7AR4

Crystal structure of beta-catenin in complex with cyclic peptide inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.203 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

Bicyclic beta-Sheet Mimetics that Target the Transcriptional Coactivator beta-Catenin and Inhibit Wnt Signaling.

Wendt, M.Bellavita, R.Gerber, A.Efrem, N.L.van Ramshorst, T.Pearce, N.M.Davey, P.R.J.Everard, I.Vazquez-Chantada, M.Chiarparin, E.Grieco, P.Hennig, S.Grossmann, T.N.

(2021) Angew Chem Int Ed Engl 60: 13937-13944

  • DOI: 10.1002/anie.202102082
  • Primary Citation of Related Structures:  
    7AR4

  • PubMed Abstract: 
  • Protein complexes are defined by the three-dimensional structure of participating binding partners. Knowledge about these structures can facilitate the design of peptidomimetics which have been applied e.g. as inhibitors of protein-protein interactions (PPIs) ...

    Protein complexes are defined by the three-dimensional structure of participating binding partners. Knowledge about these structures can facilitate the design of peptidomimetics which have been applied e.g. as inhibitors of protein-protein interactions (PPIs). Even though β-sheets participate widely in PPIs, they have only rarely served as the basis for peptidomimetic PPI inhibitors, in particular when addressing intracellular targets. Here, we present the structure-based design of β-sheet mimetics targeting the intracellular protein β-catenin, a central component of the Wnt signaling pathway. Based on a protein binding partner of β-catenin, a macrocyclic peptide was designed and its crystal structure in complex with β-catenin obtained. Using this structure, we designed a library of bicyclic β-sheet mimetics employing a late-stage diversification strategy. Several mimetics were identified that compete with transcription factor binding to β-catenin and inhibit Wnt signaling in cells. The presented design strategy can support the development of inhibitors for other β-sheet-mediated PPIs.


    Organizational Affiliation

    VU Universtity Amsterdam, Chemistry and Pharmaceutical Sciences, De Boelelaan 1108, 1081 HZ, Amsterdam, NETHERLANDS.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Catenin beta-1A [auth AAA]536Homo 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
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Cadherin-1B [auth PaP]16Mus musculusMutation(s): 8 
Gene Names: Cdh1
UniProt & NIH Common Fund Data Resources
Find proteins for P09803 (Mus musculus)
Explore P09803 
Go to UniProtKB:  P09803
IMPC:  MGI:88354
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EPE
Query on EPE

Download Ideal Coordinates CCD File 
C [auth AAA]4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
D [auth AAA]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.38α = 90
b = 85.62β = 90
c = 142.71γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research Council (ERC)--

Revision History  (Full details and data files)

  • Version 1.0: 2021-04-07
    Type: Initial release
  • Version 1.1: 2021-04-14
    Changes: Database references
  • Version 2.0: 2021-06-16
    Changes: Atomic model, Database references