4WCD

Trypanosoma brucei PTR1 in complex with inhibitor 10


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.68 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.182 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Exploiting the 2-Amino-1,3,4-thiadiazole Scaffold To Inhibit Trypanosoma brucei Pteridine Reductase in Support of Early-Stage Drug Discovery.

Linciano, P.Dawson, A.Pohner, I.Costa, D.M.Sa, M.S.Cordeiro-da-Silva, A.Luciani, R.Gul, S.Witt, G.Ellinger, B.Kuzikov, M.Gribbon, P.Reinshagen, J.Wolf, M.Behrens, B.Hannaert, V.Michels, P.A.M.Nerini, E.Pozzi, C.di Pisa, F.Landi, G.Santarem, N.Ferrari, S.Saxena, P.Lazzari, S.Cannazza, G.Freitas-Junior, L.H.Moraes, C.B.Pascoalino, B.S.Alcantara, L.M.Bertolacini, C.P.Fontana, V.Wittig, U.Muller, W.Wade, R.C.Hunter, W.N.Mangani, S.Costantino, L.Costi, M.P.

(2017) ACS Omega 2: 5666-5683

  • DOI: 10.1021/acsomega.7b00473
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Pteridine reductase-1 (PTR1) is a promising drug target for the treatment of trypanosomiasis. We investigated the potential of a previously identified class of thiadiazole inhibitors of Leishmania major PTR1 for activity against Trypanosoma brucei (T ...

    Pteridine reductase-1 (PTR1) is a promising drug target for the treatment of trypanosomiasis. We investigated the potential of a previously identified class of thiadiazole inhibitors of Leishmania major PTR1 for activity against Trypanosoma brucei (Tb). We solved crystal structures of several TbPTR1-inhibitor complexes to guide the structure-based design of new thiadiazole derivatives. Subsequent synthesis and enzyme- and cell-based assays confirm new, mid-micromolar inhibitors of TbPTR1 with low toxicity. In particular, compound 4m, a biphenyl-thiadiazole-2,5-diamine with IC50 = 16 μM, was able to potentiate the antitrypanosomal activity of the dihydrofolate reductase inhibitor methotrexate (MTX) with a 4.1-fold decrease of the EC50 value. In addition, the antiparasitic activity of the combination of 4m and MTX was reversed by addition of folic acid. By adopting an efficient hit discovery platform, we demonstrate, using the 2-amino-1,3,4-thiadiazole scaffold, how a promising tool for the development of anti-T. brucei agents can be obtained.


    Organizational Affiliation

    Dipartimento di Scienze della Vita, Università degli Studi di Modena e Reggio Emilia, Via Campi 103, 41125 Modena, Italy.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Pteridine reductase
A, B, C, D
268Trypanosoma brucei bruceiMutation(s): 0 
Gene Names: PTR1
Find proteins for O76290 (Trypanosoma brucei brucei)
Go to UniProtKB:  O76290
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
3KH
Query on 3KH

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Download CCD File 
A, B, D
5-(1H-benzotriazol-6-yl)-1,3,4-thiadiazol-2-amine
C8 H6 N6 S
QEDRDOHUKCLXOP-UHFFFAOYSA-N
 Ligand Interaction
ACT
Query on ACT

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Download CCD File 
A, C
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

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Download CCD File 
B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
NAP
Query on NAP

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Download CCD File 
A, B, D
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE
C21 H28 N7 O17 P3
XJLXINKUBYWONI-NNYOXOHSSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.68 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.182 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 74.860α = 90.00
b = 89.230β = 115.53
c = 82.650γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
MOLREPphasing
REFMACrefinement
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-09-30
    Type: Initial release
  • Version 1.1: 2017-09-27
    Type: Database references, Structure summary
  • Version 1.2: 2017-10-18
    Type: Database references