9QX6 | pdb_00009qx6

Crystal structure of RXR alpha LBD bound to a synthetic agonist FN537 and a coactivator fragment


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.46 Å
  • R-Value Free: 
    0.213 (Depositor), 0.213 (DCC) 
  • R-Value Work: 
    0.182 (Depositor), 0.182 (DCC) 
  • R-Value Observed: 
    0.183 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Development of an RXR Agonist Scaffold with Pronounced Homodimer Preference.

Nawa, F.Kardanov, A.Kasch, T.Lewandowski, M.Wein, T.Hofner, G.Marschner, J.A.Morozov, V.Merk, D.

(2025) J Med Chem 68: 16172-16187

  • DOI: https://doi.org/10.1021/acs.jmedchem.5c01090
  • Primary Citation of Related Structures:  
    9QX6, 9RMR

  • PubMed Abstract: 

    The activation of retinoid X receptors (RXRs) presents promising therapeutic potential in diverse conditions, such as cancer, inflammation, metabolic dysfunction, and neurodegeneration. However, RXRs play a central role in nuclear receptor signaling and act in various dimeric forms with multiple other ligand-activated transcription factors giving rise to promiscuous effects of RXR agonists. Here we identified a new RXR ligand chemotype addressing only part of RXR's molecular activities. Optimization provided a new RXR modulator scaffold fully activating the RXR homodimer with nanomolar potency but displaying markedly reduced RXR heterodimer activation compared to bexarotene. Co-crystal structure analysis revealed different molecular effects on the RXR LBD conformation than bexarotene possibly mediating the selective activity. The new RXR modulator type enables studies on selective RXR homodimer activation effects and suggests that different molecular mechanisms of RXR activity can be selectively addressed with ligands.


  • Organizational Affiliation
    • Ludwig-Maximilians-Universität München, Department of Pharmacy, 81377 Munich, Germany.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Retinoic acid receptor RXR-alpha235Homo sapiensMutation(s): 0 
Gene Names: RXRANR2B1
UniProt & NIH Common Fund Data Resources
Find proteins for P19793 (Homo sapiens)
Explore P19793 
Go to UniProtKB:  P19793
PHAROS:  P19793
GTEx:  ENSG00000186350 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP19793
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Nuclear receptor coactivator 210Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q15596 (Homo sapiens)
Explore Q15596 
Go to UniProtKB:  Q15596
PHAROS:  Q15596
GTEx:  ENSG00000140396 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ15596
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1JHO (Subject of Investigation/LOI)
Query on A1JHO

Download Ideal Coordinates CCD File 
D [auth A]6S,6aS,7R,10S,10aR)-6-(3,5-bis(trifluoromethyl)phenyl)-5,6,6a,7,8,9,10,10a-octahydro-7,10-methanophenanthridine-3-carboxylic acid
C23 H19 F6 N O2
GGGBDYORXLHJAW-QRHYTPHYSA-N
A1JAT (Subject of Investigation/LOI)
Query on A1JAT

Download Ideal Coordinates CCD File 
C [auth A](6R,6aR,7S,10R,10aS)-6-(3,5-bis(trifluoromethyl)phenyl)-5,6,6a,7,8,9,10,10a-octahydro-7,10-methanophenanthridine-3-carboxylic acid
C23 H19 F6 N O2
GGGBDYORXLHJAW-JMDSXHSASA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.46 Å
  • R-Value Free:  0.213 (Depositor), 0.213 (DCC) 
  • R-Value Work:  0.182 (Depositor), 0.182 (DCC) 
  • R-Value Observed: 0.183 (Depositor) 
Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 64.055α = 90
b = 64.055β = 90
c = 111.626γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata 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: 2025-08-13
    Type: Initial release
  • Version 1.1: 2025-08-27
    Changes: Database references