3CDP

Crystal structure of PPAR-gamma LBD complexed with a partial agonist, analogue of clofibric acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.298 
  • R-Value Work: 0.236 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Synthesis, biological evaluation and molecular investigation of fluorinated peroxisome proliferator-activated receptors alpha/gamma dual agonists

Fracchiolla, G.Laghezza, A.Piemontese, L.Parente, M.Lavecchia, A.Pochetti, G.Montanari, R.Di Giovanni, C.Carbonara, G.Tortorella, P.Novellino, E.Loiodice, F.

(2012) Bioorg.Med.Chem. 20: 2141-2151

  • DOI: 10.1016/j.bmc.2012.01.025

  • PubMed Abstract: 
  • PPARs are transcription factors that govern lipid and glucose homeostasis and play a central role in cardiovascular disease, obesity, and diabetes. Thus, there is significant interest in developing new agonists for these receptors. Given that the int ...

    PPARs are transcription factors that govern lipid and glucose homeostasis and play a central role in cardiovascular disease, obesity, and diabetes. Thus, there is significant interest in developing new agonists for these receptors. Given that the introduction of fluorine generally has a profound effect on the physical and/or biological properties of the target molecule, we synthesized a series of fluorinated analogs of the previously reported compound 2, some of which turned out to be remarkable PPARα and PPARγ dual agonists. Docking experiments were also carried out to gain insight into the interactions of the most active derivatives with both receptors.


    Related Citations: 
    • Structural determinants of ligand binding selectivity between the peroxisome proliferator-activated receptors
      Xu, H.E.,Lambert, M.H.,Montana, V.G.,Plunket, K.D.,Moore, L.B.,Collins, J.L.,Oplinger, J.A.,Kliewer, S.A.,Gampe, R.T.,McKee, D.D.,Moore, J.T.,Willson, T.M.
      (2001) Proc.Natl.Acad.Sci.Usa 98: 13919


    Organizational Affiliation

    Dipartimento Farmaco-Chimico, Università degli Studi di Bari 'Aldo Moro', Via Orabona 4, 70126 Bari, 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: 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
YRG
Query on YRG

Download SDF File 
Download CCD File 
A
(2S)-2-(4-chlorophenoxy)-3-phenylpropanoic acid
C15 H13 Cl O3
CPBLTMSKPQDJPW-AWEZNQCLSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
YRGEC50: 2700 - 9600 nM (99) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.298 
  • R-Value Work: 0.236 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 93.210α = 90.00
b = 61.650β = 103.01
c = 118.360γ = 90.00
Software Package:
Software NamePurpose
ADSCdata collection
MOSFLMdata reduction
SCALAdata scaling
CNSrefinement
CNSphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-01-13
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2013-12-25
    Type: Database references