8PF3 | pdb_00008pf3

Crystal structure of Trypanosoma brucei trypanothione reductase in complex with 1-(3,4-dichlorobenzyl)-4-(((5-((4-fluorophenethyl)carbamoyl)furan-2-yl)methyl)(4-fluorophenyl)carbamoyl)-1-(3-phenylpropyl)piperazin-1-ium


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 
    0.224 (Depositor), 0.228 (DCC) 
  • R-Value Work: 
    0.179 (Depositor), 0.186 (DCC) 
  • R-Value Observed: 
    0.181 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history

Literature

Fragment Merging, Growing, and Linking Identify New Trypanothione Reductase Inhibitors for Leishmaniasis.

Exertier, C.Salerno, A.Antonelli, L.Fiorillo, A.Ocello, R.Seghetti, F.Caciolla, J.Uliassi, E.Masetti, M.Fiorentino, E.Orsini, S.Di Muccio, T.Ilari, A.Bolognesi, M.L.

(2024) J Med Chem 67: 402-419

  • DOI: https://doi.org/10.1021/acs.jmedchem.3c01439
  • Primary Citation Related Structures: 
    8PF3, 8PF4, 8PF5

  • PubMed Abstract: 

    Trypanothione reductase (TR) is a suitable target for drug discovery approaches against leishmaniasis, although the identification of potent inhibitors is still challenging. Herein, we harnessed a fragment-based drug discovery (FBDD) strategy to develop new TR inhibitors. Previous crystallographic screening identified fragments 1 - 3 , which provided ideal starting points for a medicinal chemistry campaign. In silico investigations revealed critical hotspots in the TR binding site, guiding our structure- and ligand-based structure-actvity relationship (SAR) exploration that yielded fragment-derived compounds 4 - 14 . A trend of improvement in Leishmania infantum TR inhibition was detected along the optimization and confirmed by the crystal structures of 9 , 10 , and 14 in complex with Trypanosoma brucei TR. Compound 10 showed the best TR inhibitory profile ( K i = 0.2 μM), whereas 9 was the best one in terms of in vitro and ex vivo activity. Although further fine-tuning is needed to improve selectivity, we demonstrated the potentiality of FBDD on a classic but difficult target for leishmaniasis.


  • 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, Roma 00185, Italy.

Macromolecule Content 

  • Total Structure Weight: 220.61 kDa 
  • Atom Count: 16,115 
  • Modeled Residue Count: 1,954 
  • Deposited Residue Count: 1,980 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Trypanothione reductase
A, B, C, D
495Trypanosoma bruceiMutation(s): 0 
Gene Names: DPX39_100110900
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
E [auth A],
I [auth B],
L [auth C],
O [auth D]
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
YJ6
(Subject of Investigation/LOI)

Query on YJ6



Download:Ideal Coordinates CCD File
F [auth A],
J [auth B],
M [auth C],
P [auth D]
4-[(3,4-dichlorophenyl)methyl]-~{N}-(4-fluorophenyl)-~{N}-[[5-[2-(4-fluorophenyl)ethylcarbamoyl]furan-2-yl]methyl]-4-(3-phenylpropyl)-1,4$l^{4}-diazinane-1-carboxamide
C41 H41 Cl2 F2 N4 O3
YQJHJAGZYIUEMW-UHFFFAOYSA-N
PEG

Query on PEG



Download:Ideal Coordinates CCD File
G [auth A],
H [auth A],
N [auth C],
Q [auth D]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
IMD

Query on IMD



Download:Ideal Coordinates CCD File
K [auth B]IMIDAZOLE
C3 H5 N2
RAXXELZNTBOGNW-UHFFFAOYSA-O

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free:  0.224 (Depositor), 0.228 (DCC) 
  • R-Value Work:  0.179 (Depositor), 0.186 (DCC) 
  • R-Value Observed: 0.181 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 100.703α = 90
b = 63.742β = 97.75
c = 170.096γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Italian Ministry of EducationItalyFISR2019_03796

Revision History  (Full details and data files)

  • Version 1.0: 2024-04-03
    Type: Initial release
  • Version 1.1: 2024-11-06
    Changes: Structure summary