6DHA

Crystal Structure of Human PPARgamma Ligand Binding Domain in Complex with Hydroxy Pioglitazone (M-IV)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.88 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.220 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Structural Basis of Altered Potency and Efficacy Displayed by a Major in Vivo Metabolite of the Antidiabetic PPAR gamma Drug Pioglitazone.

Mosure, S.A.Shang, J.Eberhardt, J.Brust, R.Zheng, J.Griffin, P.R.Forli, S.Kojetin, D.J.

(2019) J. Med. Chem. 62: 2008-2023

  • DOI: 10.1021/acs.jmedchem.8b01573

  • PubMed Abstract: 
  • Pioglitazone (Pio) is a Food and Drug Administration-approved drug for type-2 diabetes that binds and activates the nuclear receptor peroxisome proliferator-activated receptor γ (PPARγ), yet it remains unclear how in vivo Pio metabolites affect PPARγ ...

    Pioglitazone (Pio) is a Food and Drug Administration-approved drug for type-2 diabetes that binds and activates the nuclear receptor peroxisome proliferator-activated receptor γ (PPARγ), yet it remains unclear how in vivo Pio metabolites affect PPARγ structure and function. Here, we present a structure-function comparison of Pio and its most abundant in vivo metabolite, 1-hydroxypioglitazone (PioOH). PioOH displayed a lower binding affinity and reduced potency in co-regulator recruitment assays. X-ray crystallography and molecular docking analysis of PioOH-bound PPARγ ligand-binding domain revealed an altered hydrogen bonding network, including the formation of water-mediated bonds, which could underlie its altered biochemical phenotype. NMR spectroscopy and hydrogen/deuterium exchange mass spectrometry analysis coupled to activity assays revealed that PioOH better stabilizes the PPARγ activation function-2 (AF-2) co-activator binding surface and better enhances co-activator binding, affording slightly better transcriptional efficacy. These results indicating that Pio hydroxylation affects its potency and efficacy as a PPARγ agonist contributes to our understanding of PPARγ-drug metabolite interactions.


    Organizational Affiliation

    Department of Integrative Structural and Computational Biology , The Scripps Research Institute , La Jolla , California 92037 , United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Peroxisome proliferator-activated receptor gamma
A, B
271Homo 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 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
KNA
Query on KNA

Download SDF File 
Download CCD File 
A
nonanoic acid
C9 H18 O2
FBUKVWPVBMHYJY-UHFFFAOYSA-N
 Ligand Interaction
GFV
Query on GFV

Download SDF File 
Download CCD File 
A, B
Hydroxy Pioglitazone (M-IV)
(5S)-5-{[4-(2-{5-[(1S)-1-hydroxyethyl]pyridin-2-yl}ethoxy)phenyl]methyl}-1,3-thiazolidine-2,4-dione
C19 H20 N2 O4 S
OXVFDZYQLGRLCD-SJCJKPOMSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.88 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.220 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 93.080α = 90.00
b = 61.850β = 102.73
c = 119.670γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
PHENIXrefinement
PHASERphasing
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney DiseaseUnited StatesR01DK101871

Revision History 

  • Version 1.0: 2019-03-13
    Type: Initial release