8RU4

Crystal structure of Human Catenin Beta-1 in complex with stitched peptide inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.13 Å
  • R-Value Free: 
    0.240 (Depositor), 0.245 (DCC) 
  • R-Value Work: 
    0.201 (Depositor), 0.208 (DCC) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

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This is version 1.2 of the entry. See complete history


Literature

Structure-Based Design of Bicyclic Helical Peptides That Target the Oncogene beta-Catenin.

Yeste-Vazquez, A.Paulussen, F.M.Wendt, M.Klintrot, R.Schulte, C.Wallraven, K.van Gijzel, L.Simeonov, B.van der Gaag, M.Gerber, A.Maric, H.M.Hennig, S.Grossmann, T.N.

(2024) Angew Chem Int Ed Engl 63: e202411749-e202411749

  • DOI: https://doi.org/10.1002/anie.202411749
  • Primary Citation of Related Structures:  
    8RU3, 8RU4

  • PubMed Abstract: 

    The inhibition of intracellular protein-protein interactions is challenging, in particular, when involved interfaces lack pronounced cavities. The transcriptional co-activator protein and oncogene β‑catenin is a prime example of such a challenging target. Despite extensive targeting efforts, available high-affinity binders comprise only large molecular weight Inhibitors. This hampers the further development of therapeutically useful compounds. Herein, we report the design of a considerably smaller peptidomimetic scaffold derived from the α-helical β‑catenin-binding motif of Axin. Sequence maturation and bicyclization provided a stitched peptide with an unprecedented crosslink architecture. The binding mode and site were confirmed by a crystal structure. Further derivatization yielded a β-catenin inhibitor with single-digit micromolar activity in a cell-based assay. This study sheds a light on how to design helix mimetics with reduced molecular weight thereby improving their biological activity.


  • Organizational Affiliation

    VU Amsterdam, Chemisty and Pharmaceutical Sciences, NETHERLANDS.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Catenin beta-1
A, B
523Homo sapiensMutation(s): 0 
Gene Names: CTNNB1CTNNBOK/SW-cl.35PRO2286
UniProt & NIH Common Fund Data Resources
Find proteins for P35222 (Homo sapiens)
Explore P35222 
Go to UniProtKB:  P35222
PHAROS:  P35222
GTEx:  ENSG00000168036 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP35222
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Axin-113Homo sapiensMutation(s): 7 
UniProt & NIH Common Fund Data Resources
Find proteins for O15169 (Homo sapiens)
Explore O15169 
Go to UniProtKB:  O15169
PHAROS:  O15169
GTEx:  ENSG00000103126 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO15169
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GLC
Query on GLC

Download Ideal Coordinates CCD File 
D [auth A]
G [auth A]
H [auth A]
M [auth B]
N [auth B]
alpha-D-glucopyranose
C6 H12 O6
WQZGKKKJIJFFOK-DVKNGEFBSA-N
TRS
Query on TRS

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A],
K [auth B],
L [auth B]
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
CL
Query on CL

Download Ideal Coordinates CCD File 
I [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA
Query on NA

Download Ideal Coordinates CCD File 
J [auth A],
Q [auth B]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
CSO
Query on CSO
A, B
L-PEPTIDE LINKINGC3 H7 N O3 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.13 Å
  • R-Value Free:  0.240 (Depositor), 0.245 (DCC) 
  • R-Value Work:  0.201 (Depositor), 0.208 (DCC) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 64.567α = 90
b = 103.617β = 90
c = 187.923γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
GDAdata collection
DIALSdata reduction
STARANISOdata scaling
MrBUMPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted GLCClick on this verticalbar to view details

Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research Council (ERC)European Union--

Revision History  (Full details and data files)

  • Version 1.0: 2024-09-04
    Type: Initial release
  • Version 1.1: 2024-11-13
    Changes: Structure summary
  • Version 1.2: 2024-11-20
    Changes: Database references