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 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.189 

wwPDB Validation 3D Report Full Report


This is version 1.1 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:  

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

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Peroxisome proliferator-activated receptor delta
A
269Homo sapiensMutation(s): 2 
Gene Names: PPARD (NR1C2, PPARB)
Find proteins for Q03181 (Homo sapiens)
Go to Gene View: PPARD
Go to UniProtKB:  Q03181
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
D32
Query on D32

Download SDF File 
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 SDF File 
Download CCD File 
A
HEPTYL-BETA-D-GLUCOPYRANOSIDE
C13 H26 O6
NIDYWHLDTIVRJT-UJPOAAIJSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
D32Ki: 4 nM BINDINGMOAD
D32IC50: 4 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.189 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 94.577α = 90.00
b = 92.129β = 90.00
c = 39.555γ = 90.00
Software Package:
Software NamePurpose
ADSCdata collection
SCALAdata scaling
PDB_EXTRACTdata extraction
MOSFLMdata reduction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-06-30
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance