3D6D

Crystal Structure of the complex between PPARgamma LBD and the LT175(R-enantiomer)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.305 
  • R-Value Work: 0.248 
  • R-Value Observed: 0.249 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Crystal Structure of the Peroxisome Proliferator-Activated Receptor gamma (PPARgamma) Ligand Binding Domain Complexed with a Novel Partial Agonist: A New Region of the Hydrophobic Pocket Could Be Exploited for Drug Design

Montanari, R.Saccoccia, F.Scotti, E.Crestani, M.Godio, C.Gilardi, F.Loiodice, F.Fracchiolla, G.Laghezza, A.Tortorella, P.Lavecchia, A.Novellino, E.Mazza, F.Aschi, M.Pochetti, G.

(2008) J Med Chem 51: 7768-7776

  • DOI: 10.1021/jm800733h
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The peroxisome proliferator-activated receptors (PPARs) are ligand-dependent transcription factors regulating glucose and lipid metabolism. The search for new PPAR ligands with reduced adverse effects with respect to the marketed antidiabetic agents ...

    The peroxisome proliferator-activated receptors (PPARs) are ligand-dependent transcription factors regulating glucose and lipid metabolism. The search for new PPAR ligands with reduced adverse effects with respect to the marketed antidiabetic agents thiazolidinediones (TZDs) and the dual-agonists glitazars is highly desired. We report the crystal structure and activity of the two enantiomeric forms of a clofibric acid analogue, respectively complexed with the ligand-binding domain (LBD) of PPARgamma, and provide an explanation on a molecular basis for their different potency and efficacy against PPARgamma. The more potent S-enantiomer is a dual PPARalpha/PPARgamma agonist which presents a partial agonism profile against PPARgamma. Docking of the S-enantiomer in the PPARalpha-LBD has been performed to explain its different subtype pharmacological profile. The hypothesis that partial agonists show differential stabilization of helix 3, when compared to full agonists, is also discussed. Moreover, the structure of the complex with the S-enantiomer reveals a new region of the PPARgamma-LBD never sampled before by other ligands.


    Related Citations: 
    • Insights into the mechanism of partial agonism: crystal structures of the peroxisome proliferator-activated receptor gamma ligand-binding domain in the complex with two enantiomeric ligands
      Pochetti, G., Godio, C., Mitro, N., Caruso, D., Galmozzi, A., Scurati, S., Loiodice, F., Fracchiolla, G., Tortorella, P., Laghezza, A., Lavecchia, A., Novellino, E., Mazza, F., Crestani, M.
      (2007) J Biol Chem 282: 17314
    • Partial agonists activate PPARgamma using a helix 12 independent mechanism
      Bruning, J.B., Chalmers, M.J., Prasad, S., Busby, S.A., Kamenecka, T.M., He, Y., Nettles, K.W., Griffin, P.R.
      (2007) Structure 15: 1258
    • Asymmetry in the PPARgamma/RXRalpha crystal structure reveals the molecular basis of heterodimerization among nuclear receptors
      Gampe, R.T., Montana, V.G., Lambert, M.H., Miller, A.B., Bledsoe, R.K., Milburn, M.V., Kliewer, S.A., Willson, T.M., Xu, H.E.
      (2000) Mol Cell 5: 545

    Organizational Affiliation

    Consiglio Nazionale delle Ricerche, Roma 00016, Italy.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Peroxisome proliferator-activated receptor gamma
A, B
286Homo sapiensMutation(s): 0 
Gene Names: PPARGNR1C3
Find proteins for P37231 (Homo sapiens)
Go to UniProtKB:  P37231
NIH Common Fund Data Resources
PHAROS  P37231
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
LRG
Query on LRG

Download CCD File 
A
(2S)-2-(biphenyl-4-yloxy)-3-phenylpropanoic acid
C21 H18 O3
TZTPJJNNACUQQR-FQEVSTJZSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
LRGEC50:  500   nM  BindingDB
LRGEC50:  550   nM  BindingDB
LRGEC50:  560   nM  BindingDB
LRGEC50:  480   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.305 
  • R-Value Work: 0.248 
  • R-Value Observed: 0.249 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 93.54α = 90
b = 61.05β = 103.49
c = 119.24γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
CNSrefinement
MOSFLMdata reduction
SCALAdata scaling
CNSphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-12-30
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance