5TYI

Grb7 SH2 with bicyclic peptide containing pY mimetic


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.207 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Discovery, Development, and Cellular Delivery of Potent and Selective Bicyclic Peptide Inhibitors of Grb7 Cancer Target.

Watson, G.M.Kulkarni, K.Sang, J.Ma, X.Gunzburg, M.J.Perlmutter, P.Wilce, M.C.J.Wilce, J.A.

(2017) J. Med. Chem. 60: 9349-9359

  • DOI: 10.1021/acs.jmedchem.7b01320
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Grb7 is a signaling protein with critical roles in tumor cell proliferation and migration and an established cancer therapeutic target. Here we explore chemical space to develop a new bicyclic peptide inhibitor, incorporating thioether and lactam lin ...

    Grb7 is a signaling protein with critical roles in tumor cell proliferation and migration and an established cancer therapeutic target. Here we explore chemical space to develop a new bicyclic peptide inhibitor, incorporating thioether and lactam linkers that binds with affinity (K D = 1.1 μM) and specificity to the Grb7-SH2 domain. Structural analysis of the Grb7-SH2/peptide complex revealed an unexpected binding orientation underlying the binding selectivity by this new scaffold. We further incorporated carboxymethylphenylalanine and carboxyphenylalanine phosphotyrosine mimetics and arrived at an optimized inhibitor that potently binds Grb7-SH2 (K D = 0.13 μM) under physiological conditions. X-ray crystal structures of these Grb7-SH2/peptide complexes reveal the structural basis for the most potent and specific inhibitors of Grb7 developed to date. Finally, we demonstrate that cell permeable versions of these peptides successfully block Grb7 mediated interactions in a breast cancer cell line, establishing the potential of these peptides in the development of novel therapeutics targeted to Grb7.


    Organizational Affiliation

    Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University , Wellington Road, Clayton, VIC 3800, Australia.,School of Chemistry, Monash University , Wellington Road, Clayton, VIC 3800, Australia.,Department of Physiology, School of Medicine, Jiangsu University , Zhenjiang, Jiangsu 212013, P.R. China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Growth factor receptor-bound protein 7
A, B, C, D
120Homo sapiensMutation(s): 0 
Gene Names: GRB7
Find proteins for Q14451 (Homo sapiens)
Go to Gene View: GRB7
Go to UniProtKB:  Q14451
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Peptide inhibitor
L, M, N, P
9N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
48V
Query on 48V
L, M, N, P
peptide-likeC5 H10 N2 O3 S

--

99Y
Query on 99Y
L, M, N, P
peptide linkingC10 H11 N O4

--

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.207 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 45.070α = 90.00
b = 107.610β = 101.38
c = 48.012γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
PHENIXrefinement
XSCALEdata scaling
XDSdata reduction
Aimlessdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Health and Medical Research Council (NHMRC, Australia)Australia--

Revision History 

  • Version 1.0: 2017-11-15
    Type: Initial release
  • Version 1.1: 2019-01-09
    Type: Data collection, Database references
  • Version 1.2: 2020-01-08
    Type: Author supporting evidence