8Z5J | pdb_00008z5j

Beta-catenin Crystal Structure


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 
    0.264 (Depositor), 0.234 (DCC) 
  • R-Value Work: 
    0.198 (Depositor) 
  • R-Value Observed: 
    0.224 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.2 of the entry. See complete history

Literature

Discovery of Novel 1-Phenylpiperidine Urea-Containing Derivatives Inhibiting beta-Catenin/BCL9 Interaction and Exerting Antitumor Efficacy through the Activation of Antigen Presentation of cDC1 Cells.

Zhu, W.Liu, C.Xi, K.Li, A.Shen, L.A.Li, Y.Jia, M.He, Y.Chen, G.Liu, C.Chen, Y.Chen, K.Sun, F.Zhang, D.Duan, C.Wang, H.Wang, D.Zhao, Y.Meng, X.Zhu, D.

(2024) J Med Chem 67: 12485-12520

  • DOI: https://doi.org/10.1021/acs.jmedchem.3c02079
  • Primary Citation Related Structures: 
    8Z5J, 8Z61

  • PubMed Abstract: 

    Aberrant activation of the Wnt/β-catenin signaling is associated with tumor development, and blocking β-catenin/BCL9 is a novel strategy for oncogenic Wnt/β-catenin signaling. Herein, we presented two novel β-catenin variations and exposed conformational dynamics in several β-catenin crystal structures at the BCL9 binding site. Furthermore, we identified a class of novel urea-containing compounds targeting β-catenin/BCL9 interaction. Notably, the binding modalities of inhibitors were greatly affected by the conformational dynamics of β-catenin. Among them, 28 had a strong affinity for β-catenin ( K d = 82 nM), the most potent inhibitor reported. In addition, 13 and 35 not only activate T cells but also promote the antigen presentation of cDC1, showing robust antitumor efficacy in the CT26 model. Collectively, our study demonstrated a series of potent small-molecule inhibitors targeting β-catenin/BCL9, which can enhance antigen presentation and activate cDC1 cells, delivering a potential strategy for boosting innate and adaptive immunity to overcome immunotherapy resistance.


  • Organizational Affiliation
    • Anhui University of Chinese Medicine, Hefei 230012, China.

Macromolecule Content 

  • Total Structure Weight: 60.19 kDa 
  • Atom Count: 3,772 
  • Modeled Residue Count: 505 
  • Deposited Residue Count: 549 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Catenin beta-1549Homo 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

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free:  0.264 (Depositor), 0.234 (DCC) 
  • R-Value Work:  0.198 (Depositor) 
  • R-Value Observed: 0.224 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.85α = 90
b = 103.15β = 90
c = 185.64γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASESphasing

Structure Validation

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Entry History 

& Funding Information

Deposition Data

  • Released Date: 2024-05-22 
  • Deposition Author(s): Tim, F.

Funding OrganizationLocationGrant Number
Other private--

Revision History  (Full details and data files)

  • Version 1.0: 2024-05-22
    Type: Initial release
  • Version 1.1: 2024-07-24
    Changes: Database references
  • Version 1.2: 2024-08-21
    Changes: Database references