5TWO

Peroxisome proliferator-activated receptor gamma ligand binding domain in complex with a novel selectively PPAR gamma-modulating ligand VSP-51


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.927 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.209 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Identification of a novel selective PPAR gamma ligand with a unique binding mode and improved therapeutic profile in vitro.

Yi, W.Shi, J.Zhao, G.Zhou, X.E.Suino-Powell, K.Melcher, K.Xu, H.E.

(2017) Sci Rep 7: 41487-41487

  • DOI: 10.1038/srep41487

  • PubMed Abstract: 
  • Thiazolidinediones (TZD) function as potent anti-diabetic drugs through their direct action on the nuclear receptor peroxisome proliferator-activated receptor γ (PPARγ), but their therapeutic benefits are compromised by severe side effects. To addres ...

    Thiazolidinediones (TZD) function as potent anti-diabetic drugs through their direct action on the nuclear receptor peroxisome proliferator-activated receptor γ (PPARγ), but their therapeutic benefits are compromised by severe side effects. To address this concern, here we developed a potent "hit" compound, VSP-51, which is a novel selective PPARγ-modulating ligand with improved therapeutic profiles in vitro compared to the multi-billion dollar TZD drug rosiglitazone (Rosi). Unlike Rosi, VSP-51 is a partial agonist of PPARγ with improved insulin sensitivity due to its ability to bind PPARγ with high affinity without stimulating adipocyte differentiation and the expression of adipogenesis-related genes. We have determined the crystal structure of the PPARγ ligand-binding domain (LBD) in complex with VSP-51, which revealed a unique mode of binding for VSP-51 and provides the molecular basis for the discrimination between VSP-51 from TZDs and other ligands such as telmisartan, SR1663 and SR1664. Taken together, our findings demonstrate that: a) VSP-51 can serve as a promising candidate for anti-diabetic drug discovery; and b) provide a rational basis for the development of future pharmacological agents targeting PPARγ with advantages over current TZD drugs.


    Organizational Affiliation

    Laboratory of Structural Sciences, Program of Structural Biology and Drug Discovery, Van Andel Research Institute, Grand Rapids, Michigan 49503, USA.,School of Pharmaceutical Sciences, Guangzhou Medical University, Xinzao, Panyu District, Guangzhou 511436, P. R. China.,VARI/SIMM Center, Center for Structure and Function of Drug Targets, CAS-Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, P. R. China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Peroxisome proliferator-activated receptor gamma
A
272Homo sapiensMutation(s): 0 
Gene Names: PPARG (NR1C3)
Find proteins for P37231 (Homo sapiens)
Go to Gene View: PPARG
Go to UniProtKB:  P37231
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
PRO-SER-LEU-LEU-LYS-LYS-LEU-LEU-LEU-ALA-PRO
B
15Homo sapiensMutation(s): 0 
Gene Names: PPARGC1A (LEM6, PGC1, PGC1A, PPARGC1)
Find proteins for Q9UBK2 (Homo sapiens)
Go to Gene View: PPARGC1A
Go to UniProtKB:  Q9UBK2
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
7MV
Query on 7MV

Download SDF File 
Download CCD File 
A
N-benzyl-1-[(4-chloro-3-fluorophenyl)methyl]-1H-indole-5-carboxamide
C23 H18 Cl F N2 O
BYYJMWFBVAZQMV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.927 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.209 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 56.893α = 90.00
b = 88.504β = 90.00
c = 122.163γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
SCALAdata scaling
PHENIXrefinement
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Youth Innovation Promotion Association CAS, the Shanghai Municipal Natural Science FoundationChina15ZR1447800
the Chinese Postdoctoral Science FoundationChina2014M560363

Revision History 

  • Version 1.0: 2017-02-08
    Type: Initial release
  • Version 1.1: 2018-10-24
    Type: Data collection, Structure summary