Benzamidine in complex with bovine trypsin varinat X(SSAI)bT.D1

Experimental Data Snapshot

  • Resolution: 1.80 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.190 

wwPDB Validation   3D Report Full Report

This is version 1.2 of the entry. See complete history


Understanding protein-ligand interactions: the price of protein flexibility

Rauh, D.Klebe, G.Stubbs, M.T.

(2004) J Mol Biol 335: 1325-1341

  • DOI: 10.1016/j.jmb.2003.11.041
  • Primary Citation of Related Structures:  
    1V2L, 1V2K, 1V2J, 1V2T, 1V2S, 1V2R, 1V2Q, 1V2P, 1V2O, 1V2N

  • PubMed Abstract: 
  • In order to design selective, high-affinity ligands to a target protein, it is advantageous to understand the structural determinants for protein-ligand complex formation at the atomic level. In a model system, we have successively mapped the factor ...

    In order to design selective, high-affinity ligands to a target protein, it is advantageous to understand the structural determinants for protein-ligand complex formation at the atomic level. In a model system, we have successively mapped the factor Xa binding site onto trypsin, showing that certain mutations influence both protein structure and inhibitor specificity. Our previous studies have shown that introduction of the 172SSFI175 sequence of factor Xa into rat or bovine trypsin results in the destabilisation of the intermediate helix with burial of Phe174 (the down conformation). Surface exposure of the latter residue (the up conformation) is critical for the correct formation of the aromatic box found in factor Xa-ligand complexes. In the present study, we investigate the influence of aromatic residues in position 174. Replacement with the bulky tryptophan (SSWI) shows reduced affinity for benzamidine-based inhibitors (1) and (4), whereas removal of the side-chain (alanine, SSAI) or exchange with a hydrophilic residue (arginine, SSRI) leads to a significant loss in affinity for all inhibitors studied. The variants could be crystallised in the presence of different inhibitors in multiple crystal forms. Structural characterisation of the variants revealed three different conformations of the intermediate helix and 175 loop in SSAI (down, up and super-up), as well as a complete disorder of this region in one crystal form of SSRI, suggesting that the compromised affinity of these variants is related to conformational flexibility. The influence of Glu217, peripheral to the ligand-binding site in factor Xa, was investigated. Introduction of Glu217 into trypsin variants containing the SSFI sequence exhibited enhanced affinity for the factor Xa ligands (2) and (3). The crystal structures of these variants also exhibited the down and super-up conformations, the latter of which could be converted to up upon soaking and binding of inhibitor (2). The improved affinity of the Glu217-containing variants appears to be due to a shift towards the up conformation. Thus, the reduction in affinity caused by conformational variability of the protein target can be partially or wholly offset by compensatory binding to the up conformation. The insights provided by these studies will be helpful in improving our understanding of ligand binding for the drug design process.

    Related Citations: 
    • ZZ made EZ: influence of inhibitor configuration on enzyme selectivity.
      Rauh, D., Klebe, G., Sturzebecher, J., Stubbs, M.T.
      (2003) J Mol Biol 330: 761
    • Trypsin mutants for structure-based drug design: expression, refolding and crystallisation.
      Rauh, D., Reyda, S., Klebe, G., Stubbs, M.T.
      (2002) Biol Chem 383: 1309
    • Reconstructing the Binding Site of Factor Xa in Trypsin Reveals Ligand-Induced Structural Plasticity.
      Reyda, S., Sohn, C., Klebe, G., Rall, K., Ullmann, D., Jakubke, H.D., Stubbs, M.T.
      (2003) J Mol Biol 325: 963
    • pH-dependent binding modes observed in trypsin crystals: lessons for structure-based drug design.
      Stubbs, M.T., Reyda, S., Dullweber, F., Moller, M., Klebe, G., Dorsch, D., Mederski, W.W., Wurziger, H.
      (2002) Chembiochem 3: 246
    • Structural and functional analyses of benzamidine-based inhibitors in complex with trypsin: implications for the inhibition of factor Xa, tPA, and urokinase.
      Renatus, M., Bode, W., Huber, R., Sturzebecher, J., Stubbs, M.T.
      (1998) J Med Chem 41: 5445

    Organizational Affiliation

    Institut für Pharmazeutische Chemie der Philipps, Universität Marburg, Marbacher Weg 6, D35032 Marburg, Germany.

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
TrypsinT223Bos taurusMutation(s): 4 
Find proteins for P00760 (Bos taurus)
Explore P00760 
Go to UniProtKB:  P00760
Protein Feature View
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
Query on BEN

Download Ideal Coordinates CCD File 
C7 H8 N2
 Ligand Interaction
Query on SO4

Download Ideal Coordinates CCD File 
O4 S
 Ligand Interaction
Query on CA

Download Ideal Coordinates CCD File 
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
BENKi:  427000   nM  Binding MOAD
BENKi :  427000   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Resolution: 1.80 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.190 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.55α = 90
b = 54.55β = 90
c = 136.8γ = 120
Software Package:
Software NamePurpose
CrystalCleardata collection
CrystalCleardata reduction
CrystalCleardata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-06-01
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance