7ZRB

Crystal structure of Beta-catenin Armadillo repeats domain in complex with the inhibitor RS6452


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.43 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.233 
  • R-Value Observed: 0.236 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Novel N -(Heterocyclylphenyl)benzensulfonamide Sharing an Unreported Binding Site with T-Cell Factor 4 at the beta-Catenin Armadillo Repeats Domain as an Anticancer Agent.

Nalli, M.Di Magno, L.Wen, Y.Liu, X.D'Ambrosio, M.Puxeddu, M.Parisi, A.Sebastiani, J.Sorato, A.Coluccia, A.Ripa, S.Di Pastena, F.Capelli, D.Montanari, R.Masci, D.Urbani, A.Naro, C.Sette, C.Orlando, V.D'Angelo, S.Biagioni, S.Bigogno, C.Dondio, G.Pastore, A.Stornaiuolo, M.Canettieri, G.Liu, T.Silvestri, R.La Regina, G.

(2023) Acs Pharmacol Transl Sci 6: 1087-1103

  • DOI: https://doi.org/10.1021/acsptsci.3c00092
  • Primary Citation of Related Structures:  
    7ZRB

  • PubMed Abstract: 

    Despite intensive efforts, no inhibitors of the Wnt/β-catenin signaling pathway have been approved so far for the clinical treatment of cancer. We synthesized novel N -(heterocyclylphenyl)benzenesulfonamides as β-catenin inhibitors. Compounds 5 - 10 showed strong inhibition of the luciferase activity. Compounds 5 and 6 inhibited the MDA-MB-231, HCC1806, and HCC1937 TNBC cells. Compound 9 induced in vitro cell death in SW480 and HCT116 cells and in vivo tumorigenicity of a human colorectal cancer line HCT116. In a co-immunoprecipitation study in HCT116 cells transfected with Myc-tagged T-cell factor 4 (Tcf-4), compound 9 abrogated the association between β-catenin and Tcf-4. The crystallographic analysis of the β-catenin Armadillo repeats domain revealed that compound 9 and Tcf-4 share a common binding site within the hotspot binding region close to Lys508. To our knowledge, compound 9 is the first small molecule ligand of this region to be reported. These results highlight the potential of this novel class of β-catenin inhibitors as anticancer agents.


  • Organizational Affiliation

    Laboratory affiliated to Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Department of Drug Chemistry and Technologies, Sapienza University of Rome, Piazzale Aldo Moro 5, I-00185 Rome, Italy.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Catenin beta-1
A, B
539Homo sapiensMutation(s): 0 
Gene Names: CTNNB1
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
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
JKI (Subject of Investigation/LOI)
Query on JKI

Download Ideal Coordinates CCD File 
C [auth A]4-bromanyl-~{N}-(3-pyridin-2-ylphenyl)benzenesulfonamide
C17 H13 Br N2 O2 S
FVCLFXCNULYHND-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.43 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.233 
  • R-Value Observed: 0.236 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.88α = 90
b = 160.24β = 99.63
c = 79.97γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
SAINTdata scaling
AMoREphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Italian Association for Cancer ResearchItaly--

Revision History  (Full details and data files)

  • Version 1.0: 2023-05-17
    Type: Initial release
  • Version 1.1: 2023-07-19
    Changes: Database references
  • Version 1.2: 2023-08-02
    Changes: Database references
  • Version 1.3: 2024-02-07
    Changes: Data collection, Refinement description