1979-98-2|2-(Methylthio)pyrimidine-4,6-diol| Ambeed

Structure of 1979-98-2

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Quality Control of [ 1979-98-2 ] Purity: 97% SDS Specification

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Product Details of [ 1979-98-2 ]

CAS No. :	1979-98-2
Formula :	C₅H₆N₂O₂S
M.W :	158.18
SMILES Code :	CSC1=NC(O)=CC(O)=N1
MDL No. :	MFCD00006087

Safety of [ 1979-98-2 ]

GHS Pictogram:
Signal Word:	Warning
Hazard Statements:	H315-H319-H335
Precautionary Statements:	P261-P305+P351+P338

Computational Chemistry of [ 1979-98-2 ] Show Less

Physicochemical Properties

Num. heavy atoms	10
Num. arom. heavy atoms	6
Fraction Csp3	0.2
Num. rotatable bonds	1
Num. H-bond acceptors	4.0
Num. H-bond donors	2.0
Molar Refractivity	37.8
TPSA ? Topological Polar Surface Area: Calculated from Ertl P. et al. 2000 J. Med. Chem.	91.54 Å²

Lipophilicity

Log P_o/w (iLOGP)? iLOGP: in-house physics-based method implemented from Daina A et al. 2014 J. Chem. Inf. Model.	1.51
Log P_o/w (XLOGP3)? XLOGP3: Atomistic and knowledge-based method calculated by XLOGP program, version 3.2.2, courtesy of CCBG, Shanghai Institute of Organic Chemistry	1.0
Log P_o/w (WLOGP)? WLOGP: Atomistic method implemented from Wildman SA and Crippen GM. 1999 J. Chem. Inf. Model.	0.61
Log P_o/w (MLOGP)? MLOGP: Topological method implemented from Moriguchi I. et al. 1992 Chem. Pharm. Bull. Moriguchi I. et al. 1994 Chem. Pharm. Bull. Lipinski PA. et al. 2001 Adv. Drug. Deliv. Rev.	-0.63
Log P_o/w (SILICOS-IT)? SILICOS-IT: Hybrid fragmental/topological method calculated by FILTER-IT program, version 1.0.2, courtesy of SILICOS-IT, http://www.silicos-it.com	0.54
Consensus Log P_o/w? Consensus Log P_o/w: Average of all five predictions	0.6

Water Solubility

Log S (ESOL):? ESOL: Topological method implemented from Delaney JS. 2004 J. Chem. Inf. Model.	-1.83
Solubility	2.35 mg/ml ; 0.0148 mol/l
Class? Solubility class: Log S scale Insoluble < -10 < Poorly < -6 < Moderately < -4 < Soluble < -2 Very < 0 < Highly	Very soluble
Log S (Ali)? Ali: Topological method implemented from Ali J. et al. 2012 J. Chem. Inf. Model.	-2.51
Solubility	0.487 mg/ml ; 0.00308 mol/l
Class? Solubility class: Log S scale Insoluble < -10 < Poorly < -6 < Moderately < -4 < Soluble < -2 Very < 0 < Highly	Soluble
Log S (SILICOS-IT)? SILICOS-IT: Fragmental method calculated by FILTER-IT program, version 1.0.2, courtesy of SILICOS-IT, http://www.silicos-it.com	-0.99
Solubility	16.3 mg/ml ; 0.103 mol/l
Class? Solubility class: Log S scale Insoluble < -10 < Poorly < -6 < Moderately < -4 < Soluble < -2 Very < 0 < Highly	Soluble

Pharmacokinetics

GI absorption? Gatrointestinal absorption: according to the white of the BOILED-Egg	High
BBB permeant? BBB permeation: according to the yolk of the BOILED-Egg	No
P-gp substrate? P-glycoprotein substrate: SVM model built on 1033 molecules (training set) and tested on 415 molecules (test set) 10-fold CV: ACC=0.72 / AUC=0.77 External: ACC=0.88 / AUC=0.94	No
CYP1A2 inhibitor? Cytochrome P450 1A2 inhibitor: SVM model built on 9145 molecules (training set) and tested on 3000 molecules (test set) 10-fold CV: ACC=0.83 / AUC=0.90 External: ACC=0.84 / AUC=0.91	No
CYP2C19 inhibitor? Cytochrome P450 2C19 inhibitor: SVM model built on 9272 molecules (training set) and tested on 3000 molecules (test set) 10-fold CV: ACC=0.80 / AUC=0.86 External: ACC=0.80 / AUC=0.87	No
CYP2C9 inhibitor? Cytochrome P450 2C9 inhibitor: SVM model built on 5940 molecules (training set) and tested on 2075 molecules (test set) 10-fold CV: ACC=0.78 / AUC=0.85 External: ACC=0.71 / AUC=0.81	No
CYP2D6 inhibitor? Cytochrome P450 2D6 inhibitor: SVM model built on 3664 molecules (training set) and tested on 1068 molecules (test set) 10-fold CV: ACC=0.79 / AUC=0.85 External: ACC=0.81 / AUC=0.87	No
CYP3A4 inhibitor? Cytochrome P450 3A4 inhibitor: SVM model built on 7518 molecules (training set) and tested on 2579 molecules (test set) 10-fold CV: ACC=0.77 / AUC=0.85 External: ACC=0.78 / AUC=0.86	No
Log Kp (skin permeation)? Skin permeation: QSPR model implemented from Potts RO and Guy RH. 1992 Pharm. Res.	-6.55 cm/s

Druglikeness

Lipinski? Lipinski (Pfizer) filter: implemented from Lipinski CA. et al. 2001 Adv. Drug Deliv. Rev. MW ≤ 500 MLOGP ≤ 4.15 N or O ≤ 10 NH or OH ≤ 5	0.0
Ghose? Ghose filter: implemented from Ghose AK. et al. 1999 J. Comb. Chem. 160 ≤ MW ≤ 480 -0.4 ≤ WLOGP ≤ 5.6 40 ≤ MR ≤ 130 20 ≤ atoms ≤ 70	None
Veber? Veber (GSK) filter: implemented from Veber DF. et al. 2002 J. Med. Chem. Rotatable bonds ≤ 10 TPSA ≤ 140	0.0
Egan? Egan (Pharmacia) filter: implemented from Egan WJ. et al. 2000 J. Med. Chem. WLOGP ≤ 5.88 TPSA ≤ 131.6	0.0
Muegge? Muegge (Bayer) filter: implemented from Muegge I. et al. 2001 J. Med. Chem. 200 ≤ MW ≤ 600 -2 ≤ XLOGP ≤ 5 TPSA ≤ 150 Num. rings ≤ 7 Num. carbon > 4 Num. heteroatoms > 1 Num. rotatable bonds ≤ 15 H-bond acc. ≤ 10 H-bond don. ≤ 5	1.0
Bioavailability Score? Abbott Bioavailability Score: Probability of F > 10% in rat implemented from Martin YC. 2005 J. Med. Chem.	0.55

Medicinal Chemistry

PAINS? Pan Assay Interference Structures: implemented from Baell JB. & Holloway GA. 2010 J. Med. Chem.	0.0 alert
Brenk? Structural Alert: implemented from Brenk R. et al. 2008 ChemMedChem	0.0 alert: heavy_metal
Leadlikeness? Leadlikeness: implemented from Teague SJ. 1999 Angew. Chem. Int. Ed. 250 ≤ MW ≤ 350 XLOGP ≤ 3.5 Num. rotatable bonds ≤ 7	No; 1 violation:MW<1.0
Synthetic accessibility? Synthetic accessibility score: from 1 (very easy) to 10 (very difficult) based on 1024 fragmental contributions (FP2) modulated by size and complexity penaties, trained on 12'782'590 molecules and tested on 40 external molecules (r² = 0.94)	1.74

Application In Synthesis of [ 1979-98-2 ]

* All experimental methods are cited from the reference, please refer to the original source for details. We do not guarantee the accuracy of the content in the reference.

Downstream synthetic route of [ 1979-98-2 ]

[ 1979-98-2 ] Synthesis Path-Downstream 1~35

1
[ 120-46-7 ]
[ 1979-98-2 ]
2-methylsulfanyl-5,7-diphenyl-pyrano[2,3-d]pyrimidin-4-one; perchlorate [ No CAS ]

References: [1]Chemistry of Heterocyclic Compounds,1977,vol. 13,p. 1185 - 1187.
Khimiya Geterotsiklicheskikh Soedinenii,1977,vol. 13,p. 1484 - 1486.

2
[ 123-54-6 ]
[ 1979-98-2 ]
5,7-dimethyl-2-methylsulfanyl-pyrano[2,3-d]pyrimidin-4-one; perchlorate [ No CAS ]

References: [1]Chemistry of Heterocyclic Compounds,1977,vol. 13,p. 1185 - 1187.
Khimiya Geterotsiklicheskikh Soedinenii,1977,vol. 13,p. 1484 - 1486.

3
[ 93-91-4 ]
[ 1979-98-2 ]
5-methyl-2-methylsulfanyl-7-phenyl-pyrano[2,3-d]pyrimidin-4-one; perchlorate [ No CAS ]

References: [1]Chemistry of Heterocyclic Compounds,1977,vol. 13,p. 1185 - 1187.
Khimiya Geterotsiklicheskikh Soedinenii,1977,vol. 13,p. 1484 - 1486.

4
[ 108-24-7 ]
[ 1979-98-2 ]
[ 865139-53-3 ]

References: [1]Chemistry of Heterocyclic Compounds,2004,vol. 40,p. 1070 - 1076.

5
[ 1979-98-2 ]
[ 1979-97-1 ]

Yield	Reaction Conditions	Operation in experiment
88.75%	With nitric acid; at 20 - 50℃; for 5h;	This embodiment is a method for synthesizing 2-methylthio-4,6-dichloro-5-nitropyrimidine. The synthetic steps are as follows:(1) Take 200g of 2-methylthio-4,6-dihydroxypyrimidine in batches and add it to 600ml of fuming nitric acid, and stir at room temperatureAfter 1h, heat to 50 C for 4h;(2) After the heating reaction is completed, drop to room temperature, slowly pour it into ice water, stir for 1 h, and filter. Wash the filter cake to neutrality. After digging out the filter cake, dry to obtain 240 g of compound B. The purity is greater than 95%. Rate 88.75%;(3) Disperse 100 g of compound B in 450 ml of phosphorous oxychloride, and dropwise add 60 ml of diisopropylethylamine at room temperature. After the addition of diisopropylethylamine is completed, raise the reflux temperature to chlorination reaction 2 -5h;(4) After the chlorination reaction is completed, the obtained mixture is cooled and decompressed, and concentrated to remove excess phosphorus oxychloride. The residue is slowly poured into 1 kg of crushed ice and stirred for 1 h, and extracted with 200 ml of ethyl acetate 2-3 times The organic phases were combined, washed with a saturated aqueous sodium bicarbonate solution to neutral pH, washed once with a saturated aqueous sodium chloride solution, then dried over anhydrous sodium sulfate, filtered to remove the drying agent, and concentrated to obtain a crude product, which was obtained by recrystallization from n-hexane. 118g pure product, purity is greater than 98%, yield is 97.87%.
72%	With nitric acid; at 0℃; for 2h;	EXAMPLE 99; 4-hydroxy-4-[3-(trifluoromethy)phenyl]piperidine-1-carboxylic acid (7-methoxy-5-methylsulfanyl-thiazolo[5,4-d]pyrimidin-2-yl)-amide; Step 1: 4,6-Dihydroxy-2-methylthiopyrimidine (10.0 g, 63.22 mmol) was added over 1 hr to fuming nitric acid (30 mL) at 0 C. The red solution was stirred an additional 1 hr at 0 C. and then poured onto ice to give a light brown solid which was filtered off and washed with water and diethyl ether. The solid was dried under vacuo to give 4,6-Dihydroxy-2-methylthio-5-nitropyrimidine (9.30 g, 72%) as a light brown solid. LRMS for C5H5N3O4S (M+H)+ at m/z=203. The NMR spectrum obtained on the sample is compatible with its structure.
67%	With nitric acid; acetic acid; at 5 - 20℃; for 1h;	To 6 mL of acetic acid cooled at 5C on an ice bath were added fuming nitric acid (2.5 mL) and (22e) (2.0 g, 12.6 mmol). After 1 hour stirring at room temperature, the mixture was cooled at 5C on an ice bath, water (50 mL) was added and the resulting precipitate was filtered off. Yield: 67%.Melting point: 220-221C (decomposition).H NMR (DMSO-dg) d 2.56 (s, 3H, S CH3).13C NMR (DMSO-dg) d 13.2 (SCH3), 117.4 (C-5), 158.7 (C-4/C-6), 164.6 (C-2).

65%		A solution of 4,6-dihydroxy-2-methylthiopyrimidine (50 g, 316.09 mmol) in trifluoroacetic acid (210 mL) was stirred at RT for 30 min. The mixture was cooled to 5C then HNO3 fuming (19.5 mL, 426.73 mmol) was added drop wise at 5C. The temperature was maintained at 10-15C during the addition. The ice bath was removed and when the temperature reached 20C, a violent exothermic event occurred (from 20C to 45C in 5 seconds). The mixture was stirred at RT for 16h. The mixture was poured into a mixture of water and ice. The precipitate was filtered off and washed with water. The precipitate was dried under vacuum at 50C to give 42 g (65% yield) of intermediate S2. This intermediate was directly used in the next step without any further purification.
49%	With nitric acid; acetic acid; at 50℃; for 3h;	Step A: 2-Methylsulfanyl-5-nitro-pyrimidine-4,6-diol. 2-Methylsulfanyl-pyrimidine-4,6-diol (10 g, 63 mmol) was added portion-wise to a stirring solution of glacial acetic acid (25 mL) and concentrated nitric acid (10 mL) at 50 C. After 3 h, the reaction mixture was poured onto crushed ice and the product was isolated by filtration as a yellow solid (6 g, 49%). MS (ESI): mass calcd. for C5H5N3O4S, 203.0; m/z found, 202.4 [M-H].
49%	With nitric acid; acetic acid; In water; at 50℃; for 3h;	Intermediate 1: 2-Methylsulfanyl-5-nitro-pyrimidine-4,6-diol 2-Methylsulfanyl-pyrimidine-4,6-diol (10 g, 63 mmol) was added portion wise to a stirring solution of glacial acetic acid (25 mL) and concentrated nitric acid (10 mL) at 50 C. After 3 h, the reaction mixture was poured onto crushed ice and the product was isolated by filtration as a yellow solid (6 g, 49%). MS (ESI, negative mode): mass calcd. for C5H5N3O4S, 203.0; m/z found, 202.4 [M-H].
		Method V: 4,6-Dihydroxy-2-methylthio-5-nitropyrimidine: A solution of 4,6-dihydroxy-2-methylthiopyrimidine (42 g, 0.257 mol) in trifluoroacetic acid (91 ml, 1.186 mol) was stirred at 23 C. and warmed until all solid had gone into solution. The reaction was stirred for five hours at 23 C. Next, fuming HNO3 (15 ml, 350 mmol) was added portion wise to the reaction mixture over 25 minutes at 0 C. The reaction was stirred for twenty hours at 23 C., and treated with H2O (at 23 C.) at 80% conversion (according LC-MS). The solid precipitate was captured via filteration giving 4,6-dihydroxy-2-methylthio-5-nitropyrimidine as a tan-colored solid. The crude solid was azeotroped with toluene to give 35 g of pale tan powdery solid. 1H-NMR: 300 MHz, (CD3OD, 300 MHz) d (ppm) 2.63 (s, 3H). LCMS-ESI+: calc'd for C5H4N3O4S: 202.0 (M-H-); Found: 202.0 (M-H-).
	With nitric acid; for 2h;Cooling with ice;	EXAMPLE 176; METHYL {4,6-DIAMINO-2-[5-CHLORO-3-(2,3,6-TMFLUOROBENZYL)-1H-INDAZOL- 1 -YL]PYRIMIDiN-5-YL} CARBAMATEH3; Step A; Solid 4}6-dihydroxy-2-(methylmio)pyrimidine (lOg, 63.mmol) was added in portions over 30min, to fuming nitric acid (30ml) cooled in an ice bath. After stirring for 90min in an ice bath the solution was poured over ice. The product was collected by filtration, washed with a small amount of ice water and air dried on the filter. NMR (400 MHz, CDC13): delta 7.02 (s, 2 H); 2.56 (s, 3 H). LC rt~= 0.49min (Method A, not ionized).
42 g	With nitric acid; trifluoroacetic acid; at 5 - 45℃;	A solution of F-2 (50 g, 316.09 mmol) in TFA (210 mL) was stirred at RT for 30 min. The mixture was cooled to 5C then HN03 fuming (19.5 mL, 426.73 mmol) was added drop wise at 5C. The temperature was maintained at 10-15C during the addition. The ice bath was removed and when the temperature reached 20C, a violent exothermic event occurred (from 20C to 45C in 5 seconds). The mixture was stirred at RT for 16h. The mixture was poured into a mixture of water and ice. The precipitate was filtered off and washed with water. The precipitate was dried under vacuum at 50C to give 42 g (65% yield) of intermediate G-2. This intermediate was directly used in the next step without any further purification.

References: [1]Patent: CN110372605,2019,A .Location in patent: Paragraph 0014-0016.
[2]Patent: US2007/270433,2007,A1 .Location in patent: Page/Page column 51.
[3]Patent: WO2019/158655,2019,A1 .Location in patent: Page/Page column 74; 75.
[4]Patent: WO2014/9509,2014,A1 .Location in patent: Page/Page column 26; 28.
[5]Bioorganic and Medicinal Chemistry Letters,2009,vol. 19,p. 1658 - 1661.
[6]Patent: US2008/4253,2008,A1 .Location in patent: Page/Page column 13.
[7]Patent: US2009/156599,2009,A1 .Location in patent: Page/Page column 12.
[8]Patent: US2010/143301,2010,A1 .Location in patent: Page/Page column 45.
[9]Patent: WO2011/119518,2011,A1 .Location in patent: Page/Page column 39; 80-81.
[10]Patent: WO2013/68438,2013,A1 .Location in patent: Page/Page column 29.

6
[ 1979-98-2 ]
[ 865139-54-4 ]

References: [1]Chemistry of Heterocyclic Compounds,2004,vol. 40,p. 1070 - 1076.

7
[ 1979-98-2 ]
rac-5-(2-acetyl-6,7-dimethoxy-1,2,3,4-tetrahydro-1-isoquinolyl)-4-hydroxy-2-methylthio-1,6-dihydro-6-pyrimidinone [ No CAS ]

References: [1]Chemistry of Heterocyclic Compounds,2004,vol. 40,p. 1070 - 1076.

8
[ 1979-98-2 ]
4-chloro-6-(N-isobutyloamino)-2-methylmercaptopyrimidine [ No CAS ]