9OLC | pdb_00009olc

Crystal structure of PPARg ligand-binding domain in complex with NCoR1 peptide and FTX-6746


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.83 Å
  • R-Value Free: 
    0.298 (Depositor), 0.299 (DCC) 
  • R-Value Work: 
    0.231 (Depositor), 0.235 (DCC) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history

Literature

Covalent PPAR gamma inverse agonism by FX-909 reveals mechanistic insights into therapeutic targeting of PPAR gamma /RXR alpha-activated urothelial carcinoma.

Stuckey, J.I.Mertz, J.A.Wilson, J.E.Williamson, K.E.Li, Y.Kuljanin, M.Setser, J.W.DeLaBarre, B.Chenail, G.Nguyen, P.A.Scott, M.E.Geier, M.J.Bailey, C.M.Motley, W.W.Audia, J.E.Sims 3rd, R.J.

(2026) Cell Chem Biol 33: 837-847.e14

  • DOI: https://doi.org/10.1016/j.chembiol.2026.04.017
  • Primary Citation Related Structures: 
    9OLC

  • PubMed Abstract: 

    We investigated the conformational mechanisms underlying PPARγ activation in muscle-invasive urothelial carcinoma (MIUC) and sought to develop covalent inverse agonists to therapeutically reinforce a repressive state. The integration of mutational, structural, and biochemical analyses of PPARγ and RXRα guided the discovery of FX-909, a first-in-class clinical PPARγ inverse agonist that enforces a repressive conformational state, even in highly activated biological contexts. FX-909 is a potent, highly selective, and powerful suppressor of PPARγ transcriptional activity through the enhancement of PPARγ-nuclear co-repressor (NCOR) binding affinity. Treatment with FX-909 resulted in selective growth inhibition in PPARγ-activated MIUC cell lines and durable regressions in xenograft models of MIUC. FX-909 is capable of recapitulating PPARG genetic knockout phenotypes in vivo and is currently in clinical development for the treatment of intractable MIUC.


  • Organizational Affiliation
    • Flare Therapeutics Inc. 400 Technology Square Suite 501, Cambridge, MA 02139, USA. Electronic address: jstuckey@flaretx.com.

Macromolecule Content 

  • Total Structure Weight: 133.79 kDa 
  • Atom Count: 7,913 
  • Modeled Residue Count: 977 
  • Deposited Residue Count: 1,164 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Peroxisome proliferator-activated receptor gamma
A, B, C, D
278Homo 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
Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Nuclear receptor corepressor 1 peptide
E, F, G, H
13Homo sapiensMutation(s): 0 
Gene Names: NCOR1KIAA1047
UniProt & NIH Common Fund Data Resources
Find proteins for O75376 (Homo sapiens)
Explore O75376 
Go to UniProtKB:  O75376
PHAROS:  O75376
GTEx:  ENSG00000141027 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO75376
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.83 Å
  • R-Value Free:  0.298 (Depositor), 0.299 (DCC) 
  • R-Value Work:  0.231 (Depositor), 0.235 (DCC) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.13α = 101.193
b = 70.33β = 106.579
c = 92.68γ = 104.98
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
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: 2026-04-22
    Type: Initial release
  • Version 1.1: 2026-08-26
    Changes: Database references