7NVP | pdb_00007nvp

Trypanothione reductase from Trypanosoma brucei in complex with N-{4-methoxy-3-[(4-methoxyphenyl)sulfamoyl]phenyl}-5-nitrothiophene-2-carboxamide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 
    0.278 (Depositor), 0.280 (DCC) 
  • R-Value Work: 
    0.240 (Depositor), 0.243 (DCC) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 7NVP

Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

Optimization of Potent and Specific Trypanothione Reductase Inhibitors: A Structure-Based Drug Discovery Approach.

Battista, T.Federico, S.Brogi, S.Pozzetti, L.Khan, T.Butini, S.Ramunno, A.Fiorentino, E.Orsini, S.Di Muccio, T.Fiorillo, A.Exertier, C.Di Risola, D.Colotti, G.Gemma, S.Ilari, A.Campiani, G.

(2022) ACS Infect Dis 8: 1687-1699

  • DOI: https://doi.org/10.1021/acsinfecdis.2c00325
  • Primary Citation Related Structures: 
    7NVP

  • PubMed Abstract: 

    Leishmania spp. are responsible for up to 1 million new cases each year. The current therapeutic arsenal against Leishmania is largely inadequate, and there is an urgent need for better drugs. Trypanothione reductase (TR) represents a druggable target since it is essential for the parasite and not shared by the human host. Here, we report the optimization of a novel class of potent and selective Li TR inhibitors realized through a concerted effort involving X-ray crystallography, synthesis, structure-activity relationship (SAR) investigation, molecular modeling, and in vitro phenotypic assays. 5-Nitrothiophene-2-carboxamides 3 , 6e , and 8 were among the most potent and selective TR inhibitors identified in this study. 6e and 8 displayed leishmanicidal activity in the low micromolar range coupled to SI > 50. Our studies could pave the way for the use of TR inhibitors not only against leishmaniasis but also against other trypanosomatidae due to the structural similarity of TR enzymes.


  • Organizational Affiliation
    • Institute of Molecular Biology and Pathology (IBPM) of the National Research Council of Italy (CNR), c/o Department of Biochemical Sciences, Sapienza University of Rome, Piazzale A. Moro 5, 00185Roma, Italy.

Macromolecule Content 

  • Total Structure Weight: 109.97 kDa 
  • Atom Count: 7,868 
  • Modeled Residue Count: 979 
  • Deposited Residue Count: 986 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
N(1),N(8)-bis(glutathionyl)spermidine reductaseA [auth AAA],
B [auth BBB]
493Trypanosoma brucei brucei TREU927Mutation(s): 0 
Gene Names: Tb10.406.0520
EC: 1.8.1.12
UniProt
Find proteins for Q389T8 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
Explore Q389T8 
Go to UniProtKB:  Q389T8
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ389T8
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FAD

Query on FAD



Download:Ideal Coordinates CCD File
C [auth AAA],
J [auth BBB]
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
UT2
(Subject of Investigation/LOI)

Query on UT2



Download:Ideal Coordinates CCD File
D [auth AAA],
K [auth BBB]
N-{4-methoxy-3-[(4-methoxyphenyl)sulfamoyl]phenyl}-5-nitrothiophene-2-carboxamide
C19 H17 N3 O7 S2
DYOXCKGIGMXWNR-UHFFFAOYSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
F [auth AAA]
G [auth AAA]
H [auth AAA]
I [auth AAA]
L [auth BBB]
F [auth AAA],
G [auth AAA],
H [auth AAA],
I [auth AAA],
L [auth BBB],
M [auth BBB],
N [auth BBB]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL

Query on GOL



Download:Ideal Coordinates CCD File
E [auth AAA]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free:  0.278 (Depositor), 0.280 (DCC) 
  • R-Value Work:  0.240 (Depositor), 0.243 (DCC) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.096α = 90
b = 133.334β = 90
c = 158.912γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Italian Ministry of EducationItalyFISR2019_03796 PROLEISH

Revision History  (Full details and data files)

  • Version 1.0: 2022-03-30
    Type: Initial release
  • Version 1.1: 2022-10-26
    Changes: Database references, Derived calculations
  • Version 1.2: 2024-01-31
    Changes: Data collection, Refinement description
  • Version 1.3: 2024-10-23
    Changes: Structure summary