3LJJ

Bovine trypsin in complex with UB-THR 10


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Work: 0.253 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Congeneric but still distinct: how closely related trypsin ligands exhibit different thermodynamic and structural properties.

Brandt, T.Holzmann, N.Muley, L.Khayat, M.Wegscheid-Gerlach, C.Baum, B.Heine, A.Hangauer, D.Klebe, G.

(2011) J Mol Biol 405: 1170-1187

  • DOI: https://doi.org/10.1016/j.jmb.2010.11.038
  • Primary Citation of Related Structures:  
    2ZDK, 2ZDL, 2ZDM, 2ZDN, 2ZFS, 2ZFT, 2ZHD, 2ZQ1, 2ZQ2, 3LJJ, 3LJO

  • PubMed Abstract: 

    A congeneric series of benzamidine-type ligands with a central proline moiety and a terminal cycloalkyl group--linked by a secondary amine, ether, or methylene bridge--was synthesized as trypsin inhibitors. This series of inhibitors was investigated by isothermal titration calorimetry, crystal structure analysis in two crystal forms, and molecular dynamics simulations. Even though all of these congeneric ligands exhibited essentially the same affinity for trypsin, their binding profiles at the structural, dynamic, and thermodynamic levels are very distinct. The ligands display a pronounced enthalpy/entropy compensation that results in a nearly unchanged free energy of binding, even though individual enthalpy and entropy terms change significantly across the series. Crystal structures revealed that the secondary amine-linked analogs scatter over two distinct conformational families of binding modes that occupy either the inside or of the outside the protein's S3/S4 specificity pocket. In contrast, the ether-linked and methylene-linked ligands preferentially occupy the hydrophobic specificity pocket. This also explains why the latter ligands could only be crystallized in the conformationally restricting closed crystal form whereas the derivative with the highest residual mobility in the series escaped our attempts to crystallize it in the closed form; instead, a well-resolved structure could only be achieved in the open form with the ligand in disordered orientation. These distinct binding modes are supported by molecular dynamics simulations and correlate with the shifting enthalpic/entropic signatures of ligand binding. The examples demonstrate that, at the molecular level, binding modes and thermodynamic binding signatures can be very different even for closely related ligands. However, deviating binding profiles provide the opportunity to optimally address a given target.


  • Organizational Affiliation

    Department of Pharmaceutical Chemistry, Philipps University Marburg, Marbacher Weg 6, 35032 Marburg, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cationic trypsin223Bos taurusMutation(s): 0 
EC: 3.4.21.4
UniProt
Find proteins for P00760 (Bos taurus)
Explore P00760 
Go to UniProtKB:  P00760
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00760
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
10U PDBBind:  3LJJ Kd: 300 (nM) from 1 assay(s)
Binding MOAD:  3LJJ Kd: 300 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Work: 0.253 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.6α = 90
b = 63.7β = 90
c = 69.2γ = 90
Software Package:
Software NamePurpose
SHELXL-97refinement
CNSrefinement
CrystalCleardata collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-10-06
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2012-12-12
    Changes: Other
  • Version 1.3: 2019-07-17
    Changes: Data collection, Refinement description
  • Version 1.4: 2023-09-06
    Changes: Data collection, Database references, Derived calculations, Refinement description