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 3V9Y | pdb_00003v9y

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 
    0.252 (Depositor), 0.253 (DCC) 
  • R-Value Work: 
    0.206 (Depositor), 0.204 (DCC) 
  • R-Value Observed: 
    0.206 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history. 

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

  • PubMed Abstract: 

    Peroxisome proliferator-activated receptor gamma (PPARÎģ) is a potential drug target for treating type 2 diabetes. The selective PPARÎģ modulators (SPPARMs), which partially activate the PPARÎģ transcriptional activity, are considered to improve the plasma glucose level with attenuated PPARÎģ related adverse effects. However, the relationships between desired pharmacological profiles and ligand specific PPARÎģ transcriptional profiles have been unclear. And there is also little knowledge of how to control ligand specific PPARÎģ 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 PPARÎģ 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

Macromolecule Content 

  • Total Structure Weight: 34.76 kDa 
  • Atom Count: 2,407 
  • Modeled Residue Count: 272 
  • Deposited Residue Count: 298 
  • Unique protein chains: 2

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Peroxisome proliferator-activated receptor gamma283Homo sapiensMutation(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 Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP37231
Sequence Annotations
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Peptide from Nuclear receptor coactivator 115Homo sapiensMutation(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 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ15788
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
24L

Query on 24L


Download:Ideal Coordinates CCD File
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 (Depositor), 0.253 (DCC) 
  • R-Value Work:  0.206 (Depositor), 0.204 (DCC) 
  • R-Value Observed: 0.206 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 38.7Îą = 90
b = 52.776Îē = 91.1
c = 65.891Îģ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

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