2I4P

Crystal structure of the complex between PPARgamma and the partial agonist LT127 (ureidofibrate derivative). Structure obtained from crystals of the apo-form soaked for 30 days.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.272 
  • R-Value Observed: 0.273 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

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: 17314-17324

  • DOI: 10.1074/jbc.M702316200
  • Primary Citation of Related Structures:  
    2I4P, 2I4Z, 2I4J

  • PubMed Abstract: 
  • The peroxisome proliferator-activated receptors (PPARs) are transcriptional regulators of glucose and lipid metabolism. They are activated by natural ligands, such as fatty acids, and are also targets of synthetic antidiabetic and hypolipidemic drugs ...

    The peroxisome proliferator-activated receptors (PPARs) are transcriptional regulators of glucose and lipid metabolism. They are activated by natural ligands, such as fatty acids, and are also targets of synthetic antidiabetic and hypolipidemic drugs. By using cell-based reporter assays, we studied the transactivation activity of two enantiomeric ureidofibrate-like derivatives. In particular, we show that the R-enantiomer, (R)-1, is a full agonist of PPARgamma, whereas the S-enantiomer, (S)-1, is a less potent partial agonist. Most importantly, we report the x-ray crystal structures of the PPARgamma ligand binding domain complexed with the R- and the S-enantiomer, respectively. The analysis of the two crystal structures shows that the different degree of stabilization of the helix 12 induced by the ligand determines its behavior as full or partial agonist. Another crystal structure of the PPARgamma.(S)-1 complex, only differing in the soaking time of the ligand, is also presented. The comparison of the two structures of the complexes with the partial agonist reveals significant differences and is suggestive of the possible coexistence in solution of transcriptionally active and inactive forms of helix 12 in the presence of a partial agonist. Mutation analysis confirms the importance of Leu(465), Leu(469), and Ile(472) in the activation by (R)-1 and underscores the key role of Gln(286) in the PPARgamma activity.


    Related Citations: 
    • Ligand binding and co-activator assembly of the peroxisome proliferator-activated receptor-gamma
      Nolte, R.T., Wisely, G.B., Westin, S., Cobb, J.E., Lambert, M.H., Kurokawa, R., Rosenfeld, M.G., Willson, T.M., Glass, C.K., Milburn, M.V.
      (1998) Nature 395: 137
    • A peroxisome proliferator-activated receptor ligand inhibits adipocyte differentiation
      Oberfield, J.L., Collins, J.L., Holmes, C.P., Goreham, D.M., Cooper, J.P., Cobb, J.E., Lenhard, J.M., Hull-Ryde, E.A., Mohr, C.P., Blanchard, S.G., Parks, D.J., Moore, L.B., Lehmann, J.M., Plunket, K., Miller, A.B., Milburn, M.V., Kliewer, S.A., Willson, T.M.
      (1999) Proc Natl Acad Sci U S A 96: 6102

    Organizational Affiliation

    Istituto di Cristallografia, Consiglio Nazionale delle Ricerche, Montelibretti, 00016 Monterotondo Stazione, Roma, Italia. giorgio.pochetti@ic.cnr.it



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Peroxisome proliferator-activated receptor gammaAB286Homo sapiensMutation(s): 0 
Gene Names: PPARGNR1C3
Find proteins for P37231 (Homo sapiens)
Explore P37231 
Go to UniProtKB:  P37231
NIH Common Fund Data Resources
PHAROS  P37231
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DRH
Query on DRH

Download CCD File 
A
(2S)-2-(4-{2-[1,3-BENZOXAZOL-2-YL(HEPTYL)AMINO]ETHYL}PHENOXY)-2-METHYLBUTANOIC ACID
C27 H36 N2 O4
QPKIEBNVIOELIR-MHZLTWQESA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
DRHKi:  971   nM  BindingDB
DRHKd :  1978   nM  PDBBind
DRHKd:  1978   nM  BindingDB
DRHKd:  2000   nM  BindingDB
DRHEC50:  590   nM  BindingDB
DRHEC50:  593   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.272 
  • R-Value Observed: 0.273 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 93.54α = 90
b = 60.91β = 103.08
c = 118.35γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACTdata extraction
MAR345data collection
CNSphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-04-17
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-18
    Changes: Advisory, Refinement description