4P9Z

Grb2 SH2 complexed with a pTyr-Ac6c-Asn tripeptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.181 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Protein-ligand interactions: Probing the energetics of a putative cation-pi interaction.

Myslinski, J.M.Clements, J.H.Martin, S.F.

(2014) Bioorg.Med.Chem.Lett. 24: 3164-3167

  • DOI: 10.1016/j.bmcl.2014.04.114
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • In order to probe the energetics associated with a putative cation-π interaction, thermodynamic parameters are determined for complex formation between the Grb2 SH2 domain and tripeptide derivatives of RCO-pTyr-Ac6c-Asn wherein the R group is varied ...

    In order to probe the energetics associated with a putative cation-π interaction, thermodynamic parameters are determined for complex formation between the Grb2 SH2 domain and tripeptide derivatives of RCO-pTyr-Ac6c-Asn wherein the R group is varied to include different alkyl, cycloalkyl, and aryl groups. Although an indole ring is reputed to have the strongest interaction with a guanidinium ion, binding free energies, ΔG°, for derivatives of RCO-pTyr-Ac6c-Asn bearing cyclohexyl and phenyl groups were slightly more favorable than their indolyl analog. Crystallographic analysis of two complexes reveals that test ligands bind in similar poses with the notable exception of the relative orientation and proximity of the phenyl and indolyl rings relative to an arginine residue of the domain. These spatial orientations are consistent with those observed in other cation-π interactions, but there is no net energetic benefit to such an interaction in this biological system. Accordingly, although cation-π interactions are well documented as important noncovalent forces in molecular recognition, the energetics of such interactions may be mitigated by other nonbonded interactions and solvation effects in protein-ligand associations.


    Organizational Affiliation

    The Department of Chemistry, The Institute of Cellular and Molecular Biology, and the Texas Institute of Drug and Diagnostic Development, The University of Texas, Austin, TX 78712, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Growth factor receptor-bound protein 2
A
117Homo 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
NMI-PTR-02K-ASN-NH2
B
5N/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
ACT
Query on ACT

Download SDF File 
Download CCD File 
A
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
CL
Query on CL

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Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

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Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  4 Unique
IDChainsTypeFormula2D DiagramParent
02K
Query on 02K
B
PEPTIDE LINKINGC7 H13 N O2ALA
NH2
Query on NH2
B
NON-POLYMERH2 N

--

PTR
Query on PTR
B
L-PEPTIDE LINKINGC9 H12 N O6 PTYR
NMI
Query on NMI
B
NON-POLYMERC12 H13 N O2

--

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.181 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 41.905α = 90.00
b = 41.905β = 90.00
c = 107.642γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM 84965
National Science Foundation (United States)United StatesCHE 0750329
Robert A. Welch FoundationUnited StatesF-652

Revision History 

  • Version 1.0: 2014-06-18
    Type: Initial release
  • Version 1.1: 2014-07-16
    Type: Database references
  • Version 1.2: 2017-08-09
    Type: Database references, Derived calculations, Other, Source and taxonomy, Structure summary
  • Version 1.3: 2017-09-27
    Type: Author supporting evidence