4BCR

Structure of PPARalpha in complex with WY14643


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.174 

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This is version 1.3 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: https://doi.org/10.1016/j.jmb.2013.05.010
  • Primary Citation of Related Structures:  
    4BCR

  • 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 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PEROXISOME PROLIFERATOR-ACTIVATED RECEPTOR ALPHA
A, B
274Homo sapiensMutation(s): 0 
EC: 2.3.1.48
UniProt & NIH Common Fund Data Resources
Find proteins for Q07869 (Homo sapiens)
Explore Q07869 
Go to UniProtKB:  Q07869
PHAROS:  Q07869
GTEx:  ENSG00000186951 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ07869
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
WY1 BindingDB:  4BCR Ki: min: 100, max: 4500 (nM) from 3 assay(s)
Kd: 19 (nM) from 1 assay(s)
IC50: min: 1.01e+4, max: 3.63e+4 (nM) from 2 assay(s)
EC50: min: 40, max: 3.98e+4 (nM) from 27 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.174 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.061α = 90
b = 62.359β = 90
c = 180.048γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-05-29
    Type: Initial release
  • Version 1.1: 2013-06-05
    Changes: Database references
  • Version 1.2: 2013-08-07
    Changes: Database references
  • Version 1.3: 2024-05-08
    Changes: Data collection, Database references, Derived calculations, Other