1V2M

Benzamidine in complex with bovine trypsin variant X(triple.Glu)bT.A1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.213 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Understanding protein-ligand interactions: the price of protein flexibility

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

(2004) J.Mol.Biol. 335: 1325-1341

  • Primary Citation of Related Structures:  1V2J, 1V2K, 1V2L, 1V2N, 1V2O, 1V2P, 1V2Q, 1V2R, 1V2S, 1V2T, 1V2U, 1V2V, 1V2W

  • 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: 
    • 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
    • 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
    • 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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Trypsin
T
223Bos taurusEC: 3.4.21.4
Find proteins for P00760 (Bos taurus)
Go to UniProtKB:  P00760
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
T
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
BEN
Query on BEN

Download SDF File 
Download CCD File 
T
BENZAMIDINE
C7 H8 N2
PXXJHWLDUBFPOL-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
BDNKi: 31 - 39000 nM (96) BINDINGDB
BENKi: 51000 nM BINDINGMOAD
BENKi: 51000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.213 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 54.930α = 90.00
b = 54.930β = 90.00
c = 108.410γ = 120.00
Software Package:
Software NamePurpose
CrystalCleardata scaling
CrystalCleardata collection
CNSphasing
CrystalCleardata reduction
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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