5EBK

Trypanothione reductase in complex with 6-(sec-butoxy)-2-((3-chlorophenyl)thio)pyrimidin-4-amine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.51 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.208 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Inhibition of Leishmania infantum trypanothione reductase by diaryl sulfide derivatives.

Saccoliti, F.Angiulli, G.Pupo, G.Pescatori, L.Madia, V.N.Messore, A.Colotti, G.Fiorillo, A.Scipione, L.Gramiccia, M.Di Muccio, T.Di Santo, R.Costi, R.Ilari, A.

(2017) J Enzyme Inhib Med Chem 32: 304-310

  • DOI: 10.1080/14756366.2016.1250755

  • PubMed Abstract: 
  • The study presented here aimed at identifying a new class of compounds acting against Leishmania parasites, the causative agent of Leishmaniasis. For this purpose, the thioether derivatives of our in-house library have been evaluated in whole-cell sc ...

    The study presented here aimed at identifying a new class of compounds acting against Leishmania parasites, the causative agent of Leishmaniasis. For this purpose, the thioether derivatives of our in-house library have been evaluated in whole-cell screening assays in order to determine their in vitro activity against Leishmania protozoan. Among them, promising results have been achieved with compound RDS 777 (6-(sec-butoxy)-2-((3-chlorophenyl)thio)pyrimidin-4-amine) (IC50 = 29.43 µM), which is able to impair the mechanism of the parasite defence against the reactive oxygen species by inhibiting the trypanothione reductase (TR) with high efficiency (Ki 0.25 ± 0.18 µM). The X-ray structure of L. infantum TR in complex with RDS 777 disclosed the mechanism of action of this compound that binds to the catalytic site and engages in hydrogen bonds the residues more involved in the catalysis, namely Glu466', Cys57 and Cys52, thereby inhibiting the trypanothione binding and avoiding its reduction.


    Organizational Affiliation

    a Istituto Pasteur-Fondazione Cenci Bolognetti , Dipartimento di Chimica e Tecnologie del Farmaco , "Sapienza" Università di Roma , Roma , Italia.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Trypanothione reductase
A, B
511Leishmania infantumMutation(s): 0 
Gene Names: TRYR
EC: 1.8.1.12
Find proteins for A4HSF7 (Leishmania infantum)
Go to UniProtKB:  A4HSF7
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

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

Download SDF File 
Download CCD File 
A, B
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
 Ligand Interaction
RDS
Query on RDS

Download SDF File 
Download CCD File 
A, B
6-sec-Butoxy-2-[(3-chlorophenyl)sulfanyl]-4-pyrimidinamine
C14 H16 Cl N3 O S
YBCXWCRIGXVZRG-SECBINFHSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.51 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.208 
  • Space Group: P 41
Unit Cell:
Length (Å)Angle (°)
a = 102.500α = 90.00
b = 102.500β = 90.00
c = 192.000γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
MOLREPphasing
MxCuBEdata collection
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-10-26
    Type: Initial release
  • Version 1.1: 2017-11-01
    Type: Database references