8CPI | pdb_00008cpi

Crystal structure of PPAR gamma (PPARG) in complex with WY-14643


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 
    0.282 (Depositor), 0.285 (DCC) 
  • R-Value Work: 
    0.222 (Depositor), 0.229 (DCC) 
  • R-Value Observed: 
    0.225 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Targeting the Alternative Vitamin E Metabolite Binding Site Enables Noncanonical PPAR gamma Modulation.

Arifi, S.Marschner, J.A.Pollinger, J.Isigkeit, L.Heitel, P.Kaiser, A.Obeser, L.Hofner, G.Proschak, E.Knapp, S.Chaikuad, A.Heering, J.Merk, D.

(2023) J Am Chem Soc 145: 14802-14810

  • DOI: https://doi.org/10.1021/jacs.3c03417
  • Primary Citation Related Structures: 
    8ATY, 8ATZ, 8CPH, 8CPI, 8CPJ

  • PubMed Abstract: 

    The lipid-sensing transcription factor PPARγ is the target of antidiabetic thiazolidinediones (TZD). At two sites within its ligand binding domain, it also binds oxidized vitamin E metabolites and the vitamin E mimetic garcinoic acid. While the canonical interaction within the TZD binding site mediates classical PPARγ activation, the effects of the second binding on PPARγ activity remain elusive. Here, we identified an agonist mimicking dual binding of vitamin E metabolites and developed a selective ligand of the second site, unveiling potential noncanonical regulation of PPARγ activities. We found that this alternative binding event can simultaneously occur with orthosteric ligands and it exerted different effects on PPARγ-cofactor interactions compared to both orthosteric PPARγ agonists and antagonists, indicating the diverse roles of the two binding sites. Alternative site binding lacked the pro-adipogenic effect of TZD and mediated no classical PPAR signaling in differential gene expression analysis but markedly diminished FOXO signaling, suggesting potential therapeutic applications.


  • Organizational Affiliation
    • Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, D-60438 Frankfurt, Germany.

Macromolecule Content 

  • Total Structure Weight: 32.32 kDa 
  • Atom Count: 2,310 
  • Modeled Residue Count: 277 
  • Deposited Residue Count: 277 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Peroxisome proliferator-activated receptor gamma277Homo 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
WY1
(Subject of Investigation/LOI)

Query on WY1



Download:Ideal Coordinates CCD File
B [auth A],
C [auth A]
2-({4-CHLORO-6-[(2,3-DIMETHYLPHENYL)AMINO]PYRIMIDIN-2-YL}SULFANYL)ACETIC ACID
C14 H14 Cl N3 O2 S
SZRPDCCEHVWOJX-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
WY1 BindingDB:  8CPI Kd: min: 1297, max: 1340 (nM) from 2 assay(s)
IC50: 5.37e+4 (nM) from 1 assay(s)
EC50: min: 1600, max: 6.00e+4 (nM) from 8 assay(s)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free:  0.282 (Depositor), 0.285 (DCC) 
  • R-Value Work:  0.222 (Depositor), 0.229 (DCC) 
  • R-Value Observed: 0.225 (Depositor) 
Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.595α = 90
b = 65.595β = 90
c = 157.264γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2023-07-12
    Type: Initial release
  • Version 1.1: 2023-07-19
    Changes: Database references
  • Version 1.2: 2024-06-19
    Changes: Data collection