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


Ligand Structure Quality Assessment 


This is version 1.3 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: https://doi.org/10.1016/j.bmc.2012.01.025
  • Primary Citation of Related Structures:  
    3CDP

  • 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 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.


  • Organizational Affiliation

    Dipartimento Farmaco-Chimico, Università degli Studi di Bari 'Aldo Moro', Via Orabona 4, 70126 Bari, Italy.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Peroxisome proliferator-activated receptor gamma
A, B
286Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P37231 (Homo sapiens)
Explore P37231 
Go to UniProtKB:  P37231
PHAROS:  P37231
GTEx:  ENSG00000132170 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP37231
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
YRG
Query on YRG

Download Ideal Coordinates CCD File 
C [auth A](2S)-2-(4-chlorophenoxy)-3-phenylpropanoic acid
C15 H13 Cl O3
CPBLTMSKPQDJPW-AWEZNQCLSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
YRG BindingDB:  3CDP EC50: min: 2692, max: 9600 (nM) from 4 assay(s)
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



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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
  • Version 1.3: 2024-03-13
    Changes: Data collection, Database references, Derived calculations