4A4W

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.203 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural Characterization of Amorfrutins Bound to the Peroxisome Proliferator-Activated Receptor Gamma.

De Groot, J.C.Weidner, C.Krausze, J.Kawamoto, K.Schroeder, F.C.Sauer, S.Bussow, K.

(2013) J.Med.Chem. 56: 1535

  • DOI: 10.1021/jm3013272
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Amorfrutins are a family of natural products with high affinity to the peroxisome proliferator-activated receptor γ (PPARγ), a nuclear receptor regulating lipid and glucose metabolism. The PPARγ agonist rosiglitazone increases insulin sensitivity and ...

    Amorfrutins are a family of natural products with high affinity to the peroxisome proliferator-activated receptor γ (PPARγ), a nuclear receptor regulating lipid and glucose metabolism. The PPARγ agonist rosiglitazone increases insulin sensitivity and is effective against type II diabetes but has severe adverse effects including weight gain. Amorfrutins improve insulin sensitivity and dyslipidemia but do not enhance undesired fat storage. They bear potential as therapeutics or prophylactic dietary supplements. We identified amorfrutin B as a novel partial agonist of PPARγ with a considerably higher affinity than that of previously reported amorfrutins, similar to that of rosiglitazone. Crystal structures reveal the geranyl side chain of amorfrutin B as the cause of its particularly high affinity. Typical for partial agonists, amorfrutins 1, 2, and B bind helix H3 and the β-sheet of PPARγ but not helix H12.


    Organizational Affiliation

    Department of Molecular Structural Biology, Helmholtz Centre for Infection Research, 38214 Braunschweig, 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
YFB
Query on YFB

Download SDF File 
Download CCD File 
A, B
AMORFRUTIN B
C26 H32 O4
DKNIJLWIVUCTHW-CPNJWEJPSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
YFBKd: 19 nM (99) BINDINGDB
YFBEC50: 50 - 73 nM (99) BINDINGDB
YFBKd: 19 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.203 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 92.140α = 90.00
b = 60.860β = 102.58
c = 117.600γ = 90.00
Software Package:
Software NamePurpose
XSCALEdata scaling
MOLREPphasing
REFMACrefinement
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-10-03
    Type: Initial release
  • Version 1.1: 2014-02-05
    Type: Database references