3LMP

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.203 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Discovery of a novel selective PPARgamma modulator from (-)-Cercosporamide derivatives

Furukawa, A.Arita, T.Satoh, S.Wakabayashi, K.Hayashi, S.Matsui, Y.Araki, K.Kuroha, M.Ohsumi, J.

(2010) Bioorg.Med.Chem.Lett. 20: 2095-2098

  • DOI: 10.1016/j.bmcl.2010.02.073

  • PubMed Abstract: 
  • In an investigation of (-)-Cercosporamide derivatives with a plasma glucose-lowering effect, we found that N-benzylcarboxamide derivative 4 was a partial agonist of PPARgamma. A SAR study of the substituents on carboxamide nitrogen afforded the N-(1- ...

    In an investigation of (-)-Cercosporamide derivatives with a plasma glucose-lowering effect, we found that N-benzylcarboxamide derivative 4 was a partial agonist of PPARgamma. A SAR study of the substituents on carboxamide nitrogen afforded the N-(1-naphthyl)methylcarboxamide derivative 23 as the most potent selective PPARgamma modulator. An X-ray crystallography study revealed that compound 23 bounded to the PPARgamma ligand binding domain in a unique way without any interaction with helix12. Compound 23 displayed a potent plasma glucose-lowering effect in db/db mice without the undesirable increase in body fluid and heart weight that is typically observed when PPARgamma full agonists are administrated.


    Organizational Affiliation

    Shinagawa R&D Center, Daiichi Sankyo Co., Ltd, 1-2-58, Hiromachi, Shinagawa-ku, Tokyo, Japan. furukawa.akihiro.zy@daiichisankyo.co.jp




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Peroxisome proliferator-activated receptor gamma
A
283Homo sapiensMutation(s): 0 
Gene Names: PPARG (NR1C3)
Find proteins for P37231 (Homo sapiens)
Go to Gene View: PPARG
Go to UniProtKB:  P37231
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Peptide of Nuclear receptor coactivator 1
C
15Homo sapiensMutation(s): 0 
Gene Names: NCOA1 (BHLHE74, SRC1)
EC: 2.3.1.48
Find proteins for Q15788 (Homo sapiens)
Go to Gene View: NCOA1
Go to UniProtKB:  Q15788
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CEK
Query on CEK

Download SDF File 
Download CCD File 
A
(9aS)-8-acetyl-1,7-dihydroxy-3-methoxy-9a-methyl-N-(1-naphthylmethyl)-9-oxo-9,9a-dihydrodibenzo[b,d]furan-4-carboxamide
(9aS)-8-acetyl-1,7-dihydroxy-3-methoxy-9a-methyl-N-(naphthalen-1-ylmethyl)-9-oxo-9,9a-dihydrodibenzo[b,d]furan-4-carboxamide
C28 H23 N O7
GHOGOLYMMHFNIT-MUUNZHRXSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
CEKKi: 14 nM BINDINGMOAD
CEKIC50: 620 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.203 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 38.767α = 90.00
b = 53.975β = 92.37
c = 66.531γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
HKL-2000data reduction
DENZOdata reduction
HKL-2000data scaling
CNXrefinement
PDB_EXTRACTdata extraction
CNSrefinement
X-PLORphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-04-14
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2017-11-01
    Type: Refinement description