6C1I

Crystal Structure of Human PPARgamma Ligand Binding Domain in Complex with T0070907


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.26 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.215 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

A structural mechanism for directing corepressor-selective inverse agonism of PPAR gamma.

Brust, R.Shang, J.Fuhrmann, J.Mosure, S.A.Bass, J.Cano, A.Heidari, Z.Chrisman, I.M.Nemetchek, M.D.Blayo, A.L.Griffin, P.R.Kamenecka, T.M.Hughes, T.S.Kojetin, D.J.

(2018) Nat Commun 9: 4687-4687

  • DOI: 10.1038/s41467-018-07133-w

  • PubMed Abstract: 
  • Small chemical modifications can have significant effects on ligand efficacy and receptor activity, but the underlying structural mechanisms can be difficult to predict from static crystal structures alone. Here we show how a simple phenyl-to-pyridyl ...

    Small chemical modifications can have significant effects on ligand efficacy and receptor activity, but the underlying structural mechanisms can be difficult to predict from static crystal structures alone. Here we show how a simple phenyl-to-pyridyl substitution between two common covalent orthosteric ligands targeting peroxisome proliferator-activated receptor (PPAR) gamma converts a transcriptionally neutral antagonist (GW9662) into a repressive inverse agonist (T0070907) relative to basal cellular activity. X-ray crystallography, molecular dynamics simulations, and mutagenesis coupled to activity assays reveal a water-mediated hydrogen bond network linking the T0070907 pyridyl group to Arg288 that is essential for corepressor-selective inverse agonism. NMR spectroscopy reveals that PPARγ exchanges between two long-lived conformations when bound to T0070907 but not GW9662, including a conformation that prepopulates a corepressor-bound state, priming PPARγ for high affinity corepressor binding. Our findings demonstrate that ligand engagement of Arg288 may provide routes for developing corepressor-selective repressive PPARγ ligands.


    Organizational Affiliation

    Center for Biomolecular Structure and Dynamics, University of Montana, Missoula, MT, 59812, USA.,Department of Integrative Structural and Computational Biology, The Scripps Research Institute, Jupiter, FL, 33458, USA.,Department of Integrative Structural and Computational Biology, The Scripps Research Institute, Jupiter, FL, 33458, USA. dkojetin@scripps.edu.,High School Student Summer Internship Program, The Scripps Research Institute, Jupiter, FL, 33458, USA.,Skaggs Graduate School of Chemical and Biological Sciences, The Scripps Research Institute, Jupiter, FL, 33458, USA.,Department of Biomedical and Pharmaceutical Sciences, University of Montana, Missoula, MO, 59812, USA.,Biochemistry and Biophysics Graduate Program, University of Montana, Missoula, MT, 59812, USA.,Department of Molecular Medicine, The Scripps Research Institute, Jupiter, FL, 33458, USA. dkojetin@scripps.edu.,Department of Molecular Medicine, The Scripps Research Institute, Jupiter, FL, 33458, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Peroxisome proliferator-activated receptor gamma
A, B
275Homo 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 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
KNA
Query on KNA

Download SDF File 
Download CCD File 
A, B
nonanoic acid
C9 H18 O2
FBUKVWPVBMHYJY-UHFFFAOYSA-N
 Ligand Interaction
EEY
Query on EEY

Download SDF File 
Download CCD File 
A, B
2-chloro-5-nitro-N-(pyridin-4-yl)benzamide
C12 H8 Cl N3 O3
FRPJSHKMZHWJBE-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.26 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.215 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 92.990α = 90.00
b = 61.690β = 102.31
c = 118.660γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney DiseaseUnited StatesR01DK101871

Revision History 

  • Version 1.0: 2018-12-12
    Type: Initial release
  • Version 1.1: 2019-02-20
    Type: Author supporting evidence, Data collection