7WOX | pdb_00007wox

PPARgamma antagonist (MMT-160)- PPARgamma LBD complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 
    0.273 (Depositor), 0.301 (DCC) 
  • R-Value Work: 
    0.215 (Depositor) 
  • R-Value Observed: 
    0.218 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Arylalkynyl amide-type peroxisome proliferator-activated receptor gamma (PPAR gamma )-selective antagonists covalently bind to the PPAR gamma ligand binding domain with a unique binding mode.

Yoshizawa, M.Aoyama, T.Itoh, T.Miyachi, H.

(2022) Bioorg Med Chem Lett 64: 128676-128676

  • DOI: https://doi.org/10.1016/j.bmcl.2022.128676
  • Primary Citation Related Structures: 
    7WOX

  • PubMed Abstract: 

    Peroxisome proliferator-activated receptor γ (PPARγ) antagonists are drug candidates for the treatment of type 2 diabetes, obesity, and osteoporosis. Previously, we have designed and synthesized a series of substituted phenylalkynyl amide-type PPARγ antagonists. The representative compound, MMT-160, exhibited nanomolar-order PPARγ antagonistic activity. To understand the antagonistic mode of action of MMT-160, mass spectrometric and X-ray crystallographic analysis of MMT-160 in the presence of the PPARγ ligand binding domain (LBD) were performed. The mass spectrometry results clearly indicated that alkynyl amide-type PPARγ antagonists were covalently bound to the PPARγ LBD. The X-ray crystallographic analysis indicated that MMT-160 acted as a Michael acceptor and covalently bound to the PPARγ LBD via Cys285. In addition, MMT-160 bound to the PPARγ LBD with a binding mode that was different from the binding modes observed for PPARγ agonists and partial agonists.


  • Organizational Affiliation
    • Laboratory of Drug Design and Medicinal Chemistry, Showa Pharmaceutical University, 3-3165 Higashi-Tamagawagakuen, Machida, Tokyo 194-8543, Japan.

Macromolecule Content 

  • Total Structure Weight: 63.39 kDa 
  • Atom Count: 3,973 
  • Modeled Residue Count: 507 
  • Deposited Residue Count: 552 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Peroxisome proliferator-activated receptor gamma
A, B
276Homo sapiensMutation(s): 0 
Gene Names: PPARGNR1C3
UniProt & NIH Common Fund Data Resources
Find proteins for P37231 (Homo sapiens)
Explore P37231 
Go to UniProtKB:  P37231
PHAROS:  P37231
GTEx:  ENSG00000132170 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP37231
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
5YW

Query on 5YW



Download:Ideal Coordinates CCD File
C [auth A]N-[[5-(3-phenylprop-2-ynoylamino)-2-propoxy-phenyl]methyl]-4-pyrimidin-2-yl-benzamide
C30 H26 N4 O3
LLWADQIEAQTMON-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free:  0.273 (Depositor), 0.301 (DCC) 
  • R-Value Work:  0.215 (Depositor) 
  • R-Value Observed: 0.218 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 93.51α = 90
b = 61.75β = 101.93
c = 119.62γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
MOSFLMdata reduction
REFMACphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Agency for Medical Research and Development (AMED)JapanJP20am0101087j0005 support number 2244

Revision History  (Full details and data files)

  • Version 1.0: 2022-04-13
    Type: Initial release
  • Version 1.1: 2023-11-29
    Changes: Data collection, Refinement description
  • Version 1.2: 2024-10-30
    Changes: Structure summary