6T97 | pdb_00006t97

Trypanothione Reductase from Leismania infantum in complex with TRL190

PDB DOI: https://doi.org/10.2210/pdb6T97/pdb

Classification: FLAVOPROTEIN
Organism(s): Leishmania infantum
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2019-10-26 Released: 2020-11-18
Deposition Author(s): Carriles, A., Hermoso, J.A.
Funding Organization(s): Spanish Ministry of Economy and Competitiveness

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free:
0.258 (Depositor), 0.259 (DCC)
R-Value Work:
0.204 (Depositor), 0.208 (DCC)
R-Value Observed:
0.207 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Scaffold hopping identifies new triazole-and triazolium-based inhibitors of Leishmania infantum Trypanothione Reductase with potent and selective antileishmanial activity

Revuelto, A., de Lucio, H., Carriles, A., Garcia Soriano, J.C., Sanchez-Murcia, P.A., Hermoso, J.A., Gago, F., Camarasa, M.J., Jimenez-Ruiz, A., Velazquez, S.

To be published.

Macromolecule Content

Total Structure Weight: 54.95 kDa
Atom Count: 4,060
Modeled Residue Count: 489
Deposited Residue Count: 489
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Trypanothione reductase	A	489	Leishmania infantum	Mutation(s): 0 Gene Names: TRYR, LINF_050008500, LINJ_05_0350 EC: 1.8.1.12
UniProt
Find proteins for A4HSF7 (Leishmania infantum) Explore A4HSF7 Go to UniProtKB: A4HSF7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A4HSF7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FAD Query on FAD Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
MWW (Subject of Investigation/LOI) Query on MWW Download:Ideal Coordinates CCD File SDF format, chain K [auth A] MOL2 format, chain K [auth A] mmCIF format, chain K [auth A]	K [auth A]	4-[1-[4-[4-(2-phenylethyl)-1,3-thiazol-2-yl]-3-(2-piperidin-4-ylethoxy)phenyl]-1,2,3-triazol-4-yl]butan-1-amine C₃₀ H₃₈ N₆ O S YMQYETVMOWEEHG-UHFFFAOYSA-N		Interactions Focus chain K [auth A] Interactions & Density Focus chain K [auth A]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A]	C [auth A] D [auth A] E [auth A] F [auth A] G [auth A] C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A]	I [auth A], J [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain J [auth A] Interactions & Density Focus chain I [auth A] Focus chain J [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free: 0.258 (Depositor), 0.259 (DCC)
R-Value Work: 0.204 (Depositor), 0.208 (DCC)
R-Value Observed: 0.207 (Depositor)

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 103.11	α = 90
b = 103.11	β = 90
c = 191.675	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2020-11-18

Deposition Author(s):

Carriles, A.

Hermoso, J.A.

Funding Organization	Location	Grant Number
Spanish Ministry of Economy and Competitiveness	Spain	--

Revision History (Full details and data files)

Version 1.0: 2020-11-18
Type: Initial release
Version 1.1: 2021-06-02
Changes: Refinement description
Version 1.2: 2024-01-24
Changes: Data collection, Database references, Refinement description
Version 1.3: 2024-10-16
Changes: Structure summary

6T97 | pdb_00006t97

Trypanothione Reductase from Leismania infantum in complex with TRL190

Literature

Scaffold hopping identifies new triazole-and triazolium-based inhibitors of Leishmania infantum Trypanothione Reductase with potent and selective antileishmanial activity

Biological Assembly 1

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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