Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 63.06 kDa 
• Atom Count: 4463 
• Residue Count: 518 
• Unique protein chains: 1

6DHA

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

• DOI: 10.2210/pdb6DHA/pdb

• Classification: transcription/transcription inhibitor
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2018-05-18 Released: 2019-03-13 
• Deposition Author(s): Shang, J., Mosure, S.A., Kojetin, D.J.
• Funding Organization(s): National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.88 Å
• R-Value Free: 0.255 
• R-Value Work: 0.220 
• R-Value Observed: 0.222 

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

• PubMed: 30676741 
• DOI: 10.1021/acs.jmedchem.8b01573
• Primary Citation of Related Structures:  
  6DHA


• 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 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peroxisome proliferator-activated receptor gamma	A, B	271	Homo sapiens	Mutation(s): 0  Gene Names: PPARG, NR1C3
Find proteins for P37231 (Homo sapiens) Explore P37231  Go to UniProtKB:  P37231
NIH Common Fund Data Resources
PHAROS:  P37231 GTEx:  ENSG00000132170

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GFV	A, B	Hydroxy Pioglitazone (M-IV) C19 H20 N2 O4 S OXVFDZYQLGRLCD-SJCJKPOMSA-N
KNA	A	nonanoic acid C9 H18 O2 FBUKVWPVBMHYJY-UHFFFAOYSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
GFV	Kd:  708   nM  Binding MOAD

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.88 Å
• R-Value Free: 0.255 
• R-Value Work: 0.220 
• R-Value Observed: 0.222 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 93.08	α = 90
b = 61.85	β = 102.73
c = 119.67	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
SCALA	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction
MOSFLM	data reduction

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2018-05-18 
• Released Date: 2019-03-13 
Deposition Author(s): Shang, J., Mosure, S.A., Kojetin, D.J.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)	United States	R01DK101871

Revision History 

• Version 1.0: 2019-03-13
  Type: Initial release
  
• Version 1.1: 2019-12-25
  Changes: Author supporting evidence