3GWX

MOLECULAR RECOGNITION OF FATTY ACIDS BY PEROXISOME PROLIFERATOR-ACTIVATED RECEPTORS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.301 
  • R-Value Work: 0.242 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Molecular recognition of fatty acids by peroxisome proliferator-activated receptors.

Xu, H.E.Lambert, M.H.Montana, V.G.Parks, D.J.Blanchard, S.G.Brown, P.J.Sternbach, D.D.Lehmann, J.M.Wisely, G.B.Willson, T.M.Kliewer, S.A.Milburn, M.V.

(1999) Mol Cell 3: 397-403

  • DOI: https://doi.org/10.1016/s1097-2765(00)80467-0
  • Primary Citation of Related Structures:  
    1GWX, 2GWX, 3GWX

  • PubMed Abstract: 

    The peroxisome proliferator-activated receptors (PPARs) are nuclear receptors for fatty acids (FAs) that regulate glucose and lipid homeostasis. We report the crystal structure of the PPAR delta ligand-binding domain (LBD) bound to either the FA eicosapentaenoic acid (EPA) or the synthetic fibrate GW2433. The carboxylic acids of EPA and GW2433 interact directly with the activation function 2 (AF-2) helix. The hydrophobic tail of EPA adopts two distinct conformations within the large hydrophobic cavity. GW2433 occupies essentially the same space as EPA bound in both conformations. These structures provide molecular insight into the propensity for PPARs to interact with a variety of synthetic and natural compounds, including FAs that vary in both chain length and degree of saturation.


  • Organizational Affiliation

    Glaxo Wellcome Research and Development, Research Triangle Park, North Carolina 27709, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PROTEIN (PEROXISOME PROLIFERATOR ACTIVATED RECEPTOR (PPAR-DELTA))
A, B
271Homo sapiensMutation(s): 0 
Gene Names: PPARD
UniProt & NIH Common Fund Data Resources
Find proteins for Q03181 (Homo sapiens)
Go to UniProtKB:  Q03181
PHAROS:  Q03181
GTEx:  ENSG00000112033 
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
EPA
Query on EPA

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
5,8,11,14,17-EICOSAPENTAENOIC ACID
C20 H30 O2
JAZBEHYOTPTENJ-JLNKQSITSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
EPA BindingDB:  3GWX IC50: 4000 (nM) from 1 assay(s)
PDBBind:  3GWX IC50: 4000 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.301 
  • R-Value Work: 0.242 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 39.379α = 90
b = 95.543β = 97.89
c = 96.181γ = 90
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2000-04-26
    Type: Initial release
  • Version 1.1: 2008-04-26
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-12-27
    Changes: Data collection, Database references, Derived calculations