5NBX

ENAH EVH1 in complex with Ac-[2-Cl-F]-PP-[ProM-9]-OH


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.168 

wwPDB Validation   3D Report Full Report


This is version 2.1 of the entry. See complete history


Literature

Designed nanomolar small-molecule inhibitors of Ena/VASP EVH1 interaction impair invasion and extravasation of breast cancer cells.

Barone, M.Muller, M.Chiha, S.Ren, J.Albat, D.Soicke, A.Dohmen, S.Klein, M.Bruns, J.van Dinther, M.Opitz, R.Lindemann, P.Beerbaum, M.Motzny, K.Roske, Y.Schmieder, P.Volkmer, R.Nazare, M.Heinemann, U.Oschkinat, H.Ten Dijke, P.Schmalz, H.G.Kuhne, R.

(2020) Proc Natl Acad Sci U S A 117: 29684-29690

  • DOI: https://doi.org/10.1073/pnas.2007213117
  • Primary Citation of Related Structures:  
    5N91, 5N9C, 5N9P, 5NAJ, 5NBF, 5NBX, 5NC2, 5NC7, 5NCF, 5NCG, 5NCP, 5ND0, 5NDU, 5NEG, 6RCF, 6RCJ, 6RD2, 6XVT, 6XXR, 7A5M, 7AKI

  • PubMed Abstract: 

    Battling metastasis through inhibition of cell motility is considered a promising approach to support cancer therapies. In this context, Ena/VASP-depending signaling pathways, in particular interactions with their EVH1 domains, are promising targets for pharmaceutical intervention. However, protein-protein interactions involving proline-rich segments are notoriously difficult to address by small molecules. Hence, structure-based design efforts in combination with the chemical synthesis of additional molecular entities are required. Building on a previously developed nonpeptidic micromolar inhibitor, we determined 22 crystal structures of ENAH EVH1 in complex with inhibitors and rationally extended our library of conformationally defined proline-derived modules (ProMs) to succeed in developing a nanomolar inhibitor ([Formula: see text] Da). In contrast to the previous inhibitor, the optimized compounds reduced extravasation of invasive breast cancer cells in a zebrafish model. This study represents an example of successful, structure-guided development of low molecular weight inhibitors specifically and selectively addressing a proline-rich sequence-recognizing domain that is characterized by a shallow epitope lacking defined binding pockets. The evolved high-affinity inhibitor may now serve as a tool in validating the basic therapeutic concept, i.e., the suppression of cancer metastasis by inhibiting a crucial protein-protein interaction involved in actin filament processing and cell migration.


  • Organizational Affiliation

    Oncode Institute, Department of Cell and Chemical Biology, Leiden University Medical Center, 2333 Leiden, The Netherlands; kuehne@fmp-berlin.de p.ten_dijke@lumc.nl schmalz@uni-koeln.de.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Protein enabled homolog
A, B
113Homo sapiensMutation(s): 0 
Gene Names: ENAHMENA
UniProt & NIH Common Fund Data Resources
Find proteins for Q8N8S7 (Homo sapiens)
Explore Q8N8S7 
Go to UniProtKB:  Q8N8S7
GTEx:  ENSG00000154380 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8N8S7
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
ACY-2L5-PRO-PRO-8SN
C, D
5synthetic constructMutation(s): 0 
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
BR
Query on BR

Download Ideal Coordinates CCD File 
E [auth A]BROMIDE ION
Br
CPELXLSAUQHCOX-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.168 
  • Space Group: C 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 90.214α = 90
b = 131.615β = 90
c = 35.704γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-03-21
    Type: Initial release
  • Version 1.1: 2020-11-25
    Changes: Database references, Derived calculations
  • Version 1.2: 2022-10-26
    Changes: Advisory, Database references
  • Version 2.0: 2023-11-15
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Polymer sequence, Source and taxonomy, Structure summary
  • Version 2.1: 2024-02-07
    Changes: Refinement description