1BMB

GRB2-SH2 DOMAIN IN COMPLEX WITH KPFY*VNVEF (PKF270-974)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.187 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural and conformational requirements for high-affinity binding to the SH2 domain of Grb2(1).

Ettmayer, P.France, D.Gounarides, J.Jarosinski, M.Martin, M.S.Rondeau, J.M.Sabio, M.Topiol, S.Weidmann, B.Zurini, M.Bair, K.W.

(1999) J.Med.Chem. 42: 971-980

  • DOI: 10.1021/jm9811007
  • Primary Citation of Related Structures:  1BM2

  • PubMed Abstract: 
  • Following earlier work on cystine-bridged peptides, cyclic phosphopeptides containing nonreducible mimics of cystine were synthesized that show high affinity and specificity toward the Src homology (SH2) domain of the growth factor receptor-binding p ...

    Following earlier work on cystine-bridged peptides, cyclic phosphopeptides containing nonreducible mimics of cystine were synthesized that show high affinity and specificity toward the Src homology (SH2) domain of the growth factor receptor-binding protein (Grb2). Replacement of the cystine in the cyclic heptapeptide cyclo(CYVNVPC) by D-alpha-acetylthialysine or D-alpha-lysine gave cyclo(YVNVP(D-alpha-acetyl-thiaK)) (22) and cyclo(YVNVP(D-alpha-acetyl-K)) (30), which showed improved binding 10-fold relative to that of the control peptide KPFYVNVEF (1). NMR spectroscopy and molecular modeling experiments indicate that a beta-turn conformation centered around YVNV is essential for high-affinity binding. X-ray structure analyses show that the linear peptide 1 and the cyclic compound 21 adopt a similar binding mode with a beta-turn conformation. Our data confirm the unique structural requirements of the ligand binding site of the SH2 domain of Grb2. Moreover, the potency of our cyclic lactams can be explained by the stabilization of the beta-turn conformation by three intramolecular hydrogen bonds (one mediated by an H2O molecule). These stable and easily accessible cyclic peptides can serve as templates for the evaluation of phosphotyrosine surrogates and further chemical elaboration.


    Organizational Affiliation

    Novartis Forschungsinstitut, Brunnerstrasse 59, Vienna A-1235, Austria. peter.ettmayer@pharma.novartis.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (GROWTH FACTOR RECEPTOR BOUND PROTEIN 2)
A
123Homo sapiensGene Names: GRB2 (ASH)
Find proteins for P62993 (Homo sapiens)
Go to Gene View: GRB2
Go to UniProtKB:  P62993
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (PKF270-974)
I
9N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
PTR
Query on PTR
I
L-PEPTIDE LINKINGC9 H12 N O6 PTYR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.187 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 51.130α = 90.00
b = 51.130β = 90.00
c = 90.250γ = 90.00
Software Package:
Software NamePurpose
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1998-07-29
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance