1ZFP

GROWTH FACTOR RECEPTOR BINDING PROTEIN SH2 DOMAIN COMPLEXED WITH A PHOSPHOTYROSYL PENTAPEPTIDE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structural basis for the high affinity of amino-aromatic SH2 phosphopeptide ligands.

Rahuel, J.Garcia-Echeverria, C.Furet, P.Strauss, A.Caravatti, G.Fretz, H.Schoepfer, J.Gay, B.

(1998) J.Mol.Biol. 279: 1013-1022

  • DOI: 10.1006/jmbi.1998.1790

  • PubMed Abstract: 
  • An anthranyl moiety placed at the N terminus of a phosphotyrosine peptide potentiates the inhibitory effect of this small peptide on the binding of the Grb2 SH2 domain to the EGF receptor. Using molecular modeling procedures based on the Lck SH2 doma ...

    An anthranyl moiety placed at the N terminus of a phosphotyrosine peptide potentiates the inhibitory effect of this small peptide on the binding of the Grb2 SH2 domain to the EGF receptor. Using molecular modeling procedures based on the Lck SH2 domain structure, this observation was rationalized in terms of a suitably favorable pi-pi stacking interaction between the anthranyl moiety and the arginine alphaA2 (ArgalphaA2) residue side-chain of Grb2 SH2. The crystal structure of the Grb2 SH2 domain in complex with the inhibitor 2-Abz-EpYINQ-NH2 (IC50 26 nM) has been solved in two different crystal forms at 2.1 and 1.8 A resolution. This structure confirms the modeling based on the Lck SH2 domain. The ArgalphaA2 residue is conserved in most SH2 domains. Thus, as expected, the anthranyl group also confers high affinity to small peptide ligands of other SH2 domains such as Lck-, PLC-gamma-amino-terminal and p85 amino-terminal SH2 domains as demonstrated by structure affinity relationships (SAR) data. These potent peptides with an amino-terminal surrogate group and the structure of Grb2 SH2 domain in complex with one such peptide represent good starting points for the design and optimization of new inhibitors of many SH2 domains.


    Organizational Affiliation

    Core Technology Area, Novartis Pharma AG, Core Technology Area and Oncology, Research Department, CH-4002, Basel Switzerland.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
GROWTH FACTOR RECEPTOR BINDING PROTEIN
E
98Homo sapiensMutation(s): 0 
Gene Names: GRB2 (ASH)
Find proteins for P62993 (Homo sapiens)
Go to Gene View: GRB2
Go to UniProtKB:  P62993
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
EPIDERMAL GROWTH FACTOR RECEPTOR-DERIVED PEPTIDE
I
7N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
E
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  3 Unique
IDChainsTypeFormula2D DiagramParent
NH2
Query on NH2
I
NON-POLYMERH2 N

--

BE2
Query on BE2
I
L-PEPTIDE LINKINGC7 H7 N O2

--

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
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 49.900α = 90.00
b = 113.700β = 90.00
c = 46.600γ = 90.00
Software Package:
Software NamePurpose
TFFCmodel building
MADNESdata reduction
TFFCphasing
TNTrefinement
CCP4data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 1998-03-26 
  • Released Date: 1999-03-30 
  • Deposition Author(s): Rahuel, J.

Revision History 

  • Version 1.0: 1999-03-30
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2018-04-18
    Type: Data collection, Other