3V9T

Crystal structure of the PPARgamma-LBD complexed with a cercosporamide derivative modulator


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.203 

wwPDB Validation 3D Report Full Report



Literature

Substituents at the naphthalene C3 position of (-)-Cercosporamide derivatives significantly affect the maximal efficacy as PPAR(gamma) partial agonists

Furukawa, A.Arita, T.Fukuzaki, T.Satoh, S.Mori, M.Honda, T.Matsui, Y.Wakabayashi, K.Hayashi, S.Araki, K.Ohsumi, J.

(2012) Bioorg Med Chem Lett 22: 1348-1351

  • DOI: 10.1016/j.bmcl.2011.12.066
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Peroxisome proliferator-activated receptor gamma (PPARγ) is a potential drug target for treating type 2 diabetes. The selective PPARγ modulators (SPPARMs), which partially activate the PPARγ transcriptional activity, are considered to improve the pla ...

    Peroxisome proliferator-activated receptor gamma (PPARγ) is a potential drug target for treating type 2 diabetes. The selective PPARγ modulators (SPPARMs), which partially activate the PPARγ transcriptional activity, are considered to improve the plasma glucose level with attenuated PPARγ related adverse effects. However, the relationships between desired pharmacological profiles and ligand specific PPARγ transcriptional profiles have been unclear. And there is also little knowledge of how to control ligand specific PPARγ transcriptional profiles. Herein, we present synthesis of novel derivatives containing substituent at naphthalene C3 position of compound 1. The novel derivatives showed various maximal efficacies as PPARγ partial agonist.


    Organizational Affiliation

    Shinagawa R&D Center, Daiichi Sankyo Co., Ltd, 1-2-58, Hiromachi, Shinagawa-ku, Tokyo, Japan. furukawa.akihiro.zy@daiichisankyo.co.jp



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Peroxisome proliferator-activated receptor gamma
A
283Homo sapiensMutation(s): 0 
Gene Names: PPARGNR1C3
Find proteins for P37231 (Homo sapiens)
Go to UniProtKB:  P37231
NIH Common Fund Data Resources
PHAROS  P37231
Protein Feature View
  • Reference Sequence
  • Find similar proteins by: Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Peptide from Peroxisome proliferator-activated receptor gamma coactivator 1-alpha
C
19Homo sapiensMutation(s): 0 
Gene Names: PPARGC1ALEM6PGC1PGC1APPARGC1
Find proteins for Q9UBK2 (Homo sapiens)
Go to UniProtKB:  Q9UBK2
NIH Common Fund Data Resources
PHAROS  Q9UBK2
Protein Feature View
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
17L
Query on 17L

Download CCD File 
A
(9aS)-8-acetyl-N-[(3-ethoxynaphthalen-1-yl)methyl]-1,7-dihydroxy-3-methoxy-9a-methyl-9-oxo-9,9a-dihydrodibenzo[b,d]furan-4-carboxamide
C30 H27 N O8
YMVHWNQNRJLTTN-SSEXGKCCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.203 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 38.889α = 90
b = 54.614β = 92.35
c = 66.797γ = 90
Software Package:
Software NamePurpose
CrystalCleardata collection
CNSrefinement
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-02-01
    Type: Initial release