Crystal Structure of Peroxisome Proliferator-Activated Receptor Delta (PPARd) in Complex with a Full Agonist

Experimental Data Snapshot

  • Resolution: 2.00 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.192 

wwPDB Validation   3D Report Full Report

This is version 1.2 of the entry. See complete history


Identification of a PPARdelta agonist with partial agonistic activity on PPARgamma.

Connors, R.V.Wang, Z.Harrison, M.Zhang, A.Wanska, M.Hiscock, S.Fox, B.Dore, M.Labelle, M.Sudom, A.Johnstone, S.Liu, J.Walker, N.P.Chai, A.Siegler, K.Li, Y.Coward, P.

(2009) Bioorg Med Chem Lett 19: 3550-3554

  • DOI: 10.1016/j.bmcl.2009.04.151
  • Primary Citation of Related Structures:  
    3H0A, 3GZ9

  • PubMed Abstract: 
  • The discovery and optimization of a series of potent PPARdelta full agonists with partial agonistic activity against PPARgamma is described.

    Organizational Affiliation

    Department of Chemistry, Amgen, 1120 Veterans Blvd., South San Francisco, CA 94080, USA. rconnors@amgen.com

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Peroxisome proliferator-activated receptor deltaA269Homo sapiensMutation(s): 2 
UniProt & NIH Common Fund Data Resources
Find proteins for Q03181 (Homo sapiens)
Explore Q03181 
Go to UniProtKB:  Q03181
PHAROS:  Q03181
Protein Feature View
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
Query on D32

Download Ideal Coordinates CCD File 
C [auth A](2,3-dimethyl-4-{[2-(prop-2-yn-1-yloxy)-4-{[4-(trifluoromethyl)phenoxy]methyl}phenyl]sulfanyl}phenoxy)acetic acid
C27 H23 F3 O5 S
 Ligand Interaction
Query on B7G

Download Ideal Coordinates CCD File 
B [auth A]heptyl beta-D-glucopyranoside
C13 H26 O6
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
D32IC50 :  4   nM  PDBBind
D32Ki:  4   nM  BindingDB
D32Ki:  4   nM  Binding MOAD
D32EC50:  54   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Resolution: 2.00 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.192 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 94.577α = 90
b = 92.129β = 90
c = 39.555γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
PDB_EXTRACTdata extraction
ADSCdata collection

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-06-30
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary