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: 1.93 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.211 

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
  • Structures With Same Primary Citation

  • 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.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Peroxisome proliferator-activated receptor gamma
A
272Homo sapiensMutation(s): 0 
Gene Names: PPARGNR1C3
Find proteins for P37231 (Homo sapiens)
Go to UniProtKB:  P37231
NIH Common Fund Data Resources
PHAROS  P37231
Protein Feature View
  • Reference Sequence
  • Find similar proteins by: Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
PRO-SER-LEU-LEU-LYS-LYS-LEU-LEU-LEU-ALA-PRO
B
15unidentifiedMutation(s): 0 
Find proteins for Q9UBK2 (Homo sapiens)
Go to UniProtKB:  Q9UBK2
NIH Common Fund Data Resources
PHAROS  Q9UBK2
Protein Feature View
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
7MV
Query on 7MV

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: 1.93 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.211 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.893α = 90
b = 88.504β = 90
c = 122.163γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



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
    Changes: Data collection, Structure summary