Crystal structure of human E-Cadherin (residues 3-213) in x-dimer conformation

Experimental Data Snapshot

  • Resolution: 1.92 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.194 

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Crystal Structure of Human E-Cadherin-EC1EC2 in Complex with a Peptidomimetic Competitive Inhibitor of Cadherin Homophilic Interaction.

Nardone, V.Lucarelli, A.P.Dalle Vedove, A.Fanelli, R.Tomassetti, A.Belvisi, L.Civera, M.Parisini, E.

(2016) J Med Chem 59: 5089-5094

  • DOI: https://doi.org/10.1021/acs.jmedchem.5b01487
  • Primary Citation of Related Structures:  
    4ZT1, 4ZTE

  • PubMed Abstract: 

    Cadherins are transmembrane cell adhesion proteins whose aberrant expression often correlates with cancer development and proliferation. We report the crystal structure of an E-cadherin extracellular fragment in complex with a peptidomimetic compound that was previously shown to partially inhibit cadherin homophilic adhesion. The structure reveals an unexpected binding mode and allows the identification of a druggable cadherin interface, thus paving the way to a future structure-guided design of cell adhesion inhibitors against cadherin-expressing solid tumors.

  • Organizational Affiliation

    Dipartimento di Chimica, Università degli Studi di Milano , Via C. Golgi 19, 20133 Milano, Italy.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B
211Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P12830 (Homo sapiens)
Explore P12830 
Go to UniProtKB:  P12830
PHAROS:  P12830
GTEx:  ENSG00000039068 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP12830
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.92 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.194 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 120.446α = 90
b = 76.417β = 109.98
c = 73.02γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
XDSdata reduction

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
European UnionFP7-PEOPLE-2010-RG (N. 268231)

Revision History  (Full details and data files)

  • Version 1.0: 2016-06-01
    Type: Initial release
  • Version 1.1: 2016-06-08
    Changes: Database references
  • Version 1.2: 2024-01-10
    Changes: Data collection, Database references, Derived calculations, Refinement description