5LSG | pdb_00005lsg

PPARgamma complex with the betulinic acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 
    0.264 (Depositor), 0.260 (DCC) 
  • R-Value Work: 
    0.227 (Depositor), 0.230 (DCC) 
  • R-Value Observed: 
    0.229 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted QZQClick on this verticalbar to view details

This is version 1.1 of the entry. See complete history


Literature

Betulinic acid is a PPAR gamma antagonist that improves glucose uptake, promotes osteogenesis and inhibits adipogenesis.

Brusotti, G.Montanari, R.Capelli, D.Cattaneo, G.Laghezza, A.Tortorella, P.Loiodice, F.Peiretti, F.Bonardo, B.Paiardini, A.Calleri, E.Pochetti, G.

(2017) Sci Rep 7: 5777-5777

  • DOI: https://doi.org/10.1038/s41598-017-05666-6
  • Primary Citation of Related Structures:  
    5LSG

  • PubMed Abstract: 

    PPAR antagonists are ligands that bind their receptor with high affinity without transactivation activity. Recently, they have been demonstrated to maintain insulin-sensitizing and antidiabetic properties, and they serve as an alternative treatment for metabolic diseases. In this work, an affinity-based bioassay was found to be effective for selecting PPAR ligands from the dried extract of an African plant (Diospyros bipindensis). Among the ligands, we identified betulinic acid (BA), a compound already known for its anti-inflammatory, anti-tumour and antidiabetic properties, as a PPARγ and PPARα antagonist. Cell differentiation assays showed that BA inhibits adipogenesis and promotes osteogenesis; either down-regulates or does not affect the expression of a series of adipogenic markers; and up-regulates the expression of osteogenic markers. Moreover, BA increases basal glucose uptake in 3T3-L1 adipocytes. The crystal structure of the complex of BA with PPARγ sheds light, at the molecular level, on the mechanism by which BA antagonizes PPARγ, and indicates a unique binding mode of this antagonist type. The results of this study show that the natural compound BA could be an interesting and safe candidate for the treatment of type 2 diabetes and bone diseases.


  • Organizational Affiliation

    Dipartimento di Scienze del Farmaco, Università degli Studi di Pavia, Via Taramelli 12, 27100, Pavia, Italy.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Peroxisome proliferator-activated receptor gamma
A, B
304Homo sapiensMutation(s): 0 
Gene Names: PPARGNR1C3
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
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
QZQ
Query on QZQ

Download Ideal Coordinates CCD File 
C [auth A]Betulinic Acid
C30 H46 O3
UTRVNRSDMIXTLN-BMTJSWHCSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free:  0.264 (Depositor), 0.260 (DCC) 
  • R-Value Work:  0.227 (Depositor), 0.230 (DCC) 
  • R-Value Observed: 0.229 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 92.86α = 90
b = 60.85β = 102.48
c = 118.03γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
AMoREphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted QZQClick on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-08-09
    Type: Initial release
  • Version 1.1: 2024-01-17
    Changes: Advisory, Data collection, Database references, Refinement description