Beta-Catenin in complex with compound 6

Experimental Data Snapshot

  • Resolution: 1.81 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.230 

wwPDB Validation   3D Report Full Report

Ligand Structure Quality Assessment 

This is version 1.2 of the entry. See complete history


Getting a Grip on the Undrugged: Targeting beta-Catenin with Fragment-Based Methods.

Kessler, D.Mayer, M.Zahn, S.K.Zeeb, M.Wohrle, S.Bergner, A.Bruchhaus, J.Ciftci, T.Dahmann, G.Dettling, M.Dobel, S.Fuchs, J.E.Geist, L.Hela, W.Kofink, C.Kousek, R.Moser, F.Puchner, T.Rumpel, K.Scharnweber, M.Werni, P.Wolkerstorfer, B.Breitsprecher, D.Baaske, P.Pearson, M.McConnell, D.B.Bottcher, J.

(2021) ChemMedChem 16: 1420-1424

  • DOI: https://doi.org/10.1002/cmdc.202000839
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Aberrant WNT pathway activation, leading to nuclear accumulation of β-catenin, is a key oncogenic driver event. Mutations in the tumor suppressor gene APC lead to impaired proteasomal degradation of β-catenin and subsequent nuclear translocation. Restoring cellular degradation of β-catenin represents a potential therapeutic strategy. Here, we report the fragment-based discovery of a small molecule binder to β-catenin, including the structural elucidation of the binding mode by X-ray crystallography. The difficulty in drugging β-catenin was confirmed as the primary screening campaigns identified only few and very weak hits. Iterative virtual and NMR screening techniques were required to discover a compound with sufficient potency to be able to obtain an X-ray co-crystal structure. The binding site is located between armadillo repeats two and three, adjacent to the BCL9 and TCF4 binding sites. Genetic studies show that it is unlikely to be useful for the development of protein-protein interaction inhibitors but structural information and established assays provide a solid basis for a prospective optimization towards β-catenin proteolysis targeting chimeras (PROTACs) as alternative modality.

  • Organizational Affiliation

    Boehringer Ingelheim Pharma GmbH & Co KG, Birkendorfer Straße 65, 88397, Biberach, Germany.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Catenin beta-1167Homo 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
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
R9Q (Subject of Investigation/LOI)
Query on R9Q

Download Ideal Coordinates CCD File 
B [auth A]3-[(2~{R})-4-methyl-5-oxidanylidene-2,3-dihydro-1,4-benzoxazepin-2-yl]benzenecarbonitrile
C17 H14 N2 O2
Binding Affinity Annotations 
IDSourceBinding Affinity
R9Q Binding MOAD:  7AFW Kd: 9.15e+5 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.81 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.230 
  • Space Group: P 3 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.453α = 90
b = 53.453β = 90
c = 87.545γ = 120
Software Package:
Software NamePurpose
autoPROCdata reduction
XDSdata reduction
autoPROCdata scaling
Aimlessdata scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-12-16
    Type: Initial release
  • Version 1.1: 2021-05-19
    Changes: Database references
  • Version 1.2: 2024-01-31
    Changes: Data collection, Database references, Refinement description