8BWZ

fragment-linked stabilizer for ERa - 14-3-3 interaction (1074393)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.168 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

From Tethered to Freestanding Stabilizers of 14-3-3 Protein-Protein Interactions through Fragment Linking.

Visser, E.J.Jaishankar, P.Sijbesma, E.Pennings, M.A.M.Vandenboorn, E.M.F.Guillory, X.Neitz, R.J.Morrow, J.Dutta, S.Renslo, A.R.Brunsveld, L.Arkin, M.R.Ottmann, C.

(2023) Angew Chem Int Ed Engl 62: e202308004-e202308004

  • DOI: https://doi.org/10.1002/anie.202308004
  • Primary Citation of Related Structures:  
    8BWJ, 8BWX, 8BWZ, 8BX0, 8BX3, 8BX4, 8BXI, 8BXM, 8BXN, 8BXO, 8BXQ, 8BXS, 8BY9, 8BYB, 8BYC, 8BYD, 8BYE, 8BYF, 8BYG, 8BYO, 8BYY, 8BYZ, 8BZ0, 8BZ9, 8BZA, 8BZB, 8BZW, 8C04, 8C0K, 8C4F, 8C4G

  • PubMed Abstract: 

    Small-molecule stabilization of protein-protein interactions (PPIs) is a promising strategy in chemical biology and drug discovery. However, the systematic discovery of PPI stabilizers remains a largely unmet challenge. Herein we report a fragment-linking approach targeting the interface of 14-3-3 and a peptide derived from the estrogen receptor alpha (ERα) protein. Two classes of fragments-a covalent and a noncovalent fragment-were co-crystallized and subsequently linked, resulting in a noncovalent hybrid molecule in which the original fragment interactions were largely conserved. Supported by 20 crystal structures, this initial hybrid molecule was further optimized, resulting in selective, 25-fold stabilization of the 14-3-3/ERα interaction. The high-resolution structures of both the single fragments, their co-crystal structures and those of the linked fragments document a feasible strategy to develop orthosteric PPI stabilizers by linking to an initial tethered fragment.


  • Organizational Affiliation

    Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems (ICMS), Eindhoven University of Technology, Den Dolech 2, 5612, AZ Eindhoven, The Netherlands.


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
ERalpha peptide5Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P03372 (Homo sapiens)
Explore P03372 
Go to UniProtKB:  P03372
PHAROS:  P03372
GTEx:  ENSG00000091831 
Entity Groups  
UniProt GroupP03372
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
S3I (Subject of Investigation/LOI)
Query on S3I

Download Ideal Coordinates CCD File 
C [auth A]~{N}-[3-(5-carbamimidoylthiophen-3-yl)phenyl]-2-(4-ethanoylphenoxy)-2-methyl-propanamide
C23 H23 N3 O3 S
FIJPVTLSUVVZPW-UHFFFAOYSA-N
Modified Residues  2 Unique
IDChains TypeFormula2D DiagramParent
CSO
Query on CSO
A
L-PEPTIDE LINKINGC3 H7 N O3 SCYS
TPO
Query on TPO
B
L-PEPTIDE LINKINGC4 H10 N O6 PTHR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.168 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 82.099α = 90
b = 112.39β = 90
c = 62.596γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
DIALSdata reduction
XDSdata 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: 2023-08-02
    Type: Initial release
  • Version 1.1: 2023-08-09
    Changes: Database references
  • Version 1.2: 2023-08-30
    Changes: Data collection
  • Version 1.3: 2023-09-13
    Changes: Database references
  • Version 1.4: 2023-11-15
    Changes: Data collection