4APN

Structure of TR from Leishmania infantum in complex with a diarylpirrole-based inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.239 

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 Azole-Based Compounds: A Comparative Analysis with its Physiological Substrate by X-Ray Crystallography.

Baiocco, P.Poce, G.Alfonso, S.Cocozza, M.Porretta, G.C.Colotti, G.Biava, M.Moraca, F.Botta, M.Yardley, V.Fiorillo, A.Lantella, A.Malatesta, F.Ilari, A.

(2013) Chemmedchem 8: 1175

  • DOI: 10.1002/cmdc.201300176
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Herein we report a study aimed at discovering a new class of compounds that are able to inhibit Leishmania donovani cell growth. Evaluation of an in-house library of compounds in a whole-cell screening assay highlighted 4-((1-(4-ethylphenyl)-2-methyl ...

    Herein we report a study aimed at discovering a new class of compounds that are able to inhibit Leishmania donovani cell growth. Evaluation of an in-house library of compounds in a whole-cell screening assay highlighted 4-((1-(4-ethylphenyl)-2-methyl-5-(4-(methylthio)phenyl)-1H-pyrrol-3-yl)methyl)thiomorpholine (compound 1) as the most active. Enzymatic assays on Leishmania infantum trypanothione reductase (LiTR, belonging to the Leishmania donovani complex) shed light on both the interaction with, and the nature of inhibition by, compound 1. A molecular modeling approach based on docking studies and on the estimation of the binding free energy aided our rationalization of the biological data. Moreover, X-ray crystal structure determination of LiTR in complex with compound 1 confirmed all our results: compound 1 binds to the T(SH)2 binding site, lined by hydrophobic residues such as Trp21 and Met113, as well as residues Glu18 and Tyr110. Analysis of the structure of LiTR in complex with trypanothione shows that Glu18 and Tyr110 are also involved in substrate binding, according to a competitive inhibition mechanism.


    Organizational Affiliation

    Dipartimento di Scienze Biochimiche, Sapienza Università di Roma, Piazzale A. Moro 5, 00185 Roma, Italy.




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
JV0
Query on JV0

Download SDF File 
Download CCD File 
B
4-[[1-(4-ethylphenyl)-2-methyl-5-(4-methylsulfanylphenyl)pyrrol-3-yl]methyl]thiomorpholine
C25 H30 N2 S2
NFXQXSBKNGTIEG-UHFFFAOYSA-N
 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
NDP
Query on NDP

Download SDF File 
Download CCD File 
A, B
NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H30 N7 O17 P3
ACFIXJIJDZMPPO-NNYOXOHSSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.239 
  • Space Group: P 41
Unit Cell:
Length (Å)Angle (°)
a = 102.561α = 90.00
b = 102.561β = 90.00
c = 191.985γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
MOLREPphasing
REFMACrefinement
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-04-17
    Type: Initial release
  • Version 1.1: 2013-06-26
    Type: Database references, Refinement description
  • Version 1.2: 2013-07-10
    Type: Database references