3CDP

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.298 
  • R-Value Work: 0.236 
  • R-Value Observed: 0.237 

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
  • Structures With Same Primary Citation

  • 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 U S A 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: PPARGNR1C3
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
YRG
Query on YRG

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:  7940   nM  BindingDB
YRGEC50:  2700   nM  BindingDB
YRGEC50:  9600   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.298 
  • R-Value Work: 0.236 
  • R-Value Observed: 0.237 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 93.21α = 90
b = 61.65β = 103.01
c = 118.36γ = 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: 2009-01-13
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2013-12-25
    Changes: Database references