4APN

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.239 
  • R-Value Observed: 0.241 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.3 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: https://doi.org/10.1002/cmdc.201300176
  • Primary Citation of Related Structures:  
    4ADW, 4APN

  • 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-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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
TRYPANOTHIONE REDUCTASE
A, B
511Leishmania infantumMutation(s): 0 
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],
E [auth B]
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
NDP
Query on NDP

Download Ideal Coordinates CCD File 
D [auth A],
F [auth B]
NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H30 N7 O17 P3
ACFIXJIJDZMPPO-NNYOXOHSSA-N
JV0
Query on JV0

Download Ideal Coordinates CCD File 
G [auth B],
H [auth B],
I [auth B],
J [auth B]
4-[[1-(4-ethylphenyl)-2-methyl-5-(4-methylsulfanylphenyl)pyrrol-3-yl]methyl]thiomorpholine
C25 H30 N2 S2
NFXQXSBKNGTIEG-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.239 
  • R-Value Observed: 0.241 
  • Space Group: P 41
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 102.561α = 90
b = 102.561β = 90
c = 191.985γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-04-17
    Type: Initial release
  • Version 1.1: 2013-06-26
    Changes: Database references, Refinement description
  • Version 1.2: 2013-07-10
    Changes: Database references
  • Version 1.3: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description