4BCR

Structure of PPARalpha in complex with WY14643


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.497 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.173 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Molecular Mechanism of Peroxisome Proliferator-Activated Receptor Alpha Activation by Wy14643: A New Mode of Ligand Recognition and Receptor Stabilization

Bernardes, A.T Souza, P.C.Muniz, J.R.C.Ricci, C.G.Ayers, S.D.Parekh, N.M.Godoy, A.S.Trivella, D.B.B.Reinach, P.Webb, P.Skaf, M.S.Polikarpov, I.

(2013) J.Mol.Biol. 425: 2878

  • DOI: 10.1016/j.jmb.2013.05.010

  • PubMed Abstract: 
  • Peroxisome proliferator-activated receptors (PPARs) are members of a superfamily of nuclear transcription factors. They are involved in mediating numerous physiological effects in humans, including glucose and lipid metabolism. PPARα ligands effectiv ...

    Peroxisome proliferator-activated receptors (PPARs) are members of a superfamily of nuclear transcription factors. They are involved in mediating numerous physiological effects in humans, including glucose and lipid metabolism. PPARα ligands effectively treat dyslipidemia and have significant antiinflammatory and anti-atherosclerotic activities. These effects and their ligand-dependent activity make nuclear receptors obvious targets for drug design. Here, we present the structure of the human PPARα in complex with WY14643, a member of fibrate class of drug, and a widely used PPAR activator. The crystal structure of this complex suggests that WY14643 induces activation of PPARα in an unusual bipartite mechanism involving conventional direct helix 12 stabilization and an alternative mode that involves a second ligand in the pocket. We present structural observations, molecular dynamics and activity assays that support the importance of the second site in WY14643 action. The unique binding mode of WY14643 reveals a new pattern of nuclear receptor ligand recognition and suggests a novel basis for ligand design, offering clues for improving the binding affinity and selectivity of ligand. We show that binding of WY14643 to PPARα was associated with antiinflammatory disease in a human corneal cell model, suggesting possible applications for PPARα ligands.


    Organizational Affiliation

    Institute of Physics of São Carlos, University of São Paulo, Avenida Trabalhador Sãocarlense 400, São Carlos, SP 13560-970, Brazil.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PEROXISOME PROLIFERATOR-ACTIVATED RECEPTOR ALPHA
A, B
274Homo sapiensMutation(s): 0 
Gene Names: PPARA (NR1C1, PPAR)
Find proteins for Q07869 (Homo sapiens)
Go to Gene View: PPARA
Go to UniProtKB:  Q07869
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EDO
Query on EDO

Download SDF File 
Download CCD File 
A, B
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
WY1
Query on WY1

Download SDF File 
Download CCD File 
A, B
2-({4-CHLORO-6-[(2,3-DIMETHYLPHENYL)AMINO]PYRIMIDIN-2-YL}SULFANYL)ACETIC ACID
C14 H14 Cl N3 O2 S
SZRPDCCEHVWOJX-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
WY1Ki: 100 nM (91) BINDINGDB
WY1EC50: 40 - 2100 nM (91) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.497 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.173 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 62.061α = 90.00
b = 62.359β = 90.00
c = 180.048γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
iMOSFLMdata reduction
PHASERphasing
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-05-29
    Type: Initial release
  • Version 1.1: 2013-06-05
    Type: Database references
  • Version 1.2: 2013-08-07
    Type: Database references