Trypanosoma brucei PTR1 in complex with inhibitor 4g (F133)

Experimental Data Snapshot

  • Resolution: 1.74 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.154 
  • R-Value Observed: 0.156 

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Ligand Structure Quality Assessment 

This is version 1.3 of the entry. See complete history


Enhancement of Benzothiazoles as Pteridine Reductase-1 Inhibitors for the Treatment of Trypanosomatidic Infections.

Linciano, P.Pozzi, C.Iacono, L.D.di Pisa, F.Landi, G.Bonucci, A.Gul, S.Kuzikov, M.Ellinger, B.Witt, G.Santarem, N.Baptista, C.Franco, C.Moraes, C.B.Muller, W.Wittig, U.Luciani, R.Sesenna, A.Quotadamo, A.Ferrari, S.Pohner, I.Cordeiro-da-Silva, A.Mangani, S.Costantino, L.Costi, M.P.

(2019) J Med Chem 62: 3989-4012

  • DOI: https://doi.org/10.1021/acs.jmedchem.8b02021
  • Primary Citation of Related Structures:  
    6GCK, 6GCL, 6GCP, 6GCQ, 6GD0, 6GD4, 6GDO, 6GDP, 6GEX, 6GEY

  • PubMed Abstract: 

    2-Amino-benzo[ d]thiazole was identified as a new scaffold for the development of improved pteridine reductase-1 (PTR1) inhibitors and anti-trypanosomatidic agents. Molecular docking and crystallography guided the design and synthesis of 42 new benzothiazoles. The compounds were assessed for Trypanosoma brucei and Leishmania major PTR1 inhibition and in vitro activity against T. brucei and amastigote Leishmania infantum. We identified several 2-amino-benzo[ d]thiazoles with improved enzymatic activity ( TbPTR1 IC 50 = 0.35 μM; LmPTR1 IC 50 = 1.9 μM) and low μM antiparasitic activity against T. brucei. The ten most active compounds against TbPTR1 were able to potentiate the antiparasitic activity of methotrexate when evaluated in combination against T. brucei, with a potentiating index between 1.2 and 2.7. The compound library was profiled for early ADME toxicity, and 2-amino- N-benzylbenzo[ d]thiazole-6-carboxamide (4c) was finally identified as a novel potent, safe, and selective anti-trypanocydal agent (EC 50 = 7.0 μM). Formulation of 4c with hydroxypropyl-β-cyclodextrin yielded good oral bioavailability, encouraging progression to in vivo studies.

  • Organizational Affiliation

    Dipartimento di Scienze della Vita , University of Modena and Reggio Emilia , Via Campi 103 , 41125 Modena , Italy.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Pteridine reductase
A, B, C, D
288Trypanosoma brucei bruceiMutation(s): 0 
Gene Names: PTR1
Find proteins for O76290 (Trypanosoma brucei brucei)
Explore O76290 
Go to UniProtKB:  O76290
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO76290
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on NAP

Download Ideal Coordinates CCD File 
E [auth A],
H [auth B],
J [auth C],
K [auth D]
C21 H28 N7 O17 P3
Query on EV8

Download Ideal Coordinates CCD File 
F [auth A],
I [auth B],
L [auth D]
methyl 1-[4-[[(2-azanyl-1,3-benzothiazol-6-yl)carbonylamino]methyl]phenyl]carbonylpiperidine-4-carboxylate
C23 H24 N4 O4 S
Query on ACT

Download Ideal Coordinates CCD File 
G [auth A],
M [auth D]
C2 H3 O2
Binding Affinity Annotations 
IDSourceBinding Affinity
EV8 Binding MOAD:  6GD0 IC50: 2.18e+4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.74 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.154 
  • R-Value Observed: 0.156 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.96α = 90
b = 91.12β = 115.9
c = 82.97γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
European Commission603240

Revision History  (Full details and data files)

  • Version 1.0: 2019-04-03
    Type: Initial release
  • Version 1.1: 2019-04-17
    Changes: Data collection, Database references
  • Version 1.2: 2019-05-08
    Changes: Data collection, Database references
  • Version 1.3: 2024-01-17
    Changes: Data collection, Database references, Refinement description