8C1Y

Small molecule stabilizer for 14-3-3/ChREBP (Cmd 30)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.191 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


Literature

Molecular glues of the regulatory ChREBP/14-3-3 complex protect beta cells from glucolipotoxicity.

Katz, L.S.Visser, E.J.Plitzko, K.F.Pennings, M.Cossar, P.J.Tse, I.L.Kaiser, M.Brunsveld, L.Scott, D.K.Ottmann, C.

(2024) Biorxiv 

  • DOI: https://doi.org/10.1101/2024.02.16.580675
  • Primary Citation of Related Structures:  
    8BTQ, 8BWE, 8BWH, 8C1Y

  • PubMed Abstract: 

    The Carbohydrate Response Element Binding Protein (ChREBP) is a glucose-responsive transcription factor (TF) that is characterized by two major splice isoforms (α and β). In acute hyperglycemia, both ChREBP isoforms regulate adaptive β-expansion; however, during chronic hyperglycemia and glucolipotoxicity, ChREBPβ expression surges, leading to β-cell dedifferentiation and death. 14-3-3 binding to ChREBPα results in its cytoplasmic retention and concomitant suppression of transcriptional activity, suggesting that small molecule-mediated stabilization of this protein-protein interaction (PPI) via molecular glues may represent an attractive entry for the treatment of metabolic disease. Here, we show that structure-based optimizations of a molecular glue tool compound led not only to more potent ChREBPα/14-3-3 PPI stabilizers but also for the first time cellular active compounds. In primary human β-cells, the most active compound stabilized the ChREBPα/14-3-3 interaction and thus induced cytoplasmic retention of ChREBPα, resulting in highly efficient β-cell protection from glucolipotoxicity while maintaining β-cell identity. This study may thus not only provide the basis for the development of a unique class of compounds for the treatment of Type 2 Diabetes but also showcases an alternative 'molecular glue' approach for achieving small molecule control of notoriously difficult targetable TFs.


  • Organizational Affiliation

    Diabetes, Obesity and Metabolism Institute and Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1152, New York, 10029, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
14-3-3 protein sigma236Homo sapiensMutation(s): 0 
Gene Names: SFNHME1
UniProt & NIH Common Fund Data Resources
Find proteins for P31947 (Homo sapiens)
Explore P31947 
Go to UniProtKB:  P31947
PHAROS:  P31947
GTEx:  ENSG00000175793 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP31947
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Carbohydrate-responsive element-binding protein18Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for C9JDF5 (Homo sapiens)
Explore C9JDF5 
Go to UniProtKB:  C9JDF5
GTEx:  ENSG00000009950 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupC9JDF5
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
U0U (Subject of Investigation/LOI)
Query on U0U

Download Ideal Coordinates CCD File 
C [auth B][2-[2-[[2,2-bis(fluoranyl)-2-phenyl-ethyl]amino]-2-oxidanylidene-ethoxy]phenyl]phosphonic acid
C16 H16 F2 N O5 P
YXTJSWXZBWLQLV-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.191 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.626α = 90
b = 111.651β = 90
c = 62.827γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DIALSdata reduction
Aimlessdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Netherlands Organisation for Scientific Research (NWO)Netherlands--

Revision History  (Full details and data files)

  • Version 1.0: 2024-05-01
    Type: Initial release