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Literature summary for 1.5.1.3 extracted from

  • Cody, V.; Pace, J.; Queener, S.; Adair, O.; Gangjee, A.
    Kinetic and structural analysis for potent antifolate inhibition of Pneumocystis jirovecii, Pneumocystis carinii, and human dihydrofolate reductases and their active-site variants (2013), Antimicrob. Agents Chemother., 57, 2669-2677 .
    View publication on PubMedView publication on EuropePMC

Cloned(Commentary)

Cloned (Comment) Organism
recombinant expression of His-tagged wild-type and mutant enzymes in Escherichia coli Rosetta Gami B (DE3) Homo sapiens
recombinant expression of His-tagged wild-type and mutant enzymes in Escherichia coli Rosetta Gami B (DE3) Pneumocystis carinii
recombinant expression of His-tagged wild-type enzyme in Escherichia coli Rosetta Gami B (DE3) Pneumocystis jirovecii

Crystallization (Commentary)

Crystallization (Comment) Organism
purified recombinant detagged wild-type enzyme and mutant K37Q in complex with inhibitor 2,4-diamino-6-[(2',5'-dichloro anilino)methyl]pyrido[2,3-d]pyrimidine, hanging drop vapour diffusion method, mixing of 20.4 mg/ml protein in 20 mM MES, pH 6.0, 100 mM KCl with a 0:1 molar excess of NADPH and inhibitor, and with reservoir solution containing 100 mM K2HPO4, pH 6.9, 60-64% saturated (NH4)2SO4, and 3% (v/v) ethyl alcohol, 0.01 ml drops, 4°C, for mutant K37Q/F69N, 10.9 mg/ml protein in 10 mM MES, pH 6.0, and 100 mM KCl, is mixed with with a 0:1 molar excess of NADPH and inhibitor, and with a reservoir solution containing 33-36% PEG 2000, 50 mM MES, pH 6.0, and 100 mM KCl, 14°C, X-ray diffraction structure determination and analysis at 2.2 A resolution, modeling Pneumocystis carinii
purified recombinant detagged wild-type enzyme and mutants Q35K and Q35K/N64F in complex with inhibitor 2,4-diamino-6-[(2',5'-dichloro anilino)methyl]pyrido[2,3-d]pyrimidine, hanging drop vapour diffusion method, mixing of 6.6-9.8 mg/ml protein in 100 mM K2HPO4, pH 6.9, and 30% saturated (NH4)2SO4 with a 0:1 molar excess of NADPH and inhibitor, and with reservoir solution containing 100 mM K2HPO4, pH 6.9, 60-64% saturated (NH4)2SO4, and 3% v/v ethyl alcohol, 0.01 ml drops, 14°C X-ray diffraction structure determination and analysis at 2.2 A resolution, molecular replacement methods using the coordinates for human DHFR, PDB ID 1U72, modeling Homo sapiens

Protein Variants

Protein Variants Comment Organism
F69F site-directed mutagenesis Pneumocystis jirovecii
F69N site-directed mutagenesis Pneumocystis jirovecii
F69S site-directed mutagenesis Pneumocystis carinii
K37Q site-directed mutagenesis, the mutant exhibits increased sensitivity for inhibition by 2,4-diamino-6-[(2',5'-dichloro anilino)methyl]pyrido[2,3-d]pyrimidine compared to the wild-type enzyme Pneumocystis carinii
K37Q/F69N site-directed mutagenesis, the mutant exhibits increased sensitivity for inhibition by 2,4-diamino-6-[(2',5'-dichloro anilino)methyl]pyrido[2,3-d]pyrimidine compared to the wild-type enzyme. Structure analysis of the mutant in complex with TMP, overview Pneumocystis carinii
K37Q/F69S site-directed mutagenesis Pneumocystis carinii
K37S site-directed mutagenesis Pneumocystis carinii
K37S/F69N site-directed mutagenesis Pneumocystis carinii
K37S/F69S site-directed mutagenesis Pneumocystis carinii
N64F site-directed mutagenesis, the mutant exhibits increased sensitivity for inhibition by 2,4-diamino-6-[(2',5'-dichloro anilino)methyl]pyrido[2,3-d]pyrimidine compared to the wild-type enzyme Homo sapiens
N64S site-directed mutagenesis Homo sapiens
Q35K site-directed mutagenesis Homo sapiens
Q35K/N64F site-directed mutagenesis Homo sapiens
Q35K/N64S site-directed mutagenesis Homo sapiens
Q35S site-directed mutagenesis Homo sapiens
Q35S/N64F site-directed mutagenesis Homo sapiens
Q35S/N64S site-directed mutagenesis Homo sapiens
S37K site-directed mutagenesis Pneumocystis jirovecii
S37K/S69F site-directed mutagenesis Pneumocystis jirovecii
S37K/S69N site-directed mutagenesis Pneumocystis jirovecii
S37Q/S69F site-directed mutagenesis Pneumocystis jirovecii
S37Q/S69N site-directed mutagenesis Pneumocystis jirovecii
S73Q site-directed mutagenesis Pneumocystis jirovecii

Inhibitors

Inhibitors Comment Organism Structure
2,4-diamino-6-[(2',5'-dichloroanilino)methyl]pyrido[2,3-d]pyrimidine OAAG324, a potent inhibitor of dihydrofolate reductase, analysis of the enzyme-inhibitor structure of wild-type enzyme and mutants Homo sapiens
2,4-diamino-6-[(2',5'-dichloroanilino)methyl]pyrido[2,3-d]pyrimidine OAAG324, a potent inhibitor of dihydrofolate reductase Pneumocystis carinii
2,4-diamino-6-[(2',5'-dichloroanilino)methyl]pyrido[2,3-d]pyrimidine OAAG324, a potent inhibitor of dihydrofolate reductase Pneumocystis jirovecii
2,4-diamino-6-[(3',4',5'-trichloroanilino)methyl]pyrido[2,3-d]pyrimidine
-
Homo sapiens
2,4-diamino-6-[(3',4',5'-trichloroanilino)methyl]pyrido[2,3-d]pyrimidine
-
Pneumocystis carinii
2,4-diamino-6-[(3',4',5'-trichloroanilino)methyl]pyrido[2,3-d]pyrimidine
-
Pneumocystis jirovecii
dihydrofolic acid
-
Pneumocystis carinii
methotrexate
-
Homo sapiens
methotrexate
-
Pneumocystis carinii
methotrexate
-
Pneumocystis jirovecii
TMP structure and ligand binding conformation of TMP Homo sapiens
TMP structure and ligand binding conformation of TMP Pneumocystis carinii
TMP structure and ligand binding conformation of TMP Pneumocystis jirovecii
trimethoprim
-
Homo sapiens
trimethoprim
-
Pneumocystis carinii
trimethoprim
-
Pneumocystis jirovecii

KM Value [mM]

KM Value [mM] KM Value Maximum [mM] Substrate Comment Organism Structure
additional information
-
additional information Michaelis-Menten steady-state kinetics Homo sapiens
additional information
-
additional information Michaelis-Menten steady-state kinetics Pneumocystis carinii
additional information
-
additional information Michaelis-Menten steady-state kinetics Pneumocystis jirovecii
0.0004
-
7,8-dihydrofolate recombinant mutant Q35K/N64F, pH 7.4, 37°C Homo sapiens
0.0004
-
7,8-dihydrofolate recombinant mutant Q35S/N64S, pH 7.4, 37°C Homo sapiens
0.0005
-
7,8-dihydrofolate recombinant mutant Q35K, pH 7.4, 37°C Homo sapiens
0.0007
-
7,8-dihydrofolate recombinant wild-type enzyme, pH 7.4, 37°C Homo sapiens
0.0007
-
7,8-dihydrofolate recombinant mutant Q35K/N64S, pH 7.4, 37°C Homo sapiens
0.0007
-
7,8-dihydrofolate recombinant mutant Q35S, pH 7.4, 37°C Homo sapiens
0.0007
-
7,8-dihydrofolate recombinant mutant Q35S/N64F, pH 7.4, 37°C Homo sapiens
0.0008
-
7,8-dihydrofolate recombinant mutant N64F, pH 7.4, 37°C Homo sapiens
0.0009
-
7,8-dihydrofolate recombinant mutant N64S, pH 7.4, 37°C Homo sapiens
0.002
-
7,8-dihydrofolate recombinant wild-type enzyme, pH 7.4, 37°C Pneumocystis jirovecii
0.0024
-
7,8-dihydrofolate recombinant mutant S37K/S69N, pH 7.4, 37°C Pneumocystis jirovecii
0.003
-
7,8-dihydrofolate recombinant mutant S37Q/S69F, pH 7.4, 37°C Pneumocystis jirovecii
0.0032
-
7,8-dihydrofolate recombinant mutant S37K/S69F, pH 7.4, 37°C Pneumocystis jirovecii
0.0034
-
7,8-dihydrofolate recombinant mutant S69N, pH 7.4, 37°C Pneumocystis jirovecii
0.0035
-
7,8-dihydrofolate recombinant wild-type enzyme, pH 7.4, 37°C Pneumocystis carinii
0.0035
-
7,8-dihydrofolate recombinant mutant S37Q, pH 7.4, 37°C Pneumocystis jirovecii
0.0038
-
NADPH recombinant mutant Q35S, pH 7.4, 37°C Homo sapiens
0.0038
-
7,8-dihydrofolate recombinant mutant S37Q/S69N, pH 7.4, 37°C Pneumocystis jirovecii
0.0045
-
NADPH recombinant wild-type enzyme, pH 7.4, 37°C Homo sapiens
0.0048
-
7,8-dihydrofolate recombinant mutant S69F, pH 7.4, 37°C Pneumocystis jirovecii
0.0053
-
NADPH recombinant mutant Q35S/N64S, pH 7.4, 37°C Homo sapiens
0.0056
-
NADPH recombinant mutant Q35S/N64F, pH 7.4, 37°C Homo sapiens
0.0057
-
NADPH recombinant mutant Q35K/N64F, pH 7.4, 37°C Homo sapiens
0.0063
-
NADPH recombinant mutant N64S, pH 7.4, 37°C Homo sapiens
0.0066
-
7,8-dihydrofolate recombinant mutant F69N, pH 7.4, 37°C Pneumocystis carinii
0.0066
-
NADPH recombinant mutant K37S, pH 7.4, 37°C Pneumocystis carinii
0.0066
-
NADPH recombinant mutant Q35K/N64S, pH 7.4, 37°C Homo sapiens
0.007
-
NADPH recombinant mutant K37S/F69S, pH 7.4, 37°C Pneumocystis carinii
0.0071
-
7,8-dihydrofolate recombinant mutant F69S, pH 7.4, 37°C Pneumocystis carinii
0.0072
-
NADPH recombinant mutant K37Q, pH 7.4, 37°C Pneumocystis carinii
0.0075
-
NADPH recombinant mutant N64F, pH 7.4, 37°C Homo sapiens
0.0097
-
7,8-dihydrofolate recombinant mutant K37S/F69N, pH 7.4, 37°C Pneumocystis carinii
0.0101
-
7,8-dihydrofolate recombinant mutant K37S, pH 7.4, 37°C Pneumocystis carinii
0.0106
-
NADPH recombinant mutant K37Q/F69S, pH 7.4, 37°C Pneumocystis carinii
0.0107
-
7,8-dihydrofolate recombinant mutant K37Q/F69N, pH 7.4, 37°C Pneumocystis carinii
0.0116
-
7,8-dihydrofolate recombinant mutant K37S/F69S, pH 7.4, 37°C Pneumocystis carinii
0.0118
-
NADPH recombinant mutant S37Q, pH 7.4, 37°C Pneumocystis jirovecii
0.0125
-
NADPH recombinant mutant Q35K, pH 7.4, 37°C Homo sapiens
0.0149
-
NADPH recombinant mutant S37K/S69F, pH 7.4, 37°C Pneumocystis jirovecii
0.0162
-
NADPH recombinant mutant S69F, pH 7.4, 37°C Pneumocystis jirovecii
0.0163
-
NADPH recombinant mutant F69N, pH 7.4, 37°C Pneumocystis carinii
0.0163
-
NADPH recombinant mutant K37Q/F69N, pH 7.4, 37°C Pneumocystis carinii
0.0167
-
NADPH recombinant mutant K37S/F69N, pH 7.4, 37°C Pneumocystis carinii
0.0173
-
NADPH recombinant mutant S37Q/S69N, pH 7.4, 37°C Pneumocystis jirovecii
0.0185
-
7,8-dihydrofolate recombinant mutant K37Q/F69S, pH 7.4, 37°C Pneumocystis carinii
0.0189
-
NADPH recombinant wild-type enzyme, pH 7.4, 37°C Pneumocystis jirovecii
0.0192
-
NADPH recombinant mutant F69S, pH 7.4, 37°C Pneumocystis carinii
0.023
-
NADPH recombinant wild-type enzyme, pH 7.4, 37°C Pneumocystis carinii
0.0252
-
NADPH recombinant mutant S69N, pH 7.4, 37°C Pneumocystis jirovecii
0.0275
-
NADPH recombinant mutant S37Q/S69F, pH 7.4, 37°C Pneumocystis jirovecii
0.0864
-
NADPH recombinant mutant S37K/S69N, pH 7.4, 37°C Pneumocystis jirovecii

Natural Substrates/ Products (Substrates)

Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
7,8-dihydrofolate + NADPH + H+ Homo sapiens
-
5,6,7,8-tetrahydrofolate + NADP+
-
r
7,8-dihydrofolate + NADPH + H+ Pneumocystis carinii
-
5,6,7,8-tetrahydrofolate + NADP+
-
r
7,8-dihydrofolate + NADPH + H+ Pneumocystis jirovecii
-
5,6,7,8-tetrahydrofolate + NADP+
-
r

Organism

Organism UniProt Comment Textmining
Homo sapiens P00374
-
-
Pneumocystis carinii P16184
-
-
Pneumocystis jirovecii Q9UUP5
-
-

Purification (Commentary)

Purification (Comment) Organism
recombinant His-tagged wild-type and mutant enzymes from Escherichia coli Rosetta Gami B (DE3) by nickel affinity chromatography, and tag cleavage through the SUMO protease Ulp1, followed by another step of nickel affinity chromatography to remove the tag Homo sapiens
recombinant His-tagged wild-type and mutant enzymes from Escherichia coli Rosetta Gami B (DE3) by nickel affinity chromatography, and tag cleavage through the SUMO protease Ulp1, followed by another step of nickel affinity chromatography to remove the tag Pneumocystis carinii
recombinant His-tagged wild-type enzyme from Escherichia coli Rosetta Gami B (DE3) by nickel affinity chromatography, and tag cleavage through the SUMO protease Ulp1, followed by another step of nickel affinity chromatography to remove the tag Pneumocystis jirovecii

Substrates and Products (Substrate)

Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
7,8-dihydrofolate + NADPH + H+
-
Homo sapiens 5,6,7,8-tetrahydrofolate + NADP+
-
r
7,8-dihydrofolate + NADPH + H+
-
Pneumocystis carinii 5,6,7,8-tetrahydrofolate + NADP+
-
r
7,8-dihydrofolate + NADPH + H+
-
Pneumocystis jirovecii 5,6,7,8-tetrahydrofolate + NADP+
-
r

Synonyms

Synonyms Comment Organism
DHFR
-
Homo sapiens
DHFR
-
Pneumocystis carinii
DHFR
-
Pneumocystis jirovecii

Temperature Optimum [°C]

Temperature Optimum [°C] Temperature Optimum Maximum [°C] Comment Organism
37
-
assay at Homo sapiens
37
-
assay at Pneumocystis carinii
37
-
assay at Pneumocystis jirovecii

Turnover Number [1/s]

Turnover Number Minimum [1/s] Turnover Number Maximum [1/s] Substrate Comment Organism Structure
2 8 NADPH recombinant mutant N64F, pH 7.4, 37°C Homo sapiens
2 8 7,8-dihydrofolate recombinant mutant N64F, pH 7.4, 37°C Homo sapiens
3 6 NADPH recombinant wild-type enzyme, pH 7.4, 37°C Pneumocystis jirovecii
3 6 7,8-dihydrofolate recombinant wild-type enzyme, pH 7.4, 37°C Pneumocystis jirovecii
3 6 NADPH recombinant mutant N64S, pH 7.4, 37°C Homo sapiens
3 6 7,8-dihydrofolate recombinant mutant N64S, pH 7.4, 37°C Homo sapiens
3 6 NADPH recombinant mutant Q35K/N64S, pH 7.4, 37°C Homo sapiens
3 6 7,8-dihydrofolate recombinant mutant Q35K/N64S, pH 7.4, 37°C Homo sapiens
21
-
NADPH recombinant mutant Q35S/N64F, pH 7.4, 37°C Homo sapiens
21
-
7,8-dihydrofolate recombinant mutant Q35S/N64F, pH 7.4, 37°C Homo sapiens
23
-
NADPH recombinant mutant Q35S/N64S, pH 7.4, 37°C Homo sapiens
23
-
7,8-dihydrofolate recombinant mutant Q35S/N64S, pH 7.4, 37°C Homo sapiens
24
-
NADPH recombinant mutant Q35S, pH 7.4, 37°C Homo sapiens
24
-
7,8-dihydrofolate recombinant mutant Q35S, pH 7.4, 37°C Homo sapiens
26
-
NADPH recombinant wild-type enzyme, pH 7.4, 37°C Homo sapiens
26
-
7,8-dihydrofolate recombinant wild-type enzyme, pH 7.4, 37°C Homo sapiens
26
-
NADPH recombinant mutant S37Q/S69F, pH 7.4, 37°C Pneumocystis jirovecii
26
-
7,8-dihydrofolate recombinant mutant S37Q/S69F, pH 7.4, 37°C Pneumocystis jirovecii
38
-
NADPH recombinant mutant K37Q, pH 7.4, 37°C Pneumocystis carinii
38
-
7,8-dihydrofolate recombinant mutant K37Q, pH 7.4, 37°C Pneumocystis carinii
39
-
NADPH recombinant mutant Q35K, pH 7.4, 37°C Homo sapiens
39
-
7,8-dihydrofolate recombinant mutant Q35K, pH 7.4, 37°C Homo sapiens
43
-
NADPH recombinant mutant Q35K/N64F, pH 7.4, 37°C Homo sapiens
43
-
7,8-dihydrofolate recombinant mutant Q35K/N64F, pH 7.4, 37°C Homo sapiens
45
-
NADPH recombinant mutant K37S, pH 7.4, 37°C Pneumocystis carinii
45
-
7,8-dihydrofolate recombinant mutant K37S, pH 7.4, 37°C Pneumocystis carinii
47
-
NADPH recombinant mutant S69N, pH 7.4, 37°C Pneumocystis jirovecii
47
-
7,8-dihydrofolate recombinant mutant S69N, pH 7.4, 37°C Pneumocystis jirovecii
51
-
NADPH recombinant mutant S37Q, pH 7.4, 37°C Pneumocystis jirovecii
51
-
7,8-dihydrofolate recombinant mutant S37Q, pH 7.4, 37°C Pneumocystis jirovecii
57
-
NADPH recombinant mutant S37K/S69F, pH 7.4, 37°C Pneumocystis jirovecii
57
-
7,8-dihydrofolate recombinant mutant S37K/S69F, pH 7.4, 37°C Pneumocystis jirovecii
78
-
NADPH recombinant mutant S37K/S69N, pH 7.4, 37°C Pneumocystis jirovecii
78
-
7,8-dihydrofolate recombinant mutant S37K/S69N, pH 7.4, 37°C Pneumocystis jirovecii
83
-
NADPH recombinant mutant S69F, pH 7.4, 37°C Pneumocystis jirovecii
83
-
7,8-dihydrofolate recombinant mutant S69F, pH 7.4, 37°C Pneumocystis jirovecii
95
-
NADPH recombinant mutant S37Q/S69N, pH 7.4, 37°C Pneumocystis jirovecii
95
-
7,8-dihydrofolate recombinant mutant S37Q/S69N, pH 7.4, 37°C Pneumocystis jirovecii
157
-
NADPH recombinant mutant K37S/F69S, pH 7.4, 37°C Pneumocystis carinii
157
-
7,8-dihydrofolate recombinant mutant K37S/F69S, pH 7.4, 37°C Pneumocystis carinii
158
-
NADPH recombinant mutant K37Q/F69S, pH 7.4, 37°C Pneumocystis carinii
158
-
7,8-dihydrofolate recombinant mutant K37Q/F69S, pH 7.4, 37°C Pneumocystis carinii
190
-
NADPH recombinant mutant K37S/F69N, pH 7.4, 37°C Pneumocystis carinii
190
-
7,8-dihydrofolate recombinant mutant K37S/F69N, pH 7.4, 37°C Pneumocystis carinii
204
-
NADPH recombinant mutant F69S, pH 7.4, 37°C Pneumocystis carinii
204
-
7,8-dihydrofolate recombinant mutant F69S, pH 7.4, 37°C Pneumocystis carinii
223
-
NADPH recombinant mutant K37Q/F69N, pH 7.4, 37°C Pneumocystis carinii
223
-
7,8-dihydrofolate recombinant mutant K37Q/F69N, pH 7.4, 37°C Pneumocystis carinii
235
-
NADPH recombinant wild-type enzyme, pH 7.4, 37°C Pneumocystis carinii
235
-
7,8-dihydrofolate recombinant wild-type enzyme, pH 7.4, 37°C Pneumocystis carinii

pH Optimum

pH Optimum Minimum pH Optimum Maximum Comment Organism
7.4
-
assay at Homo sapiens
7.4
-
assay at Pneumocystis carinii
7.4
-
assay at Pneumocystis jirovecii

Cofactor

Cofactor Comment Organism Structure
NADP+
-
Homo sapiens
NADP+
-
Pneumocystis carinii
NADP+
-
Pneumocystis jirovecii
NADPH
-
Homo sapiens
NADPH
-
Pneumocystis carinii
NADPH
-
Pneumocystis jirovecii

Ki Value [mM]

Ki Value [mM] Ki Value maximum [mM] Inhibitor Comment Organism Structure
additional information
-
additional information inhibition kinetics of wild-type and mutant enzymes, comparison with the inhibition kinetics of enzymes and enzyme mutants from Homo sapiens and Pneumocystis carinii, overview Pneumocystis jirovecii
additional information
-
additional information inhibition kinetics of wild-type and mutant enzymes, comparison with the inhibition kinetics of enzymes and enzyme mutants from Homo sapiens and Pneumocystis jirovecii, overview Pneumocystis carinii
additional information
-
additional information inhibition kinetics of wild-type and mutant enzymes, comparison with the inhibition kinetics of enzymes and enzyme mutants from Pneumocystis carinii and Pneumocystis jirovecii, overview Homo sapiens
0.00000026
-
2,4-diamino-6-[(2',5'-dichloroanilino)methyl]pyrido[2,3-d]pyrimidine mutant K37Q enzyme, pH 7.4, 37°C Pneumocystis carinii
0.00000058
-
2,4-diamino-6-[(2',5'-dichloroanilino)methyl]pyrido[2,3-d]pyrimidine recombinant mutant N64F enzyme, pH 7.4, 37°C Homo sapiens
0.00000071
-
2,4-diamino-6-[(2',5'-dichloroanilino)methyl]pyrido[2,3-d]pyrimidine mutant K37Q/F69N enzyme, pH 7.4, 37°C Pneumocystis carinii
0.0000008
-
2,4-diamino-6-[(2',5'-dichloroanilino)methyl]pyrido[2,3-d]pyrimidine mutant K37S enzyme, pH 7.4, 37°C Pneumocystis jirovecii
0.00000142
-
2,4-diamino-6-[(2',5'-dichloroanilino)methyl]pyrido[2,3-d]pyrimidine mutant K37S/F69S enzyme, pH 7.4, 37°C Pneumocystis jirovecii
0.0000027
-
2,4-diamino-6-[(2',5'-dichloroanilino)methyl]pyrido[2,3-d]pyrimidine wild-type enzyme, pH 7.4, 37°C Pneumocystis jirovecii
0.0000063
-
2,4-diamino-6-[(2',5'-dichloroanilino)methyl]pyrido[2,3-d]pyrimidine wild-type enzyme, pH 7.4, 37°C Pneumocystis carinii
0.0000244
-
2,4-diamino-6-[(2',5'-dichloroanilino)methyl]pyrido[2,3-d]pyrimidine recombinant wild-type enzyme, pH 7.4, 37°C Homo sapiens

General Information

General Information Comment Organism
additional information homology model of enzyme pjDHFR in ternary complex with NADPH and inhibitor 2,4-diamino-6-[(2',5'-dichloro anilino)methyl]pyrido[2,3-d]pyrimidine Pneumocystis jirovecii