3GY3

A comparative study on the inhibition of bovine beta-trypsin by bis-benzamidines diminazene and pentamidine by X-ray crystallography and ITC


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.175 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural binding evidence of the trypanocidal drugs Berenil and Pentacarinate active principles to a serine protease model.

Perilo, C.S.Pereira, M.T.Santoro, M.M.Nagem, R.A.

(2010) Int.J.Biol.Macromol. 46: 502-511

  • DOI: 10.1016/j.ijbiomac.2010.03.006
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Bovine trypsin is a model system for the serine protease class of enzymes, which is an important target for contemporary medicinal chemistry. Some structural and thermodynamic reports are available on its interaction with benzamidine-based compounds ...

    Bovine trypsin is a model system for the serine protease class of enzymes, which is an important target for contemporary medicinal chemistry. Some structural and thermodynamic reports are available on its interaction with benzamidine-based compounds but no structural information is available so far on its binding modes to the active principles of the trypanocidal drugs Pentacarinate (pentamidine) and Berenil (diminazene). The crystallographic structures of bovine beta-trypsin in complex with the ligands were determined to a resolution of 1.57 A (diminazene) and 1.70 A (diminazene and pentamidine). The second benzamidine moieties in these inhibitors are bound to the enzyme in different hot spots and only few hydrogen bonds mediate these interactions. Thermodynamic parameters for the association of pentamidine with beta-trypsin reveal that this inhibitor has about 1.3-fold lower affinity than diminazene. Moreover its binding mode resembles other benzamidine-based compounds that assess the aryl binding pocket of the enzyme; however, with almost 2.5-fold higher affinity. This is the first structural evidence of the binding of Berenil and Pentacarinate active principles trypanocidal drugs to serine proteases.


    Organizational Affiliation

    Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Avenida Antônio Carlos 6627, Belo Horizonte, MG, CEP 31270-901, Brazil.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cationic trypsin
A
223Bos taurusMutation(s): 0 
EC: 3.4.21.4
Find proteins for P00760 (Bos taurus)
Go to UniProtKB:  P00760
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PNT
Query on PNT

Download SDF File 
Download CCD File 
A
1,5-BIS(4-AMIDINOPHENOXY)PENTANE
C19 H24 N4 O2
XDRYMKDFEDOLFX-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download SDF File 
Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download SDF File 
Download CCD File 
A
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
PNTKd: 2360 nM BINDINGMOAD
PNTKd: 2360 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.175 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 53.393α = 90.00
b = 53.393β = 90.00
c = 104.760γ = 120.00
Software Package:
Software NamePurpose
HKL-2000data collection
AMoREphasing
HKL-2000data reduction
HKL-2000data scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-03-23
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance