5N9C

ENAH EVH1 in complex with Ac-[2-Cl-F]-PP-[ProM-1]-OH


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.16 Å
  • R-Value Free: 0.169 
  • R-Value Work: 0.139 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

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: 5011-5016

  • DOI: 10.1073/pnas.1422054112
  • Primary Citation of Related Structures:  
  • Also Cited By: 5NCP, 5NEG, 5NDU, 5ND0, 5NCG, 5NC7, 5NC2, 5NBX, 5NBF, 5NAJ, 5N91

  • 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 prol ...

    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;




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Protein enabled homolog
A, B
113Homo sapiensMutation(s): 0 
Gene Names: ENAH (MENA)
Find proteins for Q8N8S7 (Homo sapiens)
Go to Gene View: ENAH
Go to UniProtKB:  Q8N8S7
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Ac-[2-Cl-F]-PP-[ProM-1]-OH
F, G, H, M
5N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
NO3
Query on NO3

Download SDF File 
Download CCD File 
A, B
NITRATE ION
N O3
NHNBFGGVMKEFGY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  3 Unique
IDChainsTypeFormula2D DiagramParent
92B
Query on 92B
F, G, H, M
NON-POLYMERC12 H16 N2 O3

--

2L5
Query on 2L5
F, G, H, M
L-PEPTIDE LINKINGC9 H10 Cl N O2

--

ACE
Query on ACE
F, G, H, M
NON-POLYMERC2 H4 O

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.16 Å
  • R-Value Free: 0.169 
  • R-Value Work: 0.139 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 34.761α = 61.40
b = 43.386β = 84.03
c = 43.593γ = 84.10
Software Package:
Software NamePurpose
XSCALEdata scaling
XDSdata reduction
PHENIXrefinement
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2017-02-24 
  • Released Date: 2017-06-14 
  • Deposition Author(s): Barone, M., Roske, Y.

Revision History 

  • Version 1.0: 2017-06-14
    Type: Initial release