PDBsum entry 3imj

Go to PDB code: 
protein ligands Protein-protein interface(s) links
Signaling protein/peptide PDB id
Protein chains
101 a.a. *
AYI ×2
Waters ×182
* Residue conservation analysis
PDB id:
Name: Signaling protein/peptide
Title: Crystal structure of the grb2 sh2 domain in complex with a cyclopropyl-constrained ac-ptyr-ile-asn-nh2 tripeptide mimi
Structure: Growth factor receptor-bound protein 2. Chain: a, b. Fragment: sh2 domain. Synonym: adapter protein grb2, sh2/sh3 adapter grb2, protei engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: grb2, ash. Expressed in: escherichia coli. Expression_system_taxid: 562.
2.02Å     R-factor:   0.200     R-free:   0.229
Authors: J.H.Clements
Key ref: J.E.DeLorbe et al. (2009). Thermodynamic and structural effects of conformational constraints in protein-ligand interactions. Entropic paradoxy associated with ligand preorganization. J Am Chem Soc, 131, 16758-16770. PubMed id: 19886660 DOI: 10.1021/ja904698q
10-Aug-09     Release date:   17-Nov-09    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
P62993  (GRB2_HUMAN) -  Growth factor receptor-bound protein 2
217 a.a.
101 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     membrane   1 term 
  Biological process     Ras protein signal transduction   1 term 
  Biochemical function     SH3/SH2 adaptor activity     1 term  


DOI no: 10.1021/ja904698q J Am Chem Soc 131:16758-16770 (2009)
PubMed id: 19886660  
Thermodynamic and structural effects of conformational constraints in protein-ligand interactions. Entropic paradoxy associated with ligand preorganization.
J.E.DeLorbe, J.H.Clements, M.G.Teresk, A.P.Benfield, H.R.Plake, L.E.Millspaugh, S.F.Martin.
Succinate- and cyclopropane-derived phosphotyrosine (pY) replacements were incorporated into a series of Grb2 SH2 binding ligands wherein the pY+1 residue was varied to determine explicitly how variations in ligand preorganization affect binding energetics and structure. The complexes of these ligands with the Grb2 SH2 domain were examined in a series of thermodynamic and structural investigations using isothermal titration calorimetry and X-ray crystallography. The binding enthalpies for all ligands were favorable, and although binding entropies for all ligands having a hydrophobic residue at the pY+1 site were favorable, binding entropies for those having a hydrophilic residue at this site were unfavorable. Preorganized ligands generally bound with more favorable Gibbs energies than their flexible controls, but this increased affinity was the consequence of relatively more favorable binding enthalpies. Unexpectedly, binding entropies of the constrained ligands were uniformly disfavored relative to their flexible controls, demonstrating that the widely held belief that ligand preorganization should result in an entropic advantage is not necessarily true. Crystallographic studies of complexes of several flexible and constrained ligands having the same amino acid at the pY+1 position revealed extensive similarities, but there were some notable differences. There are a greater number of direct polar contacts in complexes of the constrained ligands that correlate qualitatively with their more favorable binding enthalpies and Gibbs energies. There are more single water-mediated contacts between the domain and the flexible ligand of each pair; although fixing water molecules at a protein-ligand interface is commonly viewed as entropically unfavorable, entropies for forming these complexes are favored relative to those of their constrained counterparts. Crystallographic b-factors in the complexes of constrained ligands are greater than those of their flexible counterparts, an observation that seems inconsistent with our finding that entropies for forming complexes of flexible ligands are relatively more favorable. This systematic study highlights the profound challenges and complexities associated with predicting how structural changes in a ligand will affect enthalpies, entropies, and structure in protein-ligand interactions.

Literature references that cite this PDB file's key reference

  PubMed id Reference
21339062 E.Gallicchio, and R.M.Levy (2011).
Advances in all atom sampling methods for modeling protein-ligand binding affinities.
  Curr Opin Struct Biol, 21, 161-166.  
21157775 R.J.Falconer, and B.M.Collins (2011).
Survey of the year 2009: applications of isothermal titration calorimetry.
  J Mol Recognit, 24, 1.  
20944243 J.H.Clements, J.E.DeLorbe, A.P.Benfield, and S.F.Martin (2010).
Binding of flexible and constrained ligands to the Grb2 SH2 domain: structural effects of ligand preorganization.
  Acta Crystallogr D Biol Crystallogr, 66, 1101-1115.  
20733063 M.Biasini, V.Mariani, J.Haas, S.Scheuber, A.D.Schenk, T.Schwede, and A.Philippsen (2010).
OpenStructure: a flexible software framework for computational structural biology.
  Bioinformatics, 26, 2626-2628.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time.