5K6A | pdb_00005k6a

Trypanosoma brucei Pteridine reductase 1 (PTR1) in complex with compound 1

• PDB DOI: https://doi.org/10.2210/pdb5K6A/pdb

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


• Deposited: 2016-05-24 Released: 2017-03-22 
• Deposition Author(s): Landi, G., Pozzi, C., Di Pisa, F., Dello lacono, L., Mangani, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.220 (Depositor), 0.218 (DCC) 
• R-Value Work: 
  0.180 (Depositor) 
• R-Value Observed: 
  0.182 (Depositor) 

Starting Model: experimental

Literature

Chroman-4-One Derivatives Targeting Pteridine Reductase 1 and Showing Anti-Parasitic Activity.

Di Pisa, F., Landi, G., Dello Iacono, L., Pozzi, C., Borsari, C., Ferrari, S., Santucci, M., Santarem, N., Cordeiro-da-Silva, A., Moraes, C.B., Alcantara, L.M., Fontana, V., Freitas-Junior, L.H., Gul, S., Kuzikov, M., Behrens, B., Pohner, I., Wade, R.C., Costi, M.P., Mangani, S.

(2017) Molecules 22

• PubMed: 28282886 
• DOI: https://doi.org/10.3390/molecules22030426
• Primary Citation Related Structures: 
  5K6A, 5L42, 5L4N


• PubMed Abstract: 
  

  Flavonoids have previously been identified as antiparasitic agents and pteridine reductase 1 (PTR1) inhibitors. Herein, we focus our attention on the chroman-4-one scaffold. Three chroman-4-one analogues ( 1 - 3 ) of previously published chromen-4-one derivatives were synthesized and biologically evaluated against parasitic enzymes ( Trypanosoma brucei PTR1- Tb PTR1 and Leishmania major-Lm PTR1) and parasites ( Trypanosoma brucei and Leishmania infantum ). A crystal structure of Tb PTR1 in complex with compound 1 and the first crystal structures of Lm PTR1-flavanone complexes (compounds 1 and 3 ) were solved. The inhibitory activity of the chroman-4-one and chromen-4-one derivatives was explained by comparison of observed and predicted binding modes of the compounds. Compound 1 showed activity both against the targeted enzymes and the parasites with a selectivity index greater than 7 and a low toxicity. Our results provide a basis for further scaffold optimization and structure-based drug design aimed at the identification of potent anti-trypanosomatidic compounds targeting multiple PTR1 variants.

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Organizational Affiliation: 
• Department of Biotechnology, Chemistry and Pharmacy, University of Siena, 53100 Siena, Italy. [e-mail].
Department of Biotechnology, Chemistry and Pharmacy, University of Siena, 53100 Siena, Italy. [e-mail].
Department of Biotechnology, Chemistry and Pharmacy, University of Siena, 53100 Siena, Italy. [e-mail].
Department of Biotechnology, Chemistry and Pharmacy, University of Siena, 53100 Siena, Italy. [e-mail].
Department of Life Sciences, University of Modena and Reggio Emilia, Via Campi 103, 41125 Modena, Italy. [e-mail].
Department of Life Sciences, University of Modena and Reggio Emilia, Via Campi 103, 41125 Modena, Italy. [e-mail].
Department of Life Sciences, University of Modena and Reggio Emilia, Via Campi 103, 41125 Modena, Italy. [e-mail].
Institute for Molecular and Cell Biology, 4150-180 Porto, Portugal and Instituto de Investigação e Inovação em Saúde, Universidade do Porto and Institute for Molecular and Cell Biology, 4150-180 Porto, Portugal. [e-mail].
Institute for Molecular and Cell Biology, 4150-180 Porto, Portugal and Instituto de Investigação e Inovação em Saúde, Universidade do Porto and Institute for Molecular and Cell Biology, 4150-180 Porto, Portugal. [e-mail].
Laboratório Nacional de Biociências (LNBio), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas SP13083-100, Brazil. [e-mail].
Laboratório Nacional de Biociências (LNBio), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas SP13083-100, Brazil. [e-mail].
Laboratório Nacional de Biociências (LNBio), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas SP13083-100, Brazil. [e-mail].
Laboratório Nacional de Biociências (LNBio), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas SP13083-100, Brazil. [e-mail].
GARDE, Instituto Butantan, São Paulo SP05503-900, Brazil. [e-mail].
Fraunhofer Institute for Molecular Biology and Applied Ecology Screening Port, D-22525 Hamburg, Germany. [e-mail].
Fraunhofer Institute for Molecular Biology and Applied Ecology Screening Port, D-22525 Hamburg, Germany. [e-mail].
Fraunhofer Institute for Molecular Biology and Applied Ecology Screening Port, D-22525 Hamburg, Germany. [e-mail].
Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies, 69118 Heidelberg, Germany. [e-mail].
Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies, 69118 Heidelberg, Germany. [e-mail].
Center for Molecular Biology (ZMBH), DKFZ-ZMBH Alliance, Heidelberg University, 69120 Heidelberg, Germany. [e-mail].
Interdisciplinary Center for Scientific Computing (IWR), Heidelberg University, 69120 Heidelberg, Germany. [e-mail].
Department of Life Sciences, University of Modena and Reggio Emilia, Via Campi 103, 41125 Modena, Italy. [e-mail].
Department of Biotechnology, Chemistry and Pharmacy, University of Siena, 53100 Siena, Italy. [e-mail].
Magnetic Resonance Center CERM, University of Florence, 50019 Sesto Fiorentino (FI), Italy. [e-mail].

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: 126.91 kDa 
• Atom Count: 8,396 
• Modeled Residue Count: 981 
• Deposited Residue Count: 1,152 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pteridine reductase	A, B, D	288	Trypanosoma brucei brucei	Mutation(s): 0  Gene Names: PTR1
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	288	Trypanosoma brucei brucei	Mutation(s): 0  Gene Names: PTR1
UniProt
Find proteins for O76290 (Trypanosoma brucei brucei) Explore O76290  Go to UniProtKB:  O76290

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAP	E [auth A], H [auth B], J [auth C], M [auth D]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H28 N7 O17 P3 XJLXINKUBYWONI-NNYOXOHSSA-N
6QT	F [auth A], I [auth B], K [auth C], N [auth D]	(2~{R})-2-(3-hydroxyphenyl)-6-oxidanyl-2,3-dihydrochromen-4-one C15 H12 O4 FTDCCBIDVVGONG-OAHLLOKOSA-N
ACT	G [auth A], L [auth C]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.220 (Depositor), 0.218 (DCC) 
• R-Value Work:  0.180 (Depositor) 
• R-Value Observed: 0.182 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.72	α = 90
b = 89.894	β = 115.75
c = 82.684	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-03-22 
Deposition Author(s): Landi, G., Pozzi, C., Di Pisa, F., Dello lacono, L., Mangani, S.

Revision History  

• Version 1.0: 2017-03-22
  Type: Initial release
  
• Version 1.1: 2024-01-10
  Changes: Data collection, Database references, Refinement description