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 

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
  • 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 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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PEROXISOME PROLIFERATOR-ACTIVATED RECEPTOR ALPHAA, B274Homo sapiensMutation(s): 0 
Gene Names: PPARANR1C1PPAR
EC: 2.3.1.48
Find proteins for Q07869 (Homo sapiens)
Explore Q07869 
Go to UniProtKB:  Q07869
NIH Common Fund Data Resources
PHAROS  Q07869
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
WY1
Query on WY1

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
EDO
Query on EDO

Download CCD File 
A, B
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
WY1Kd:  0.36000001430511475   nM  BindingDB
WY1EC50:  39800   nM  BindingDB
WY1Ki:  100   nM  BindingDB
WY1EC50:  10000   nM  BindingDB
WY1EC50:  4800   nM  BindingDB
WY1EC50:  5000   nM  BindingDB
WY1EC50:  542   nM  BindingDB
WY1IC50:  36300   nM  BindingDB
WY1EC50:  13000   nM  BindingDB
WY1EC50:  740   nM  BindingDB
WY1EC50:  12000   nM  BindingDB
WY1EC50:  12600   nM  BindingDB
WY1Kd:  19   nM  BindingDB
WY1EC50:  700   nM  BindingDB
WY1EC50:  40   nM  BindingDB
WY1EC50:  630   nM  BindingDB
WY1EC50:  650   nM  BindingDB
WY1EC50:  15500   nM  BindingDB
WY1EC50:  1600   nM  BindingDB
WY1EC50:  1620   nM  BindingDB
WY1EC50:  2100   nM  BindingDB
WY1EC50:  23330   nM  BindingDB
WY1EC50:  1560   nM  BindingDB
WY1IC50:  10110   nM  BindingDB
WY1EC50:  130   nM  BindingDB
WY1EC50:  29000   nM  BindingDB
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

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • 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