4MY6

EnaH-EVH1 in complex with peptidomimetic low-molecular weight inhibitor Ac-[2-Cl-F]-[ProM-2]-[ProM-1]-OH

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.189 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history. 


Literature

A modular toolkit to inhibit proline-rich motif-mediated protein-protein interactions.

Opitz, R., Muller, 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., Kuhne, R.

(2015) Proc Natl Acad Sci U S A 112: 5011-5016

  • DOI: https://doi.org/10.1073/pnas.1422054112
  • Primary Citation of Related Structures:  
    4MY6

  • PubMed Abstract: 

    • Small-molecule competitors of protein-protein interactions are urgently needed for functional analysis of large-scale genomics and proteomics data. Particularly abundant, yet so far undruggable, targets include domains specialized in recognizing proline-rich segments, including Src-homology 3 (SH3), WW, GYF, and Drosophila enabled (Ena)/vasodilator-stimulated phosphoprotein (VASP) homology 1 (EVH1) domains ...

    Small-molecule competitors of protein-protein interactions are urgently needed for functional analysis of large-scale genomics and proteomics data. Particularly abundant, yet so far undruggable, targets include domains specialized in recognizing proline-rich segments, including Src-homology 3 (SH3), WW, GYF, and Drosophila enabled (Ena)/vasodilator-stimulated phosphoprotein (VASP) homology 1 (EVH1) domains. Here, we present a modular strategy to obtain an extendable toolkit of chemical fragments (ProMs) designed to replace pairs of conserved prolines in recognition motifs. As proof-of-principle, we developed a small, selective, peptidomimetic inhibitor of Ena/VASP EVH1 domain interactions. Highly invasive MDA MB 231 breast-cancer cells treated with this ligand showed displacement of VASP from focal adhesions, as well as from the front of lamellipodia, and strongly reduced cell invasion. General applicability of our strategy is illustrated by the design of an ErbB4-derived ligand containing two ProM-1 fragments, targeting the yes-associated protein 1 (YAP1)-WW domain with a fivefold higher affinity.

    Organizational Affiliation: 

    Leibniz-Institut für Molekulare Pharmakologie, 13125 Berlin, Germany; schmalz@uni-koeln.de kuehne@fmp-berlin.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: ENAH, MENA
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
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
3VH
Query on 3VH
Download Ideal Coordinates CCD File 
C [auth A],
F [auth B]		 (3aR,5aS,8S,10aS)-1-[(3S,6R,8aS)-1'-[(2S)-2-acetamido-3-(2-chlorophenyl)propanoyl]-5-oxidanylidene-spiro[1,2,3,8a-tetrahydroindolizine-6,2'-pyrrolidine]-3-yl]carbonyl-10-oxidanylidene-2,3,3a,5a,8,10a-hexahydrodipyrrolo[3,2-b:3',1'-f]azepine-8-carboxylic acid
C35 H38 Cl N5 O7
PORJLWGURWUCLW-QHVDBZGRSA-N		 Ligand Interaction
BR
Query on BR
Download Ideal Coordinates CCD File 
D [auth A],
E [auth A]		BROMIDE ION
Br
CPELXLSAUQHCOX-UHFFFAOYSA-M		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.189 
  • Space Group: C 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 89.83α = 90
b = 131.42β = 90
c = 35.56γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
SCALAdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-10-15
    Type: Initial release
  • Version 1.1: 2015-04-15
    Changes: Database references
  • Version 1.2: 2015-04-22
    Changes: Database references
  • Version 1.3: 2015-05-06
    Changes: Database references
  • Version 1.4: 2015-07-22
    Changes: Structure summary