4R2U

Crystal Structure of PPARgamma in complex with SR1664


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.192 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Pharmacological repression of PPAR gamma promotes osteogenesis.

Marciano, D.P.Kuruvilla, D.S.Boregowda, S.V.Asteian, A.Hughes, T.S.Garcia-Ordonez, R.Corzo, C.A.Khan, T.M.Novick, S.J.Park, H.Kojetin, D.J.Phinney, D.G.Bruning, J.B.Kamenecka, T.M.Griffin, P.R.

(2015) Nat Commun 6: 7443-7443

  • DOI: https://doi.org/10.1038/ncomms8443
  • Primary Citation of Related Structures:  
    4R2U, 4R6S

  • PubMed Abstract: 

    The nuclear receptor peroxisome proliferator-activated receptor gamma (PPARγ) is the master regulator of adipogenesis and the pharmacological target of the thiazolidinedione (TZD) class of insulin sensitizers. Activation of PPARγ by TZDs promotes adipogenesis at the expense of osteoblast formation, contributing to their associated adverse effects on bone. Recently, we reported the development of PPARγ antagonist SR1664, designed to block the obesity-induced phosphorylation of serine 273 (S273) in the absence of classical agonism, to derive insulin-sensitizing efficacy with improved therapeutic index. Here we identify the structural mechanism by which SR1664 actively antagonizes PPARγ, and extend these findings to develop the inverse agonist SR2595. Treatment of isolated bone marrow-derived mesenchymal stem cells with SR2595 promotes induction of osteogenic differentiation. Together these results identify the structural determinants of ligand-mediated PPARγ repression, and suggest a therapeutic approach to promote bone formation.


  • Organizational Affiliation

    Departments of Molecular Therapeutics, The Scripps Research Institute, Scripps Florida, Jupiter FL33458, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Peroxisome proliferator-activated receptor gammaA,
B [auth D]
275Homo sapiensMutation(s): 0 
Gene Names: NR1C3PPARG
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
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
3JX
Query on 3JX

Download Ideal Coordinates CCD File 
C [auth A],
D
4'-[(2,3-dimethyl-5-{[(1S)-1-(4-nitrophenyl)ethyl]carbamoyl}-1H-indol-1-yl)methyl]biphenyl-2-carboxylic acid
C33 H29 N3 O5
IIJDFXNUWZTHIM-NRFANRHFSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
3JX BindingDB:  4R2U IC50: 80 (nM) from 1 assay(s)
EC50: 4288 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.192 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 89.63α = 90
b = 63.67β = 103.43
c = 118.93γ = 90
Software Package:
Software NamePurpose
d*TREKdata scaling
d*TREKdata reduction
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-3000data collection

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-07-01
    Type: Initial release
  • Version 1.1: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description