2YHI

Trypanosoma brucei PTR1 in complex with inhibitor WH16


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.180 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 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: https://doi.org/10.1021/acsomega.7b00473
  • Primary Citation of Related Structures:  
    2YHI, 2YHU, 4WCD, 4WCF, 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 ). 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)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PTERIDINE REDUCTASE, PUTATIVE
A, C
288Trypanosoma bruceiMutation(s): 0 
EC: 1.5.1.33
UniProt
Find proteins for Q581W1 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
Explore Q581W1 
Go to UniProtKB:  Q581W1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ581W1
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
PTERIDINE REDUCTASE, PUTATIVE
B, D
288Trypanosoma bruceiMutation(s): 0 
EC: 1.5.1.33
UniProt
Find proteins for Q581W1 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
Explore Q581W1 
Go to UniProtKB:  Q581W1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ581W1
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAP
Query on NAP

Download Ideal Coordinates CCD File 
E [auth A],
I [auth B],
L [auth C],
O [auth D]
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H28 N7 O17 P3
XJLXINKUBYWONI-NNYOXOHSSA-N
W16
Query on W16

Download Ideal Coordinates CCD File 
F [auth A],
J [auth B],
M [auth C],
P [auth D]
5-(2-CHLOROETHYL)-1,3,4-THIADIAZOL-2-AMINE
C4 H6 Cl N3 S
XGIWQRDVHNRICP-UHFFFAOYSA-N
DTU
Query on DTU

Download Ideal Coordinates CCD File 
K [auth B](2R,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL
C4 H10 O2 S2
VHJLVAABSRFDPM-ZXZARUISSA-N
DTT
Query on DTT

Download Ideal Coordinates CCD File 
N [auth C],
Q [auth D]
2,3-DIHYDROXY-1,4-DITHIOBUTANE
C4 H10 O2 S2
VHJLVAABSRFDPM-IMJSIDKUSA-N
DTV
Query on DTV

Download Ideal Coordinates CCD File 
G [auth A](2S,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL
C4 H10 O2 S2
VHJLVAABSRFDPM-QWWZWVQMSA-N
ACT
Query on ACT

Download Ideal Coordinates CCD File 
H [auth A],
R [auth D]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
CSX
Query on CSX
A, C
L-PEPTIDE LINKINGC3 H7 N O3 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.180 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.28α = 90
b = 90.74β = 115.66
c = 84.29γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


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
  • Version 1.3: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description