5Y2O

Structure of PPARgamma ligand binding domain-pioglitazone complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.801 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.202 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Structures of PPAR gamma complexed with lobeglitazone and pioglitazone reveal key determinants for the recognition of antidiabetic drugs

Lee, M.A.Tan, L.Yang, H.Im, Y.G.Im, Y.J.

(2017) Sci Rep 7: 16837-16837

  • DOI: 10.1038/s41598-017-17082-x
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Peroxisome proliferator-activator receptor (PPAR) γ is a nuclear hormone receptor that regulates glucose homeostasis, lipid metabolism, and adipocyte function. PPARγ is a target for thiazolidinedione (TZD) class of drugs which are widely used for the ...

    Peroxisome proliferator-activator receptor (PPAR) γ is a nuclear hormone receptor that regulates glucose homeostasis, lipid metabolism, and adipocyte function. PPARγ is a target for thiazolidinedione (TZD) class of drugs which are widely used for the treatment of type 2 diabetes. Recently, lobeglitazone was developed as a highly effective TZD with reduced side effects by Chong Kun Dang Pharmaceuticals. To identify the structural determinants for the high potency of lobeglitazone as a PPARγ agonist, we determined the crystal structures of the PPARγ ligand binding domain (LBD) in complex with lobeglitazone and pioglitazone at 1.7 and 1.8 Å resolutions, respectively. Comparison of ligand-bound PPARγ structures revealed that the binding modes of TZDs are well conserved. The TZD head group forms hydrogen bonds with the polar residues in the AF-2 pocket and helix 12, stabilizing the active conformation of the LBD. The unique p-methoxyphenoxy group of lobeglitazone makes additional hydrophobic contacts with the Ω-pocket. Docking analysis using the structures of TZD-bound PPARγ suggested that lobeglitazone displays 12 times higher affinity to PPARγ compared to rosiglitazone and pioglitazone. This structural difference correlates with the enhanced affinity and the low effective dose of lobeglitazone compared to the other TZDs.


    Organizational Affiliation

    Department of Oral Medicine, Chonnam National University Dental Hospital, Gwangju, 61186, Republic of Korea.,College of Pharmacy, Chonnam National University, Gwangju, 61186, Republic of Korea. imyoungjun@jnu.ac.kr.,College of Pharmacy, Chonnam National University, Gwangju, 61186, Republic of Korea.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Peroxisome proliferator-activated receptor gamma
A, B
294Homo 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
8N6
Query on 8N6

Download SDF File 
Download CCD File 
A
(5S)-5-[[4-[2-(5-ethylpyridin-2-yl)ethoxy]phenyl]methyl]-1,3-thiazolidine-2,4-dione
Pioglitazone
C19 H20 N2 O3 S
HYAFETHFCAUJAY-KRWDZBQOSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.801 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.202 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 55.584α = 90.00
b = 88.139β = 91.24
c = 57.732γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2017-07-26 
  • Released Date: 2017-12-20 
  • Deposition Author(s): Im, Y.J., Lee, M.

Revision History 

  • Version 1.0: 2017-12-20
    Type: Initial release