(s): 0 
Gene Names: PPARGNR1C3
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
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Nuclear receptor coactivator 1 peptideB [auth C]16Homo sapiensMutation(s): 0 
Gene Names: NCOA1BHLHE74SRC1
EC: 2.3.1.48
UniProt & NIH Common Fund Data Resources
Find proteins for Q15788 (Homo sapiens)
Explore Q15788 
Go to UniProtKB:  Q15788
PHAROS:  Q15788
GTEx:  ENSG00000084676 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ15788
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
486
Query on 486

Download Ideal Coordinates CCD File 
C [auth A]11-(4-DIMETHYLAMINO-PHENYL)-17-HYDROXY-13-METHYL-17-PROP-1-YNYL-1,2,6,7,8,11,12,13,14,15,16,17-DODEC AHYDRO-CYCLOPENTA[A]PHENANTHREN-3-ONE
C29 H35 N O2
VKHAHZOOUSRJNA-GCNJZUOMSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free:  0.277 (Depositor), 0.280 (DCC) 
  • R-Value Work:  0.196 (Depositor), 0.210 (DCC) 
  • R-Value Observed: 0.200 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.22α = 90
b = 95.781β = 90
c = 125.29γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
MOLREPphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted 486Click on this verticalbar to view details

Entry History 

Deposition Data

  • Released Date: 2012-02-29 
  • Deposition Author(s): Rong, H.

Revision History  (Full details and data files)

  • Version 1.0: 2012-02-29
    Type: Initial release
  • Version 1.1: 2013-08-28
    Changes: Database references
  • Version 1.2: 2024-02-21
    Changes: Data collection, Database references, Derived calculations, Structure summary