5EEL

Grb7 SH2 with bicyclic peptide inhibitor

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.47 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.185 

wwPDB Validation 3D Report Full Report


This is version 2.0 of the entry. See complete history. 

Literature

Unexpected involvement of staple leads to redesign of selective bicyclic peptide inhibitor of Grb7.

Gunzburg, M.J., Kulkarni, K., Watson, G.M., Ambaye, N.D., Del Borgo, M.P., Brandt, R., Pero, S.C., Perlmutter, P., Wilce, M.C., Wilce, J.A.

(2016) Sci Rep 6: 27060-27060

  • DOI: 10.1038/srep27060
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • The design of potent and specific peptide inhibitors to therapeutic targets is of enormous utility for both proof-of-concept studies and for the development of potential new therapeutics. Grb7 is a key signaling molecule in the progression of HER2 po ...

    The design of potent and specific peptide inhibitors to therapeutic targets is of enormous utility for both proof-of-concept studies and for the development of potential new therapeutics. Grb7 is a key signaling molecule in the progression of HER2 positive and triple negative breast cancers. Here we report the crystal structure of a stapled bicyclic peptide inhibitor G7-B1 in complex with the Grb7-SH2 domain. This revealed an unexpected binding mode of the peptide, in which the staple forms an alternative contact with the surface of the target protein. Based on this structural information, we designed a new series of bicyclic G7 peptides that progressively constrain the starting peptide, to arrive at the G7-B4 peptide that binds with an approximately 2-fold enhanced affinity to the Grb7-SH2 domain (KD = 0.83 μM) compared to G7-B1 and shows low affinity binding to Grb2-, Grb10- and Grb14-SH2 domains (KD > 100 μM). Furthermore, we determined the structure of the G7-B4 bicyclic peptide in complex with the Grb7-SH2 domain, both before and after ring closing metathesis to show that the closed staple is essential to the target interaction. The G7-B4 peptide represents an advance in the development of Grb7 inhibitors and is a classical example of structure aided inhibitor development.

    Organizational Affiliation: 

    Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University, Wellington Road, Clayton VIC 3800, Australia.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Growth factor receptor-bound protein 7
A, B, C, D, E, F
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
Bicyclic Peptide Inhibitor
L, M, N, P, Q, R
9N/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
NA
Query on NA
Download SDF File 
Download CCD File 
A, B, C, D, E, F
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
FMT
Query on FMT
Download SDF File 
Download CCD File 
A, B, C, D, E, F
FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N
 Ligand Interaction
MLA
Query on MLA
Download SDF File 
Download CCD File 
A, C, D, E, F
MALONIC ACID
DICARBOXYLIC ACID C3; PROPANEDIOLIC ACID; METHANEDICARBOXYLIC ACID
C3 H4 O4
OFOBLEOULBTSOW-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
AEA
Query on AEA
L, M, N, P, Q, R
L-PEPTIDE LINKINGC5 H10 N2 O3 SCYS
73C
Query on 73C
L, M, N, P, Q, R
L-peptide linkingC7 H15 N O3SER
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.47 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.185 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 95.228α = 90.00
b = 95.228β = 90.00
c = 241.566γ = 90.00
Software Package:
Software NamePurpose
xia2data scaling
PDB_EXTRACTdata extraction
MOLREPphasing
PHENIXrefinement
xia2data reduction

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-06-15
    Type: Initial release
  • Version 2.0: 2018-12-26
    Type: Data collection, Derived calculations, Polymer sequence