3H0A

Crystal Structure of Peroxisome Proliferator-Activated Receptor Gamma (PPARg) and Retinoic Acid Receptor Alpha (RXRa) in Complex with 9-cis Retinoic Acid, Co-activator Peptide, and a Partial Agonist


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.342 
  • R-Value Work: 0.246 

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:  

  • 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
Retinoic acid receptor RXR-alpha
A
228Homo sapiensMutation(s): 0 
Gene Names: RXRA (NR2B1)
Find proteins for P19793 (Homo sapiens)
Go to Gene View: RXRA
Go to UniProtKB:  P19793
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Peroxisome proliferator-activated receptor gamma
D
272Homo sapiensMutation(s): 0 
Gene Names: PPARG (NR1C3)
Find proteins for P37231 (Homo sapiens)
Go to Gene View: PPARG
Go to UniProtKB:  P37231
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Nuclear receptor coactivator 1, Co-activator Peptide
B, E
12Homo sapiensMutation(s): 0 
Gene Names: NCOA1 (BHLHE74, SRC1)
EC: 2.3.1.48
Find proteins for Q15788 (Homo sapiens)
Go to Gene View: NCOA1
Go to UniProtKB:  Q15788
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
D30
Query on D30

Download SDF File 
Download CCD File 
D
[(4-{[2-(pent-2-yn-1-yloxy)-4-{[4-(trifluoromethyl)phenoxy]methyl}phenyl]sulfanyl}-5,6,7,8-tetrahydronaphthalen-1-yl)oxy]acetic acid
C31 H29 F3 O5 S
SIHDSSYICQEWRS-UHFFFAOYSA-N
 Ligand Interaction
9RA
Query on 9RA

Download SDF File 
Download CCD File 
A
4-[1-(3,5,5,8,8-pentamethyl-5,6,7,8-tetrahydronaphthalen-2-yl)ethenyl]benzoic acid
C24 H28 O2
NAVMQTYZDKMPEU-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.342 
  • R-Value Work: 0.246 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 179.258α = 90.00
b = 53.825β = 107.74
c = 67.108γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
ADSCdata collection
MOSFLMdata reduction
REFMACrefinement
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-06-09
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2014-04-02
    Type: Source and taxonomy