Protein-Ligand Interactions: Thermodynamic Effects Associated with Increasing Hydrophobic Surface Area

Experimental Data Snapshot

  • Resolution: 1.71 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.199 

wwPDB Validation   3D Report Full Report

This is version 1.3 of the entry. See complete history


Protein-ligand interactions: thermodynamic effects associated with increasing nonpolar surface area.

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

(2011) J Am Chem Soc 133: 18518-18521

  • DOI: https://doi.org/10.1021/ja2068752
  • Primary Citation of Related Structures:  
    3OV1, 3OVE, 3S8L, 3S8N, 3S8O

  • PubMed Abstract: 

    Thermodynamic parameters were determined for complex formation between the Grb2 SH2 domain and Ac-pTyr-Xaa-Asn derived tripeptides in which the Xaa residue is an α,α-cycloaliphatic amino acid that varies in ring size from three- to seven-membered. Although the six- and seven-membered ring analogs are approximately equipotent, binding affinities of those having three- to six-membered rings increase incrementally with ring size because increasingly more favorable binding enthalpies dominate increasingly less favorable binding entropies, a finding consistent with an enthalpy-driven hydrophobic effect. Crystallographic analysis reveals that the only significant differences in structures of the complexes are in the number of van der Waals contacts between the domain and the methylene groups in the Xaa residues. There is a positive correlation between buried nonpolar surface area and binding free energy and enthalpy, but not with ΔC(p). Displacing a water molecule from a protein-ligand interface is not necessarily reflected in a favorable change in binding entropy. These findings highlight some of the fallibilities associated with commonly held views of relationships of structure and energetics in protein-ligand interactions and have significant implications for ligand design.

  • Organizational Affiliation

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

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Growth factor receptor-bound protein 2117Homo 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
pYAc4cN5N/AMutation(s): 0 
Sequence Annotations
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
Query on PTR
Experimental Data & Validation

Experimental Data

  • Resolution: 1.71 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.199 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.072α = 90
b = 42.072β = 90
c = 108.755γ = 90
Software Package:
Software NamePurpose
CrystalCleardata collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-11-02
    Type: Initial release
  • Version 1.1: 2011-12-07
    Changes: Database references
  • Version 1.2: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.3: 2023-12-06
    Changes: Data collection