3GZ9

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • 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


Literature

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:  
    3GZ9, 3H0A

  • 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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Peroxisome proliferator-activated receptor deltaA269Homo sapiensMutation(s): 2 
Gene Names: PPARDNR1C2PPARB
Find proteins for Q03181 (Homo sapiens)
Explore Q03181 
Go to UniProtKB:  Q03181
NIH Common Fund Data Resources
PHAROS  Q03181
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
D32
Query on D32

Download CCD File 
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
RMMWVBYHCKSFMW-UHFFFAOYSA-N
 Ligand Interaction
B7G
Query on B7G

Download CCD File 
A
heptyl beta-D-glucopyranoside
C13 H26 O6
NIDYWHLDTIVRJT-UJPOAAIJSA-N
 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

  • Method: X-RAY DIFFRACTION
  • 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
REFMACrefinement
PDB_EXTRACTdata extraction
ADSCdata collection

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • 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