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Literature summary for 2.5.1.78 extracted from

  • Zhang, Y.; Jin, G.; Illarionov, B.; Bacher, A.; Fischer, M.; Cushman, M.
    A new series of 3-alkyl phosphate derivatives of 4,5,6,7-tetrahydro-1-D-ribityl-1H-pyrazolo[3,4-d]pyrimidinedione as inhibitors of lumazine synthase: design, synthesis, and evaluation (2007), J. Org. Chem., 72, 7176-7184.
    View publication on PubMed
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Crystallization (Commentary)

Crystallization (Comment) Organism
molecular modeling of enzyme in complex with inhibitor 3-(1,3,7-trihydro-9-D-ribityl-2,6,8-purinetrione-7-yl)pentane 1-phosphate. The pyrazolopyrimidinedione ring of the ligand is stacked with the indole ring of Trp27. The phosphate of the ligand is extensively hydrogen bonded with the one water molecule, the side chain nitrogens of Arg128, as well as the backbone nitrogens of Gln86 and Thr87 and the side-chain hydroxyl of Thr87. The ribityl hydroxyl groups are hydrogen bonded to the backbone nitrogen and oxygen of Asn114, the side-chain oxygens of Glu61, and the backbone nitrogen of Ile60. The pyrazolopyrimidinedione ring of the ligand is hydrogen bonded to the backbone nitrogen of Ala59, the backbone nitrogen of Ile83, backbone oxygen of Val81, and the side-chain nitrogen of Lys138 Mycobacterium tuberculosis
molecular modeling of enzyme in complex with inhibitor 3-(1,3,7-trihydro-9-D-ribityl-2,6,8-purinetrione-7-yl)pentane 1-phosphate. The pyrazolopyrimidinedione ring of the ligand is stacked with the indole ring of Trp27. The phosphate of the ligand is extensively hydrogen bonded with the one water molecule, the side chain nitrogens of Arg128, as well as the backbone nitrogens of Gln86 and Thr87 and the side-chain hydroxyl of Thr87. The ribityl hydroxyl groups are hydrogen bonded to the backbone nitrogen and oxygen of Asn114, the side-chain oxygens of Glu61, and the backbone nitrogen of Ile60. The pyrazolopyrimidinedione ring of the ligand is hydrogen bonded to the backbone nitrogen of Ala59, the backbone nitrogen of Ile83, backbone oxygen of Val81, and the side-chain nitrogen of Lys138 Candida albicans

Inhibitors

Inhibitors Comment Organism Structure
3-(1,3,7-trihydro-9-D-ribityl-2,6,8-purinetrione-7-yl)butane 1-phosphate competitive Candida albicans
3-(1,3,7-trihydro-9-D-ribityl-2,6,8-purinetrione-7-yl)butane 1-phosphate competitive Mycobacterium tuberculosis
3-(1,3,7-trihydro-9-D-ribityl-2,6,8-purinetrione-7-yl)butane 1-phosphate competitive Pyricularia grisea
3-(1,3,7-trihydro-9-D-ribityl-2,6,8-purinetrione-7-yl)pentane 1-phosphate competitive Candida albicans
3-(1,3,7-trihydro-9-D-ribityl-2,6,8-purinetrione-7-yl)pentane 1-phosphate competitive Mycobacterium tuberculosis
3-(1,3,7-trihydro-9-D-ribityl-2,6,8-purinetrione-7-yl)pentane 1-phosphate competitive Pyricularia grisea
3-[4,6-dioxo-4,5,6,7-tetrahydro-1-D-ribityl-1H-pyrazolo[3,4-d]pyrimidin-3-yl]propyl 1-phosphate competitive Candida albicans
3-[4,6-dioxo-4,5,6,7-tetrahydro-1-D-ribityl-1H-pyrazolo[3,4-d]pyrimidin-3-yl]propyl 1-phosphate competitive Mycobacterium tuberculosis
3-[4,6-dioxo-4,5,6,7-tetrahydro-1-D-ribityl-1H-pyrazolo[3,4-d]pyrimidin-3-yl]propyl 1-phosphate mixed type inhibition Pyricularia grisea
4-[4,6-dioxo-4,5,6,7-tetrahydro1-D-ribityl-1H-pyrazolo[3,4-d]-pyrimidin-3-yl]butyl 1-phosphate competitive Candida albicans
4-[4,6-dioxo-4,5,6,7-tetrahydro1-D-ribityl-1H-pyrazolo[3,4-d]-pyrimidin-3-yl]butyl 1-phosphate competitive Mycobacterium tuberculosis
5-[4,6-dioxo-4,5,6,7-tetrahydro-1-D-ribityl-1H-pyrazolo[3,4-d]pyrimidin-3-yl]pentyl 1-phosphate competitive Candida albicans
5-[4,6-dioxo-4,5,6,7-tetrahydro-1-D-ribityl-1H-pyrazolo[3,4-d]pyrimidin-3-yl]pentyl 1-phosphate competitive Mycobacterium tuberculosis

Organism

Organism UniProt Comment Textmining
Candida albicans
-
-
-
Mycobacterium tuberculosis
-
-
-
Pyricularia grisea
-
-
-

Temperature Optimum [°C]

Temperature Optimum [°C] Temperature Optimum Maximum [°C] Comment Organism
27
-
 assay at Mycobacterium tuberculosis
27
-
 assay at Pyricularia grisea
37
-
 assay at Candida albicans

pH Optimum

pH Optimum Minimum pH Optimum Maximum Comment Organism
7
-
 assay at Mycobacterium tuberculosis
7
-
 assay at Candida albicans
7
-
 assay at Pyricularia grisea

Ki Value [mM]

Ki Value [mM] Ki Value maximum [mM] Inhibitor Comment Organism Structure
0.0000008
-
 3-(1,3,7-trihydro-9-D-ribityl-2,6,8-purinetrione-7-yl)pentane 1-phosphate pH 7.0, 27°C Pyricularia grisea
0.0000009
-
 3-(1,3,7-trihydro-9-D-ribityl-2,6,8-purinetrione-7-yl)pentane 1-phosphate pH 7.0, 27°C Candida albicans
0.0000013
-
 4-[4,6-dioxo-4,5,6,7-tetrahydro1-D-ribityl-1H-pyrazolo[3,4-d]-pyrimidin-3-yl]butyl 1-phosphate pH 7.0, 27°C Candida albicans
0.000002
-
 3-(1,3,7-trihydro-9-D-ribityl-2,6,8-purinetrione-7-yl)butane 1-phosphate pH 7.0, 27°C Pyricularia grisea
0.0000037
-
 3-[4,6-dioxo-4,5,6,7-tetrahydro-1-D-ribityl-1H-pyrazolo[3,4-d]pyrimidin-3-yl]propyl 1-phosphate pH 7.0, 27°C Candida albicans
0.0000041
-
 4-[4,6-dioxo-4,5,6,7-tetrahydro1-D-ribityl-1H-pyrazolo[3,4-d]-pyrimidin-3-yl]butyl 1-phosphate pH 7.0, 27°C Mycobacterium tuberculosis
0.0000047
-
 5-[4,6-dioxo-4,5,6,7-tetrahydro-1-D-ribityl-1H-pyrazolo[3,4-d]pyrimidin-3-yl]pentyl 1-phosphate pH 7.0, 27°C Mycobacterium tuberculosis
0.0000077
-
 5-[4,6-dioxo-4,5,6,7-tetrahydro-1-D-ribityl-1H-pyrazolo[3,4-d]pyrimidin-3-yl]pentyl 1-phosphate pH 7.0, 27°C Candida albicans
0.000014
-
 3-(1,3,7-trihydro-9-D-ribityl-2,6,8-purinetrione-7-yl)butane 1-phosphate pH 7.0, 27°C Candida albicans
0.000015
-
 3-(1,3,7-trihydro-9-D-ribityl-2,6,8-purinetrione-7-yl)butane 1-phosphate pH 7.0, 27°C Mycobacterium tuberculosis
0.00003
-
 3-(1,3,7-trihydro-9-D-ribityl-2,6,8-purinetrione-7-yl)pentane 1-phosphate pH 7.0, 27°C Mycobacterium tuberculosis
0.00004
-
 3-[4,6-dioxo-4,5,6,7-tetrahydro-1-D-ribityl-1H-pyrazolo[3,4-d]pyrimidin-3-yl]propyl 1-phosphate pH 7.0, 27°C Mycobacterium tuberculosis
0.000101
-
 3-[4,6-dioxo-4,5,6,7-tetrahydro-1-D-ribityl-1H-pyrazolo[3,4-d]pyrimidin-3-yl]propyl 1-phosphate pH 7.0, 27°C Pyricularia grisea