3V9T | pdb_00003v9t

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


Experimental Data Snapshot

  • Method:&nbspX-RAY DIFFRACTION
  • Resolution:&nbsp1.65 Å
  • R-Value Free:&nbsp
    0.219 (Depositor), 0.220 (DCC)&nbsp
  • R-Value Work:&nbsp
    0.202 (Depositor), 0.200 (DCC)&nbsp
  • R-Value Observed:&nbsp
    0.203&nbsp(Depositor)&nbsp

Starting Model: experimental
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Ligand Structure Quality Assessment&nbsp


This is version 1.1 of the entry. See complete&nbsphistory.&nbsp


Literature

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

Furukawa, A.,&nbspArita, T.,&nbspFukuzaki, T.,&nbspSatoh, S.,&nbspMori, M.,&nbspHonda, T.,&nbspMatsui, Y.,&nbspWakabayashi, K.,&nbspHayashi, S.,&nbspAraki, K.,&nbspOhsumi, J.

(2012) Bioorg Med Chem Lett&nbsp22: 1348-1351

  • DOI:&nbsphttps://doi.org/10.1016/j.bmcl.2011.12.066
  • Primary Citation of Related Structures: &nbsp
    3V9T, 3V9V, 3V9Y

  • PubMed Abstract:&nbsp

    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:&nbsp

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Peroxisome proliferator-activated receptor gamma283Homo sapiensMutation(s): 0&nbsp
Gene Names:&nbspPPARG,&nbspNR1C3
UniProt & NIH Common Fund Data Resources
Find proteins for&nbspP37231&nbsp(Homo sapiens)
Explore&nbspP37231&nbsp
Go to UniProtKB: &nbspP37231
PHAROS: &nbspP37231
GTEx: &nbspENSG00000132170&nbsp
Entity Groups &nbsp
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP37231
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Peptide from Peroxisome proliferator-activated receptor gamma coactivator 1-alphaB [auth C]19Homo sapiensMutation(s): 0&nbsp
UniProt & NIH Common Fund Data Resources
Find proteins for&nbspQ9UBK2&nbsp(Homo sapiens)
Explore&nbspQ9UBK2&nbsp
Go to UniProtKB: &nbspQ9UBK2
PHAROS: &nbspQ9UBK2
GTEx: &nbspENSG00000109819&nbsp
Entity Groups &nbsp
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UBK2
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands&nbsp1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
17L
Query on 17L

Download Ideal Coordinates CCD File&nbsp
C [auth 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
Experimental Data & Validation

Experimental Data

  • Method:&nbspX-RAY DIFFRACTION
  • Resolution:&nbsp1.65 Å
  • R-Value Free:&nbsp 0.219 (Depositor), 0.220 (DCC)&nbsp
  • R-Value Work:&nbsp 0.202 (Depositor), 0.200 (DCC)&nbsp
  • R-Value Observed:&nbsp0.203&nbsp(Depositor)&nbsp
Space Group:&nbspP 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

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Ligand Structure Quality Assessment&nbsp


Entry History&nbsp

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