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 
  • R-Value Observed: 0.210 

wwPDB Validation   3D Report Full Report


This is version 1.2 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: https://doi.org/10.1080/14756366.2016.1250755
  • Primary Citation of Related Structures:  
    5EBK

  • 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 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) (IC 50  = 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 (K i 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Trypanothione reductase
A, B
511Leishmania infantumMutation(s): 0 
Gene Names: TRYRLINJ_05_0350
EC: 1.8.1.12
UniProt
Find proteins for A4HSF7 (Leishmania infantum)
Explore A4HSF7 
Go to UniProtKB:  A4HSF7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA4HSF7
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FAD
Query on FAD

Download Ideal Coordinates CCD File 
C [auth A],
I [auth B]
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
RDS
Query on RDS

Download Ideal Coordinates CCD File 
D [auth A]
E [auth A]
F [auth A]
H [auth B]
J [auth B]
D [auth A],
E [auth A],
F [auth A],
H [auth B],
J [auth B],
K [auth B],
L [auth B]
6-sec-Butoxy-2-[(3-chlorophenyl)sulfanyl]-4-pyrimidinamine
C14 H16 Cl N3 O S
YBCXWCRIGXVZRG-SECBINFHSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
G [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.51 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.210 
  • Space Group: P 41
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 102.5α = 90
b = 102.5β = 90
c = 192γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MxCuBEdata collection
XDSdata reduction
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-10-26
    Type: Initial release
  • Version 1.1: 2017-11-01
    Changes: Database references
  • Version 1.2: 2024-01-10
    Changes: Data collection, Database references, Refinement description