2YHU

Trypanosoma brucei PTR1 in complex with inhibitor WHF30


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.01 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.235 
  • R-Value Observed: 0.237 

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:  
    4WCD, 4WCF, 2YHU, 2YHI, 5IZC

  • 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 ( Tb ) ...

    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 Tb PTR1-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 Tb PTR1 with low toxicity. In particular, compound 4m , a biphenyl-thiadiazole-2,5-diamine with IC 50 = 16 μM, was able to potentiate the antitrypanosomal activity of the dihydrofolate reductase inhibitor methotrexate (MTX) with a 4.1-fold decrease of the EC 50 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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PTERIDINE REDUCTASEA, B, C, D288Trypanosoma bruceiMutation(s): 0 
EC: 1.5.1.33
UniProt
Find proteins for O76290 (Trypanosoma brucei brucei)
Explore O76290 
Go to UniProtKB:  O76290
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NDP
Query on NDP

Download Ideal Coordinates CCD File 
E [auth A], G [auth B], J [auth C], L [auth D]NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H30 N7 O17 P3
ACFIXJIJDZMPPO-NNYOXOHSSA-N
 Ligand Interaction
WHF
Query on WHF

Download Ideal Coordinates CCD File 
F [auth A], H [auth B], K [auth C], M [auth D]3-(5-AMINO-1,3,4-THIADIAZOL-2-YL)-1-THIOPHEN-2-YLPROPAN-1-ONE
C9 H9 N3 O S2
ODSWRTIXISBLTP-UHFFFAOYSA-N
 Ligand Interaction
ACT
Query on ACT

Download Ideal Coordinates CCD File 
I [auth B], N [auth D]ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CSX
Query on CSX
A, B, C, DL-PEPTIDE LINKINGC3 H7 N O3 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.01 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.235 
  • R-Value Observed: 0.237 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.55α = 90
b = 90.29β = 115.43
c = 82.46γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-05-23
    Type: Initial release
  • Version 1.1: 2017-09-27
    Changes: Database references, Structure summary
  • Version 1.2: 2017-10-18
    Changes: Database references