3VJI

Human PPAR gamma ligand binding domain in complex with JKPL53


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.61 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.212 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Peroxisome proliferator-activated receptors (PPARs) have multiple binding points that accommodate ligands in various conformations: phenylpropanoic acid-type PPAR ligands bind to PPAR in different conformations, depending on the subtype.

Kuwabara, N.Oyama, T.Tomioka, D.Ohashi, M.Yanagisawa, J.Shimizu, T.Miyachi, H.

(2012) J.Med.Chem. 55: 893-902

  • DOI: 10.1021/jm2014293
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Human peroxisome proliferator-activated receptors (hPPARs) are ligand-dependent transcription factors that control various biological responses, and there are three subtypes: hPPARα, hPPARδ, and hPPARγ. We report here that α-substituted phenylpropano ...

    Human peroxisome proliferator-activated receptors (hPPARs) are ligand-dependent transcription factors that control various biological responses, and there are three subtypes: hPPARα, hPPARδ, and hPPARγ. We report here that α-substituted phenylpropanoic acid-type hPPAR agonists with similar structure bind to the hPPAR ligand binding domain (LBD) in different conformations, depending on the receptor subtype. These results might indicate that hPPAR ligand binding pockets have multiple binding points that can be utilized to accommodate structurally flexible hPPAR ligands.


    Organizational Affiliation

    Graduate School of Pharmaceutical Sciences, Faculty of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Peroxisome proliferator-activated receptor gamma
A, B
286Homo sapiensMutation(s): 0 
Gene Names: PPARG (NR1C3)
Find proteins for P37231 (Homo sapiens)
Go to Gene View: PPARG
Go to UniProtKB:  P37231
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
J53
Query on J53

Download SDF File 
Download CCD File 
A
(2S)-2-{4-butoxy-3-[({4-[(3S,5S,7S)-tricyclo[3.3.1.1~3,7~]dec-1-yl]benzoyl}amino)methyl]benzyl}butanoic acid
C33 H43 N O4
DEFUFGZNKMSDHW-KVJCSQNRSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.61 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.212 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 93.150α = 90.00
b = 60.610β = 103.79
c = 118.771γ = 90.00
Software Package:
Software NamePurpose
ADSCdata collection
MOLREPphasing
HKL-2000data reduction
REFMACrefinement
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-08-29
    Type: Initial release