4K1F | pdb_00004k1f

Crystal structure of reduced tryparedoxin peroxidase from leishmania major at 2.34 A resolution

• PDB DOI: https://doi.org/10.2210/pdb4K1F/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Leishmania major
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2013-04-05 Released: 2014-04-09 
• Deposition Author(s): Ilari, A., Fiorillo, A., Di Chiaro, F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.34 Å
• R-Value Free: 
  0.247 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.194 (Depositor), 0.181 (DCC) 
• R-Value Observed: 
  0.196 (Depositor) 

Starting Model: experimental

Literature

Structure-based discovery of the first non-covalent inhibitors of Leishmania major tryparedoxin peroxidase by high throughput docking

Brindisi, M., Brogi, S., Relitti, N., Vallone, A., Butini, S., Gemma, S., Novellino, E., Colotti, G., Angiulli, G., Di Chiaro, F., Fiorillo, A., Ilari, A., Campiani, G.

(2015) Sci Rep 5: 9705-9705

• PubMed: 25951439 
• DOI: https://doi.org/10.1038/srep09705
• Primary Citation Related Structures: 
  4K1F


• PubMed Abstract: 
  

  Leishmaniasis is a neglected vector-born disease caused by a protozoan of the genus Leishmania and affecting more than 1.300.000 people worldwide. The couple tryparedoxin/tryparedoxin peroxidase is essential for parasite survival in the host since it neutralizes the hydrogen peroxide produced by macrophages during the infection. Herein we report a study aimed at discovering the first class of compounds able to non-covalently inhibit tryparedoxin peroxidase. We have solved the high-resolution structure of Tryparedoxin peroxidase I from Leishmania major (LmTXNPx) in the reduced state and in fully folded conformation. A first series of compounds able to inhibit LmTXNPx was identified by means of the high throughput docking technique. The inhibitory activity of these compounds was validated by a Horseradish peroxidase-based enzymatic assay and their affinity for LmTXNPx calculated by surface plasmon resonance experiments. On the basis of these results, the analysis of the enzyme-inhibitor docked models allowed us to rationally design and synthesize a series of N,N-disubstituted 3-aminomethyl quinolones. These compounds showed an inhibitory potency against LmTXNPx in the micromolar range. Among them, compound 12 represents the first non-covalent LmTXNPx inhibitor reported to date and could pave the way to the discovery of a new class of drugs against leishmaniasis.

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Organizational Affiliation: 
• 1] European Research Centre for Drug Discovery and Development (NatSynDrugs), University of Siena, via Aldo Moro 2, 53100, Siena [2] Dip. di Biotecnologie, Chimica e Farmacia, University of Siena, via Aldo Moro 2, 53100, Siena, Italy.
1] European Research Centre for Drug Discovery and Development (NatSynDrugs), University of Siena, via Aldo Moro 2, 53100, Siena [2] Dip. di Biotecnologie, Chimica e Farmacia, University of Siena, via Aldo Moro 2, 53100, Siena, Italy [3] Dip. di Farmacia, University of Naples Federico II, Via D. Montesano 49, 80131 Naples, Italy.
1] European Research Centre for Drug Discovery and Development (NatSynDrugs), University of Siena, via Aldo Moro 2, 53100, Siena [2] Dip. di Farmacia, University of Naples Federico II, Via D. Montesano 49, 80131 Naples, Italy.
Istituto Pasteur Fondazione Cenci-Bolognetti and Istituto di Biologia e Patologia Molecolari IBPM- CNR, c/o Dipartimento di Scienze Biochimiche, Sapienza Università di Roma Piazzale A. Moro 5, 00185 Roma (Italy).
Dipartimento di Scienze Biochimiche, Sapienza Università di Roma, Piazzale A. Moro 5, 00185 Roma (Italy).

Biological Assembly 1  

Global Symmetry: Dihedral - D5  (Explore in 3D)
Global Stoichiometry: Homo 10-mer - A10 

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

Macromolecule Content 

• Total Structure Weight: 111.89 kDa 
• Atom Count: 8,148 
• Modeled Residue Count: 987 
• Deposited Residue Count: 995 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tryparedoxin peroxidase	A, B, C, D, E	199	Leishmania major	Mutation(s): 0  Gene Names: TRYP3 EC: 1.11.1.15 (PDB Primary Data), 1.11.1.24 (UniProt)
UniProt
Find proteins for Q4QF76 (Leishmania major) Explore Q4QF76  Go to UniProtKB:  Q4QF76

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PE8	I [auth B]	3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL C16 H34 O9 GLZWNFNQMJAZGY-UHFFFAOYSA-N
PGE	F [auth A]	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N
PEG	H [auth B], J [auth C], L [auth D], N [auth E]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
CL	G [auth A], K [auth C], M [auth D], O [auth E]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.34 Å
• R-Value Free:  0.247 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.194 (Depositor), 0.181 (DCC) 
• R-Value Observed: 0.196 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 111.811	α = 90
b = 226.203	β = 90
c = 91.719	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
XDS	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-04-09 
Deposition Author(s): Ilari, A., Fiorillo, A., Di Chiaro, F.

Revision History  

• Version 1.0: 2014-04-09
  Type: Initial release
  
• Version 1.1: 2014-07-30
  Changes: Data collection
• Version 1.2: 2015-06-10
  Changes: Database references
• Version 1.3: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description