7FGX | pdb_00007fgx

Toxoplasma gondii dihydrofolate reductase thymidylate synthase (TgDHFR-TS) complexed with P39, NADPH and dUMP

PDB DOI: https://doi.org/10.2210/pdb7FGX/pdb

Classification: OXIDOREDUCTASE
Organism(s): Toxoplasma gondii
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2021-07-28 Released: 2022-06-29
Deposition Author(s): Vanichtanankul, J., Yoomuang, A., Taweechai, S., Saeyang, T., Yuvaniyama, J., Tarnchompoo, B., Yuthavong, Y., Kamchonwongpaisan, S.
Funding Organization(s): The Thailand Research Fund (TRF)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.05 Å
R-Value Free:
0.214 (Depositor), 0.213 (DCC)
R-Value Work:
0.180 (Depositor), 0.180 (DCC)
R-Value Observed:
0.182 (Depositor)

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

Structural Insight into Effective Inhibitors' Binding to Toxoplasma gondii Dihydrofolate Reductase Thymidylate Synthase.

Vanichtanankul, J., Yoomuang, A., Taweechai, S., Saeyang, T., Pengon, J., Yuvaniyama, J., Tarnchompoo, B., Yuthavong, Y., Kamchonwongpaisan, S.

(2022) ACS Chem Biol 17: 1691-1702

PubMed: 35715223 Search on PubMed
DOI: https://doi.org/10.1021/acschembio.1c00627
Primary Citation Related Structures:
7FGW, 7FGX, 7FGY, 7XI7

PubMed Abstract:
Pyrimethamine (Pyr), a known dihydrofolate reductase (DHFR) inhibitor, has long been used to treat toxoplasmosis caused by Toxoplasma gondii (Tg) infection. However, Pyr is effective only at high doses with associated toxicity to patients, calling for safer alternative treatments. In this study, we investigated a series of Pyr analogues, previously developed as DHFR inhibitors of Plasmodium falciparum bifunctional DHFR-thymidylate synthase (PfDHFR-TS), for their activity against T. gondii DHFR-TS (TgDHFR-TS). Of these, a set of compounds with a substitution at the C ⁶ position of the pyrimidine ring exhibited high binding affinities (in a low nanomolar range) against TgDHFR-TS and in vitro T. gondii inhibitory activity. Three-dimensional structures of TgDHFR-TS reported here include the ternary complexes with Pyr, P39, or P40. A comparison of these structures showed the minor steric strain between the p -chlorophenyl group of Pyr and Thr83 of TgDHFR-TS. Such a conflict was relieved in the complexes with the two analogues, P39 and P40, explaining their highest binding affinities described herein. Moreover, these structures suggested that the hydrophobic environment in the active-site pocket could be used for drug design to increase the potency and selectivity of antifolate inhibitors. These findings would accelerate the development of new antifolate drugs to treat toxoplasmosis.

Organizational Affiliation

National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), 113 Thailand Science Park, Khlong Nueng, Khlong Luang, Pathum Thani 12120, Thailand.

Macromolecule Content

Total Structure Weight: 280.67 kDa
Atom Count: 19,328
Modeled Residue Count: 2,241
Deposited Residue Count: 2,440
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bifunctional dihydrofolate reductase-thymidylate synthase	A, B, C, D	610	Toxoplasma gondii	Mutation(s): 0 EC: 1.5.1.3 (PDB Primary Data), 2.1.1.45 (PDB Primary Data)
UniProt
Find proteins for Q07422 (Toxoplasma gondii) Explore Q07422 Go to UniProtKB: Q07422
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q07422
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NDP Query on NDP Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain H [auth B] SDF format, chain K [auth C] SDF format, chain N [auth D] MOL2 format, chain E [auth A] MOL2 format, chain H [auth B] MOL2 format, chain K [auth C] MOL2 format, chain N [auth D] mmCIF format, chain E [auth A] mmCIF format, chain H [auth B] mmCIF format, chain K [auth C] mmCIF format, chain N [auth D]	E [auth A], H [auth B], K [auth C], N [auth D]	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C₂₁ H₃₀ N₇ O₁₇ P₃ ACFIXJIJDZMPPO-NNYOXOHSSA-N		Interactions Focus chain E [auth A] Focus chain H [auth B] Focus chain K [auth C] Focus chain N [auth D] Interactions & Density Focus chain E [auth A] Focus chain H [auth B] Focus chain K [auth C] Focus chain N [auth D]
UMP Query on UMP Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain M [auth C] SDF format, chain P [auth D] SDF format, chain J [auth B] MOL2 format, chain G [auth A] MOL2 format, chain M [auth C] MOL2 format, chain P [auth D] MOL2 format, chain J [auth B] mmCIF format, chain G [auth A] mmCIF format, chain M [auth C] mmCIF format, chain P [auth D] mmCIF format, chain J [auth B]	G [auth A], J [auth B], M [auth C], P [auth D]	2'-DEOXYURIDINE 5'-MONOPHOSPHATE C₉ H₁₃ N₂ O₈ P JSRLJPSBLDHEIO-SHYZEUOFSA-N		Interactions Focus chain G [auth A] Focus chain J [auth B] Focus chain M [auth C] Focus chain P [auth D] Interactions & Density Focus chain G [auth A] Focus chain J [auth B] Focus chain M [auth C] Focus chain P [auth D]
4RI (Subject of Investigation/LOI) Query on 4RI Download:Ideal Coordinates CCD File SDF format, chain L [auth C] SDF format, chain O [auth D] SDF format, chain I [auth B] SDF format, chain F [auth A] MOL2 format, chain L [auth C] MOL2 format, chain O [auth D] MOL2 format, chain I [auth B] MOL2 format, chain F [auth A] mmCIF format, chain L [auth C] mmCIF format, chain O [auth D] mmCIF format, chain I [auth B] mmCIF format, chain F [auth A]	F [auth A], I [auth B], L [auth C], O [auth D]	6-hexyl-5-phenyl-pyrimidine-2,4-diamine C₁₆ H₂₂ N₄ DBCDYKFZHWOABJ-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain I [auth B] Focus chain L [auth C] Focus chain O [auth D] Interactions & Density Focus chain F [auth A] Focus chain I [auth B] Focus chain L [auth C] Focus chain O [auth D]