2ZNP

Human PPAR delta ligand binding domain in complex with a synthetic agonist TIPP204


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.230 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Adaptability and selectivity of human peroxisome proliferator-activated receptor (PPAR) pan agonists revealed from crystal structures

Oyama, T.Toyota, K.Waku, T.Hirakawa, Y.Nagasawa, N.Kasuga, J.Hashimoto, Y.Miyachi, H.Morikawa, K.

(2009) Acta Crystallogr.,Sect.D 65: 786-795

  • DOI: 10.1107/S0907444909015935
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Peroxisome proliferator-activated receptors (PPARs) belong to the nuclear hormone receptor family, which is defined as transcriptional factors that are activated by the binding of ligands to their ligand-binding domains (LBDs). Although the three PPA ...

    Peroxisome proliferator-activated receptors (PPARs) belong to the nuclear hormone receptor family, which is defined as transcriptional factors that are activated by the binding of ligands to their ligand-binding domains (LBDs). Although the three PPAR subtypes display different tissue distribution patterns and distinct pharmacological profiles, they all are essentially related to fatty-acid and glucose metabolism. Since the PPARs share similar three-dimensional structures within the LBDs, synthetic ligands which simultaneously activate two or all of the PPARs could be potent candidates in terms of drugs for the treatment of abnormal metabolic homeostasis. The structures of several PPAR LBDs were determined in complex with synthetic ligands, derivatives of 3-(4-alkoxyphenyl)propanoic acid, which exhibit unique agonistic activities. The PPARalpha and PPARgamma LBDs were complexed with the same pan agonist, TIPP-703, which activates all three PPARs and their crystal structures were determined. The two LBD-ligand complex structures revealed how the pan agonist is adapted to the similar, but significantly different, ligand-binding pockets of the PPARs. The structures of the PPARdelta LBD in complex with an alpha/delta-selective ligand, TIPP-401, and with a related delta-specific ligand, TIPP-204, were also determined. The comparison between the two PPARdelta complexes revealed how each ligand exhibits either a ;dual selective' or ;single specific' binding mode.


    Related Citations: 
    • Improvement of the transactivation activity of phenylpropanoic acid-type peroxisome proliferator-acitvated rectpror pan agonists; effect of introduction of fluorine at the linker part
      Kasuga, J.,Oyama, T.,Hirakawa, Y.,Makishima, M.,Morikawa, K.,Hashimoto, Y.,Miyachi, H.
      () TO BE PUBLISHED --: --
    • Peroxisome proliferator-activated receptor (PPAR) agonists with a 3,4-dihydro-2H-benzo[e][1,3]oxazine and 2,3,4,5-tetrahydrobenzo[f][1,4]oxazepine skeleton: effects of the conformational restriction on PPAR agonistic acivity
      Ohkane, K.,Kasuga, J.,Oyama, T.,Hirakawa, Y.,Morikawa, K.,Makishima, M.,Hashimoto, Y.,Miyachi, H.
      () TO BE PUBLISHED --: --


    Organizational Affiliation

    The Takara Bio Endowed Division, Department of Biomolecular Recognition, Institute for Protein Research, Osaka University, Open Laboratories of Advanced Bioscience and Biotechnology, Suita, Osaka 565-0874, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Peroxisome proliferator-activated receptor delta
A, B
276Homo sapiensMutation(s): 0 
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
B7G
Query on B7G

Download SDF File 
Download CCD File 
A, B
HEPTYL-BETA-D-GLUCOPYRANOSIDE
C13 H26 O6
NIDYWHLDTIVRJT-UJPOAAIJSA-N
 Ligand Interaction
K55
Query on K55

Download SDF File 
Download CCD File 
A, B
(2S)-2-{4-butoxy-3-[({[2-fluoro-4-(trifluoromethyl)phenyl]carbonyl}amino)methyl]benzyl}butanoic acid
(S)-2-{4-butoxy-3-[(2-fluoro-4-trifluoromethylbenzoylamino)methyl]benzyl} butyric acid
C24 H27 F4 N O4
AJSFKATVCYWKJN-INIZCTEOSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.230 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 39.492α = 90.00
b = 93.149β = 97.48
c = 96.370γ = 90.00
Software Package:
Software NamePurpose
CNSphasing
CNSrefinement
HKL-2000data scaling
HKL-2000data collection
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-05-05
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2012-04-11
    Type: Database references
  • Version 1.3: 2016-03-02
    Type: Structure summary