Crystal Structure of the Grb2 SH2 Domain in Complex with a Tripeptide: Ac-pY-Ac6c-N-isohexyl

Experimental Data Snapshot

  • Resolution: 2.00 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.204 

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Some thermodynamic effects of varying nonpolar surfaces in protein-ligand interactions.

Cramer, D.L.Cheng, B.Tian, J.Clements, J.H.Wypych, R.M.Martin, S.F.

(2020) Eur J Med Chem 208: 112771-112771

  • DOI: https://doi.org/10.1016/j.ejmech.2020.112771
  • Primary Citation of Related Structures:  
    6WM1, 6WO2

  • PubMed Abstract: 

    Understanding how making structural changes in small molecules affects their binding affinities for targeted proteins is central to improving strategies for rational drug design. To assess the effects of varying the nature of nonpolar groups upon binding entropies and enthalpies, we designed and prepared a set of Grb2-SH2 domain ligands, Ac-pTyr-Ac 6 c-Asn-(CH 2 ) n -R, in which the size and electrostatic nature of R groups at the pTyr+3 site were varied. The complexes of these ligands with the Grb2-SH2 domain were evaluated in a series of studies in which the binding thermodynamics were determined using isothermal titration calorimetry, and binding interactions were examined in crystallographic studies of two different complexes. Notably, adding nonpolar groups to the pTyr+3 site leads to higher binding affinities, but the magnitude and energetic origins of these effects vary with the nature of the R substituent. For example, enhancements to binding affinities using aliphatic R groups are driven by more favorable changes in binding entropies, whereas aryl R groups improve binding free energies through a combination of more favorable changes in binding enthalpies and entropies. However, enthalpy/entropy compensation plays a significant role in these associations and mitigates against any significant variation in binding free energies, which vary by only 0.8 kcal•mol -1 , with changes in the electrostatic nature and size of the R group. Crystallographic studies show that differences in ΔG° or ΔH° correlate with buried nonpolar surface area, but they do not correlate with the total number of polar or van der Waals contacts. The relative number of ordered water molecules and relative order in the side chains at pTyr+3 correlate with differences in -TΔS°. Overall, these studies show that burial of nonpolar surface can lead to enhanced binding affinities arising from dominating entropy- or enthalpy-driven hydrophobic effects, depending upon the electrostatic nature of the apolar R group.

  • Organizational Affiliation

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

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Growth factor receptor-bound protein 2
A, B
117Homo sapiensMutation(s): 0 
Gene Names: GRB2ASH
UniProt & NIH Common Fund Data Resources
Find proteins for P62993 (Homo sapiens)
Explore P62993 
Go to UniProtKB:  P62993
PHAROS:  P62993
GTEx:  ENSG00000177885 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP62993
Sequence Annotations
  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
C, D
5synthetic constructMutation(s): 0 
Sequence Annotations
  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 32.225α = 90
b = 62.72β = 90
c = 90.137γ = 90
Software Package:
Software NamePurpose
HKL-2000data scaling
PDB_EXTRACTdata extraction

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Library of Medicine (NIH/NLM)United StatesGM 84965
National Science Foundation (NSF, United States)United StatesCHE 0750329
Robert A. Welch FoundationUnited StatesF-0652
Welch FoundationUnited StatesH-F-0032

Revision History  (Full details and data files)

  • Version 1.0: 2020-09-02
    Type: Initial release
  • Version 1.1: 2020-09-23
    Changes: Database references
  • Version 1.2: 2023-10-18
    Changes: Advisory, Data collection, Database references, Refinement description
  • Version 1.3: 2023-11-15
    Changes: Data collection