6IZM

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

• PDB DOI: https://doi.org/10.2210/pdb6IZM/pdb

• Classification: TRANSCRIPTION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2018-12-20 Released: 2019-03-27 
• Deposition Author(s): Matsui, Y., Hanzawa, H.

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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 

Starting Model: experimental

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

• PubMed: 30891140 
• DOI: https://doi.org/10.1021/acsmedchemlett.8b00645
• Primary Citation of Related Structures:  
  6IZM, 6IZN


• 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 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 34.88 kDa 
• Atom Count: 2,414 
• Modelled Residue Count: 276 
• Deposited Residue Count: 302 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peroxisome proliferator-activated receptor gamma	A	283	Homo sapiens	Mutation(s): 0  Gene Names: PPARG, NR1C3
UniProt & NIH Common Fund Data Resources
Find proteins for P37231 (Homo sapiens) Explore P37231  Go to UniProtKB:  P37231
PHAROS:  P37231 GTEx:  ENSG00000132170

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptide from Peroxisome proliferator-activated receptor gamma coactivator 1-alpha	B [auth C]	19	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UBK2 (Homo sapiens) Explore Q9UBK2  Go to UniProtKB:  Q9UBK2
PHAROS:  Q9UBK2 GTEx:  ENSG00000109819

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
B0X (Subject of Investigation/LOI)	C [auth A]	3-[[6-(2,6-dimethylpyridin-3-yl)oxy-1-methyl-benzimidazol-2-yl]methoxy]benzoic acid C23 H21 N3 O4 SWNQXLUHHMLVFL-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
B0X	BindingDB:  6IZM	EC50: 273 (nM) from 1 assay(s)

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 = 39.012	α = 90
b = 54.266	β = 92.51
c = 66.727	γ = 90

Software Package:

Software Name	Purpose
CNX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
CNX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-03-27 
Deposition Author(s): Matsui, Y., Hanzawa, H.

Revision History  

• Version 1.0: 2019-03-27
  Type: Initial release
  
• Version 1.1: 2019-11-20
  Changes: Database references
• Version 1.2: 2023-11-22
  Changes: Data collection, Database references, Refinement description