3V9Y

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

• PDB DOI: https://doi.org/10.2210/pdb3V9Y/pdb

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


• Deposited: 2011-12-28 Released: 2012-02-01 
• Deposition Author(s): Matsui, Y., Hanzawa, H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.252 
• R-Value Work: 0.206 
• R-Value Observed: 0.206 

Starting Model: experimental

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

• PubMed: 22225641 
• DOI: https://doi.org/10.1016/j.bmcl.2011.12.066
• Primary Citation of Related Structures:  
  3V9T, 3V9V, 3V9Y


• 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 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.

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Organizational Affiliation: 

Shinagawa R&D Center, Daiichi Sankyo Co., Ltd, 1-2-58, Hiromachi, Shinagawa-ku, Tokyo, Japan. [e-mail]

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: 34.76 kDa 
• Atom Count: 2,407 
• Modelled Residue Count: 272 
• Deposited Residue Count: 298 
• 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 Nuclear receptor coactivator 1	B	15	Homo sapiens	Mutation(s): 0  EC: 2.3.1.48
UniProt & NIH Common Fund Data Resources
Find proteins for Q15788 (Homo sapiens) Explore Q15788  Go to UniProtKB:  Q15788
PHAROS:  Q15788 GTEx:  ENSG00000084676

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
24L	C [auth A]	4-{4-[({[(9aS)-8-acetyl-1,7-dihydroxy-3-methoxy-9a-methyl-9-oxo-9,9a-dihydrodibenzo[b,d]furan-4-yl]carbonyl}amino)methyl]naphthalen-2-yl}butanoic acid C32 H29 N O9 AIBZQPUCRUZLOJ-JGCGQSQUSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.252 
• R-Value Work: 0.206 
• R-Value Observed: 0.206 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 38.7	α = 90
b = 52.776	β = 91.1
c = 65.891	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-02-01 
Deposition Author(s): Matsui, Y., Hanzawa, H.

Revision History  

• Version 1.0: 2012-02-01
  Type: Initial release
  
• Version 1.1: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description