2Q8S

X-ray Crystal structure of the nuclear hormone receptor PPAR-gamma in a complex with a PPAR gamma/alpha dual agonist


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.222 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Effects of modifications of the linker in a series of phenylpropanoic acid derivatives: Synthesis, evaluation as PPARalpha/gamma dual agonists, and X-ray crystallographic studies.

Casimiro-Garcia, A.Bigge, C.F.Davis, J.A.Padalino, T.Pulaski, J.Ohren, J.F.McConnell, P.Kane, C.D.Royer, L.J.Stevens, K.A.Auerbach, B.J.Collard, W.T.McGregor, C.Fakhoury, S.A.Schaum, R.P.Zhou, H.

(2008) Bioorg.Med.Chem. 16: 4883-4907

  • DOI: 10.1016/j.bmc.2008.03.043

  • PubMed Abstract: 
  • A new series of alpha-aryl or alpha-heteroarylphenyl propanoic acid derivatives was synthesized that incorporate acetylene-, ethylene-, propyl-, or nitrogen-derived linkers as a replacement of the commonly used ether moiety that joins the central phe ...

    A new series of alpha-aryl or alpha-heteroarylphenyl propanoic acid derivatives was synthesized that incorporate acetylene-, ethylene-, propyl-, or nitrogen-derived linkers as a replacement of the commonly used ether moiety that joins the central phenyl ring with the lipophilic tail. The effect of these modifications in the binding and activation of PPARalpha and PPARgamma was first evaluated in vitro. Compounds possessing suitable profiles were then evaluated in the ob/ob mouse model of type 2 diabetes. The propylene derivative 40 and the propyl derivative 53 demonstrated robust plasma glucose lowering activity in this model. Compound 53 was also evaluated in male Zucker diabetic fatty rats and was found to achieve normalization of glucose, triglycerides, and insulin levels. An X-ray crystal structure of the complex of 53 with the PPARgamma-ligand-binding domain was obtained and discussed in this report.


    Organizational Affiliation

    Department of Chemistry, Pfizer Global Research and Development, Michigan Laboratories, 2800 Plymouth Road, Ann Arbor, MI 48105, USA. agustin.casimiro-garcia@pfizer.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Peroxisome proliferator-activated receptor gamma
A, B
271Homo sapiensMutation(s): 0 
Gene Names: PPARG (NR1C3)
Find proteins for P37231 (Homo sapiens)
Go to Gene View: PPARG
Go to UniProtKB:  P37231
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
L92
Query on L92

Download SDF File 
Download CCD File 
A
(2S)-3-{4-[3-(5-METHYL-2-PHENYL-1,3-OXAZOL-4-YL)PROPYL]PHENYL}-2-(1H-PYRROL-1-YL)PROPANOIC ACID
C26 H26 N2 O3
QPJVYLQOALFBLJ-DEOSSOPVSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
L92IC50: 185 nM (100) BINDINGDB
L92EC50: 140 nM (100) BINDINGDB
L92IC50: 185 nM BINDINGMOAD
L92IC50: 185 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.222 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 93.455α = 90.00
b = 62.016β = 102.54
c = 118.660γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
MOLREPphasing
ADSCdata collection
HKL-2000data scaling
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2007-06-11 
  • Released Date: 2008-10-14 
  • Deposition Author(s): Ohren, J.F.

Revision History 

  • Version 1.0: 2008-10-14
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Version format compliance