4R6S

Crystal structure of PPARgammma in complex with SR1663


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.174 

wwPDB Validation 3D Report Full Report


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: 10.1038/ncomms8443
  • Structures With Same Primary Citation

  • 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 adi ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Peroxisome proliferator-activated receptor gamma
A, B
275Homo sapiensMutation(s): 1 
Gene Names: NR1C3PPARG
Find proteins for P37231 (Homo sapiens)
Go to UniProtKB:  P37231
NIH Common Fund Data Resources
PHAROS  P37231
Protein Feature View
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
3K2
Query on 3K2

Download CCD File 
A, B
4'-[(2,3-dimethyl-5-{[(1R)-1-(4-nitrophenyl)ethyl]carbamoyl}-1H-indol-1-yl)methyl]biphenyl-2-carboxylic acid
C33 H29 N3 O5
IIJDFXNUWZTHIM-OAQYLSRUSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
3K2IC50:  2   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.174 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 93.241α = 90
b = 61.94β = 103.44
c = 119.226γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-07-01
    Type: Initial release
  • Version 1.1: 2017-11-22
    Changes: Refinement description