Thermodynamics of Binding of 2-methoxy-3-isopropylpyrazine and 2-methoxy-3-isobutylpyrazine to the Major Urinary Protein

Experimental Data Snapshot

  • Resolution: 1.70 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.183 

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Thermodynamics of Binding of 2-Methoxy-3-isopropylpyrazine and 2-Methoxy-3-isobutylpyrazine to the Major Urinary Protein.

Bingham, R.J.Findlay, J.B.C.Hsieh, S.-Y.Kalverda, A.P.Kjellberg, A.Perazzolo, C.Phillips, S.E.V.Seshadri, K.Trinh, C.H.Turnbull, W.B.Bodenhausen, G.Homans, S.W.

(2004) J Am Chem Soc 126: 1675-1681

  • DOI: https://doi.org/10.1021/ja038461i
  • Primary Citation of Related Structures:  
    1QY0, 1QY1, 1QY2

  • PubMed Abstract: 

    In the present study we examine the thermodynamics of binding of two related pyrazine-derived ligands to the major urinary protein, MUP-I, using a combination of isothermal titration calorimetry (ITC), X-ray crystallography, and NMR backbone (15)N and methyl side-chain (2)H relaxation measurements. Global thermodynamics data derived from ITC indicate that binding is driven by favorable enthalpic contributions, rather than the classical entropy-driven hydrophobic effect. Unfavorable entropic contributions from the protein backbone and side-chain residues in the vicinity of the binding pocket are partially offset by favorable entropic contributions at adjacent positions, suggesting a "conformational relay" mechanism whereby increased rigidity of residues on ligand binding are accompanied by increased conformational freedom of side chains in adjacent positions. The principal driving force governing ligand affinity and specificity can be attributed to solvent-driven enthalpic effects from desolvation of the protein binding pocket.

  • Organizational Affiliation

    Astbury Centre for Structural Molecular Biology, School of Biochemistry & Molecular Biology, University of Leeds, LS2 9JT Leeds, UK.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Major Urinary Protein174Mus musculusMutation(s): 0 
Gene Names: MUP1
Find proteins for P11588 (Mus musculus)
Explore P11588 
Go to UniProtKB:  P11588
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP11588
Sequence Annotations
  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
PRZ Binding MOAD:  1QY1 Kd: 300 (nM) from 1 assay(s)
PDBBind:  1QY1 Kd: 300 (nM) from 1 assay(s)
BindingDB:  1QY1 -TΔS: min: 9.39, max: 19.29 (kJ/mol) from 2 assay(s)
ΔG: min: -3.85e+1, max: -2.83e+1 (kJ/mol) from 2 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.70 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.183 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.575α = 90
b = 53.575β = 90
c = 137.562γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
CCP4data scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2004-02-24
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance