9O9N | pdb_00009o9n

Crystal structure of PPARgamma ligand binding domain (LBD) in complex with NCoR1 corepressor peptide and inverse agonist FX-909

• PDB DOI: https://doi.org/10.2210/pdb9O9N/pdb

• Classification: NUCLEAR PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2025-04-18 Released: 2025-05-14 
• Deposition Author(s): Laughlin, Z.T., Dong, J., Harp, J.M., Kojetin, D.J.
• Funding Organization(s): National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.297 (Depositor), 0.298 (DCC) 
• R-Value Work: 
  0.239 (Depositor), 0.239 (DCC) 
• R-Value Observed: 
  0.245 (Depositor) 

Starting Model: experimental

Literature

Structural Basis of PPAR gamma-Mediated Transcriptional Repression by the Covalent Inverse Agonist FX-909.

Laughlin, Z.T., Arifova, L., Munoz-Tello, P., Yu, X., Giridhar, M.N.K., Dong, J., Harp, J.M., Zhu, D., Kamenecka, T.M., Kojetin, D.J.

(2025) J Med Chem 68: 17587-17597

• PubMed: 40797371 
• DOI: https://doi.org/10.1021/acs.jmedchem.5c01252
• Primary Citation Related Structures: 
  9O9N


• PubMed Abstract: 
  

  Hyperactivation of peroxisome proliferator-activated receptor γ-mediated transcription promotes tumor growth in urothelial (bladder) cancer, which can be inhibited by compounds that repress PPARγ activity. FX-909 is a covalent PPARγ inverse agonist in phase 1 clinical trials for advanced solid malignancies, including muscle-invasive bladder cancer. Here, we compared the mechanism of action of FX-909 to other covalent inverse agonists including T0070907, reported more than 20 years ago and misclassified as an antagonist, and two reported improved covalent inverse agonist analogs, SR33068 and BAY-4931. Functional profiling and NMR studies reveal that FX-909 displays improved corepressor-selective inverse agonism and better stabilizes a transcriptionally repressive PPARγ LBD conformation compared to T0070907. The crystal structure of PPARγ LBD cobound to FX-909 and the NCoR1 corepressor peptide reveals a repressive conformation shared by other covalent inverse agonists. These findings build on recent studies highlighting the pharmacological significance and clinical relevance of transcriptionally repressive PPARγ inverse agonists.

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Organizational Affiliation: 
• Department of Biochemistry, Vanderbilt University, Nashville, Tennessee 37232, United States.
Undergraduate Program in Biochemistry and Chemical Biology, Vanderbilt University, Nashville, Tennessee 37232, United States.
Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37232, United States.
Department of Molecular Medicine, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, University of Florida, Jupiter, Florida 33458, United States.
Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, Tennessee 37232, United States.
Vanderbilt-Ingram Cancer Center, Vanderbilt University, Nashville, Tennessee 37232, United States.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 34.38 kDa 
• Atom Count: 2,250 
• Modeled Residue Count: 275 
• Deposited Residue Count: 299 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peroxisome proliferator-activated receptor gamma	A [auth B]	276	Homo sapiens	Mutation(s): 0  Gene Names: PPARG, NR1C3
UniProt & NIH Common Fund Data Resources
Find proteins for P37231 (Homo sapiens) Explore P37231  Go to UniProtKB:  P37231
PHAROS:  P37231 GTEx:  ENSG00000132170

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Nuclear receptor corepressor 1	B [auth D]	23	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for O75376 (Homo sapiens) Explore O75376  Go to UniProtKB:  O75376
PHAROS:  O75376 GTEx:  ENSG00000141027

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1CAA (Subject of Investigation/LOI)	C [auth B]	(3P)-3-(5,7-difluoro-4-oxo-1,4-dihydroquinolin-2-yl)-4-(methanesulfonyl)benzonitrile C17 H10 F2 N2 O3 S RBUBBZVQPHSZEZ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.297 (Depositor), 0.298 (DCC) 
• R-Value Work:  0.239 (Depositor), 0.239 (DCC) 
• R-Value Observed: 0.245 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.043	α = 90
b = 62.043	β = 90
c = 166.259	γ = 90

Software Package:

Software Name	Purpose
PROTEUM PLUS	data collection
PROTEUM PLUS	data reduction
PROTEUM PLUS	data scaling
PHASER	phasing
PHENIX	refinement

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-05-14 
Deposition Author(s): Laughlin, Z.T., Dong, J., Harp, J.M., Kojetin, D.J.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)	United States	R01DK124870

Revision History  

• Version 1.0: 2025-05-14
  Type: Initial release
  
• Version 1.1: 2025-08-27
  Changes: Database references
• Version 1.2: 2025-09-10
  Changes: Database references