6IZM

Crystal structure of the PPARgamma-LBD complexed with compound 1l


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.225 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structure-Activity Relationship Studies of 3- or 4-Pyridine Derivatives of DS-6930.

Shinozuka, T.Tsukada, T.Fujii, K.Tokumaru, E.Matsui, Y.Wakimoto, S.Ogata, T.Araki, K.Sawamura, R.Watanabe, N.Mori, M.Tanaka, J.

(2019) ACS Med Chem Lett 10: 358-362

  • DOI: 10.1021/acsmedchemlett.8b00645
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Derivatization efforts were continued to discover backups for a potent selective PPARγ modulator, DS-6930. In this Letter, the replacement of 2-pyridine ring in DS-6930 with 3- or 4-pyridyl group is reported. As the introduction of substituents on th ...

    Derivatization efforts were continued to discover backups for a potent selective PPARγ modulator, DS-6930. In this Letter, the replacement of 2-pyridine ring in DS-6930 with 3- or 4-pyridyl group is reported. As the introduction of substituents on the pyridine ring did not provide potent partial agonists, modifications of benzimidazole ring were explored to discover potent intermediate agonists. 4'-Alkoxy substituted benzimidazoles failed to show potent efficacy in vivo, whereas 7'-fluoro benzimidazole 3g (DS19161384) was found to result in robust plasma glucose reductions with excellent DMPK profiles.


    Organizational Affiliation

    R&D Division, Daiichi Sankyo Co., Ltd., 1-2-58 Hiromachi, Shinagawa-ku, Tokyo 140-8710, Japan.



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
B0X
Query on B0X

Download CCD File 
A
3-[[6-(2,6-dimethylpyridin-3-yl)oxy-1-methyl-benzimidazol-2-yl]methoxy]benzoic acid
C23 H21 N3 O4
SWNQXLUHHMLVFL-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.225 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 39.012α = 90
b = 54.266β = 92.51
c = 66.727γ = 90
Software Package:
Software NamePurpose
CNXrefinement
HKL-2000data reduction
HKL-2000data scaling
CNXphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2019-03-27
    Type: Initial release
  • Version 1.1: 2019-11-20
    Changes: Database references