5IZC | pdb_00005izc

Trypanosoma brucei PTR1 in complex with inhibitor F032

• PDB DOI: https://doi.org/10.2210/pdb5IZC/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Trypanosoma brucei brucei
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2016-03-25 Released: 2017-04-05 
• Deposition Author(s): Pozzi, C., Landi, G., Di Pisa, F., Mangani, S.
• Funding Organization(s): European Commission

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.92 Å
• R-Value Free: 
  0.206 (Depositor), 0.216 (DCC) 
• R-Value Work: 
  0.161 (Depositor), 0.172 (DCC) 
• R-Value Observed: 
  0.163 (Depositor) 

Starting Model: experimental

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

• PubMed: 28983525 
• DOI: https://doi.org/10.1021/acsomega.7b00473
• Primary Citation 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.

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Organizational Affiliation: 
• Dipartimento di Scienze della Vita, Università degli Studi di Modena e Reggio Emilia, Via Campi 103, 41125 Modena, Italy.
Biological Chemistry & Drug Discovery, School of Life Sciences, The Wellcome Trust Building, University of Dundee, Dow Street, Dundee DD1 5EH, U.K.
Molecular and Cellular Modeling Group and Scientific Databases and Visualization (SDBV) Group, Heidelberg Institute for Theoretical Studies, Schloss-Wolfsbrunnenweg 35, D-69118 Heidelberg, Germany.
Instituto de Investigação e Inovação em Saúde, Instituto de Biologia Molecular e Celular, and Departamento de Ciências Biológicas, Universidade do Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal.
Fraunhofer-IME SP, Schnackenburgallee 114, D-22525 Hamburg, Germany.
Research Unit for Tropical Diseases, de Duve Institute and Laboratory of Biochemistry, Université catholique de Louvain, Avenue Hippocrate 74, B-1200 Brussels, Belgium.
University of Siena, Via Aldo Moro 2, 53100 Siena, Italy.
Laboratório Nacional de Biociências CNPEM, Centro Nacional de Pesquisa em Energia e Materials, Rua Giuseppe Máximo Scolfaro, 10.000, CEP 13083-970 Campinas/SP, Brasil.
Center for Molecular Biology (ZMBH), DKFZ-ZMBH Alliance, Heidelberg University, Im Neuenheimer Feld 282, D-69120 Heidelberg, Germany.
Interdisciplinary Center for Scientific Computing (IWR), Heidelberg University, Im Neuenheimer Feld 205, D-69120 Heidelberg, Germany.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 118.44 kDa 
• Atom Count: 8,206 
• Modeled Residue Count: 985 
• Deposited Residue Count: 1,072 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pteridine reductase	A, B, D	268	Trypanosoma brucei brucei	Mutation(s): 0  Gene Names: PTR1 EC: 1.5.1.33
UniProt
Find proteins for O76290 (Trypanosoma brucei brucei) Explore O76290  Go to UniProtKB:  O76290

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Pteridine reductase	C	268	Trypanosoma brucei brucei	Mutation(s): 0  Gene Names: PTR1 EC: 1.5.1.33
UniProt
Find proteins for O76290 (Trypanosoma brucei brucei) Explore O76290  Go to UniProtKB:  O76290

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAP	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
6F4	F [auth A], J [auth B], M [auth C], P [auth D]	N~2~-[(thiophen-2-yl)methyl]-1,3,4-thiadiazole-2,5-diamine C7 H8 N4 S2 KYOKGDLJKFUPBK-UHFFFAOYSA-N
GOL	K [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ACT	G [auth A], H [auth A], N [auth C]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CME	A, B, D	L-PEPTIDE LINKING	C5 H11 N O3 S2		CYS
OCS	C	L-PEPTIDE LINKING	C3 H7 N O5 S		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.92 Å
• R-Value Free:  0.206 (Depositor), 0.216 (DCC) 
• R-Value Work:  0.161 (Depositor), 0.172 (DCC) 
• R-Value Observed: 0.163 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.63	α = 90
b = 89.443	β = 115.87
c = 82.645	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SCALA	data scaling
PDB_EXTRACT	data extraction
iMOSFLM	data reduction
MOLREP	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2017-04-05 
Deposition Author(s): Pozzi, C., Landi, G., Di Pisa, F., Mangani, S.

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Funding Organization	Location	Grant Number
European Commission	Italy	603240

Revision History  

• Version 1.0: 2017-04-05
  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: 2024-01-10
  Changes: Data collection, Database references, Refinement description