6XVT

ENAH EVH1 in complex with Ac-[2-Cl-F]-PPPPTEDDL-NH2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.203 

wwPDB Validation   3D Report Full Report


This is version 1.4 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: 10.1073/pnas.2007213117
  • Primary Citation of Related Structures:  
    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 ...

    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.


    Related Citations: 
    • A modular toolkit to inhibit proline-rich motif-mediated protein-protein interactions.
      Opitz, R., Mueller, M., Reuter, C., Barone, M., Soicke, A., Roske, Y., Piotukh, K., Huy, P., Beerbaum, M., Wiesner, B., Beyermann, M., Schmieder, P., Freund, C., Volkmer, R., Oschkinat, H., Schmalz, H.G., Kuehne, R.
      (2015) Proc Natl Acad Sci U S A 112: 5011

    Organizational Affiliation

    Department of Structural Biology, Leibniz-Forschungsinstitut für Molekulare Pharmakologie, 13125 Berlin, Germany; 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
MoleculeChainsSequence LengthOrganismDetailsImage
Protein enabled homologA, B113Homo sapiensMutation(s): 0 
Gene Names: ENAHMENA
UniProt & NIH Common Fund Data Resources
Find proteins for Q8N8S7 (Homo sapiens)
Explore Q8N8S7 
Go to UniProtKB:  Q8N8S7
PHAROS:  Q8N8S7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8N8S7
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
ACY-SC1-SC2-SC3-SC4-SC5-NMEC [auth G],
D [auth H]
7synthetic constructMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.203 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 34.65α = 60.849
b = 44.28β = 84.037
c = 43.16γ = 84.005
Software Package:
Software NamePurpose
XDSdata reduction
XDSdata scaling
PHASERphasing
PHENIXrefinement

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Federal Ministry for Education and ResearchGermany16GW0186K

Revision History  (Full details and data files)

  • Version 1.0: 2020-03-18
    Type: Initial release
  • Version 1.1: 2020-11-25
    Changes: Database references
  • Version 1.2: 2020-12-02
    Changes: Database references
  • Version 1.3: 2021-02-10
    Changes: Database references
  • Version 1.4: 2021-02-17
    Changes: Database references