2YFE

Ligand binding domain of human PPAR gamma in complex with amorfrutin 1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.204 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Amorfrutins are Potent Antidiabetic Dietary Natural Products

Weidner, C.De Groot, J.C.Prasad, A.Freiwald, A.Quedenau, C.Kliem, M.Witzke, A.Kodelja, V.Han, C.-T.Giegold, S.Baumann, M.Klebl, B.Siems, K.Mueller-Kuhrt, L.Schuermann, A.Schueller, R.Pfeiffer, A.F.H.Schroeder, F.C.Buessow, K.Sauer, S.

(2012) Proc.Natl.Acad.Sci.USA 109: 7257

  • DOI: 10.1073/pnas.1116971109

  • PubMed Abstract: 
  • Given worldwide increases in the incidence of obesity and type 2 diabetes, new strategies for preventing and treating metabolic diseases are needed. The nuclear receptor PPARγ (peroxisome proliferator-activated receptor gamma) plays a central role in ...

    Given worldwide increases in the incidence of obesity and type 2 diabetes, new strategies for preventing and treating metabolic diseases are needed. The nuclear receptor PPARγ (peroxisome proliferator-activated receptor gamma) plays a central role in lipid and glucose metabolism; however, current PPARγ-targeting drugs are characterized by undesirable side effects. Natural products from edible biomaterial provide a structurally diverse resource to alleviate complex disorders via tailored nutritional intervention. We identified a family of natural products, the amorfrutins, from edible parts of two legumes, Glycyrrhiza foetida and Amorpha fruticosa, as structurally new and powerful antidiabetics with unprecedented effects for a dietary molecule. Amorfrutins bind to and activate PPARγ, which results in selective gene expression and physiological profiles markedly different from activation by current synthetic PPARγ drugs. In diet-induced obese and db/db mice, amorfrutin treatment strongly improves insulin resistance and other metabolic and inflammatory parameters without concomitant increase of fat storage or other unwanted side effects such as hepatoxicity. These results show that selective PPARγ-activation by diet-derived ligands may constitute a promising approach to combat metabolic disease.


    Organizational Affiliation

    Otto Warburg Laboratory, Max Planck Institute for Molecular Genetics, Ihnestrasse 63-73, 14195 Berlin, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PEROXISOME PROLIFERATOR-ACTIVATED RECEPTOR GAMMA
A, B
287Homo sapiensMutation(s): 0 
Gene Names: PPARG (NR1C3)
Find proteins for P37231 (Homo sapiens)
Go to Gene View: PPARG
Go to UniProtKB:  P37231
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
YFE
Query on YFE

Download SDF File 
Download CCD File 
A, B
Amorfrutin 1
C21 H24 O4
CTNFTPUIYFUXBE-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
YFEKd: 236 nM (99) BINDINGDB
YFEEC50: 458 nM (99) BINDINGDB
YFEKi: 236 nM BINDINGMOAD
YFEKi: 236 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.204 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 92.810α = 90.00
b = 61.100β = 102.78
c = 118.220γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
MOLREPphasing
XDSdata reduction
XSCALEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-04-11
    Type: Initial release
  • Version 1.1: 2012-04-25
    Type: Other
  • Version 1.2: 2012-05-02
    Type: Other
  • Version 1.3: 2012-05-23
    Type: Other