4WWQ

Apo structure of the Grb7 SH2 domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.169 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Cyclic Peptides Incorporating Phosphotyrosine Mimetics as Potent and Specific Inhibitors of the Grb7 Breast Cancer Target.

Watson, G.M.Gunzburg, M.J.Ambaye, N.D.Lucas, W.A.Traore, D.A.Kulkarni, K.Cergol, K.M.Payne, R.J.Panjikar, S.Pero, S.C.Perlmutter, P.Wilce, M.C.Wilce, J.A.

(2015) J.Med.Chem. 58: 7707-7718

  • DOI: 10.1021/acs.jmedchem.5b00609
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The Grb7 adaptor protein is a therapeutic target for both TNBC and HER2+ breast cancer. A nonphosphorylated cyclic peptide 1 (known as G7-18NATE) inhibits Grb7 via targeting the Grb7-SH2 domain, but requires the presence of phosphate ions for both af ...

    The Grb7 adaptor protein is a therapeutic target for both TNBC and HER2+ breast cancer. A nonphosphorylated cyclic peptide 1 (known as G7-18NATE) inhibits Grb7 via targeting the Grb7-SH2 domain, but requires the presence of phosphate ions for both affinity and specificity. Here we report the discovery of malonate bound in the phosphotyrosine binding pocket of the apo-Grb7-SH2 structure. Based on this, we carried out the rational design and synthesis of two analogues of peptide 1 that incorporate carboxymethylphenylalanine (cmF) and carboxyphenylalanine (cF) as mimics of phosphotyrosine (pY). Binding studies using SPR confirmed that affinity for Grb7-SH2 domain is improved up to 9-fold over peptide 1 under physiological phosphate conditions (KD = 2.1-5.7 μM) and that binding is specific for Grb7-SH2 over closely related domains (low or no detectable binding to Grb2-SH2 and Grb10-SH2). X-ray crystallographic structural analysis of the analogue bearing a cmF moiety in complex with Grb7-SH2 has identified the precise contacts conferred by the pY mimic that underpin this improved molecular interaction. Together this study identifies and characterizes the tightest specific inhibitor of Grb7 to date, representing a significant development toward a new Grb7-targeted therapeutic.


    Organizational Affiliation

    Australian Synchrotron , 800 Blackburn Road, Clayton, Victoria 3168, Australia.,School of Chemistry, The University of Sydney , Sydney, New South Wales 2006, Australia.,Department of Surgery and Vermont Cancer Center, University of Vermont , Burlington, Vermont 05401, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Growth factor receptor-bound protein 7
A, B
120Homo sapiensMutation(s): 0 
Gene Names: GRB7
Find proteins for Q14451 (Homo sapiens)
Go to Gene View: GRB7
Go to UniProtKB:  Q14451
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MLA
Query on MLA

Download SDF File 
Download CCD File 
A
MALONIC ACID
DICARBOXYLIC ACID C3; PROPANEDIOLIC ACID; METHANEDICARBOXYLIC ACID
C3 H4 O4
OFOBLEOULBTSOW-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.169 
  • Space Group: P 63
Unit Cell:
Length (Å)Angle (°)
a = 84.000α = 90.00
b = 84.000β = 90.00
c = 75.950γ = 120.00
Software Package:
Software NamePurpose
PHENIXrefinement
MOSFLMdata reduction
MOLREPphasing
PDB_EXTRACTdata extraction
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-09-23
    Type: Initial release
  • Version 1.1: 2015-10-28
    Type: Database references
  • Version 1.2: 2017-11-22
    Type: Data collection, Database references, Derived calculations, Refinement description