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CAS No. : | 1979-98-2 | MDL No. : | MFCD00006087 |
Formula : | C5H6N2O2S | Boiling Point : | - |
Linear Structure Formula : | - | InChI Key : | - |
M.W : | 158.18 | Pubchem ID : | - |
Synonyms : |
|
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 : | 91.54 Ų |
GI absorption : | High |
BBB permeant : | No |
P-gp substrate : | No |
CYP1A2 inhibitor : | No |
CYP2C19 inhibitor : | No |
CYP2C9 inhibitor : | No |
CYP2D6 inhibitor : | No |
CYP3A4 inhibitor : | No |
Log Kp (skin permeation) : | -6.55 cm/s |
Log Po/w (iLOGP) : | 1.51 |
Log Po/w (XLOGP3) : | 1.0 |
Log Po/w (WLOGP) : | 0.61 |
Log Po/w (MLOGP) : | -0.63 |
Log Po/w (SILICOS-IT) : | 0.54 |
Consensus Log Po/w : | 0.6 |
Lipinski : | 0.0 |
Ghose : | None |
Veber : | 0.0 |
Egan : | 0.0 |
Muegge : | 1.0 |
Bioavailability Score : | 0.55 |
Log S (ESOL) : | -1.83 |
Solubility : | 2.35 mg/ml ; 0.0148 mol/l |
Class : | Very soluble |
Log S (Ali) : | -2.51 |
Solubility : | 0.487 mg/ml ; 0.00308 mol/l |
Class : | Soluble |
Log S (SILICOS-IT) : | -0.99 |
Solubility : | 16.3 mg/ml ; 0.103 mol/l |
Class : | Soluble |
PAINS : | 0.0 alert |
Brenk : | 0.0 alert |
Leadlikeness : | 1.0 |
Synthetic accessibility : | 1.74 |
Signal Word: | Warning | Class: | N/A |
Precautionary Statements: | P261-P305+P351+P338 | UN#: | N/A |
Hazard Statements: | H315-H319-H335 | Packing Group: | N/A |
GHS Pictogram: |
* 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.
Yield | Reaction Conditions | Operation in experiment |
---|---|---|
97% | at 0℃; for 2.5 h; Heating / reflux | Step b: 4,6-Dichloro-2-methylsulfanyl-pyrimidine (19b) ; 2-Methylsulfanyl-pyrimidine-4,6-diol (30.0 g, 189 mmol) was added slowly to phosphorus oxychloride (350 ml ) while cooling on ice then N,N-diethylaniline (52.5 ml) was added slowly while cooling. The mixture was slowly warmed till reflux and refluxed for 2.5 hours. The mixture was evaporated and added to crushed ice. The mixture was extracted three times with ethyl acetate and the combined organic layers were washed three times with water, once with brine and concentrated. Purification by column chromatography on silica gel eluted with hexane - ethyl acetate gave the title compound (36 g, 97percent). |
65% | at 105 - 110℃; for 6 h; | A solution of 2-methylthiopyrimidine-4,6-diol (12.5 g, 79.11 mmol) in phosphorous oxychloride (60 ml) was heated to 105-110° C. for 6 hours. The phosphorous oxychloride was removed under reduced pressure to give a residue which was partitioned between dichloromethane and water. The organic layer was separated, dried and concentrated to give a residue. Purification was done by silica gel flash column chromatography (3percent ethyl acetate in hexane) to afford the desired product as a white solid (10 g, 65percent yield). 1H NMR (CDCl3, 400 MHz): δ 7.03(s, 1H), 2.58 (s, 3H). |
Yield | Reaction Conditions | Operation in experiment |
---|---|---|
95% | With sodium hydroxide In ethanol; water at 20 - 60℃; | Example 19; Step a: 2-Methylsulfanyl-pyrimidine-4,6-diol (19a) ; Methyl iodide (32,64g, 220 mmol) was added dropwise to a suspension of thiobarbituric acid (29g, 200 mmol) in EtOH (300ml) and 2M NaOH solution in water (110ml) at room temperature. The mixture was stirred at room temperature overnight and then stirred for two hours at 600C. The ethanol was removed, water was added and the mixture was allowed to stay for 2 hours on an ice bath. The solid title compound was filtered of, washed with ice cold water and dried (3Og, 95percent). |
Yield | Reaction Conditions | Operation in experiment |
---|---|---|
85 %Chromat. | With sodium hydroxide In methanol at 25 - 30℃; Autoclave | Example 7: Preparation of 2-Methylthio-4, 6-dihydroxypyrimidine 1.0m thiobarbituric acid sodium salt was dissolved in 1.5m 1 N aqueous sodium hydroxide solution and 50 ml methanol in a SS autoclave to obtain a mixture. To this 0.5m methyl chloride was fed in 1 to 2 hours. The obtained reaction mass was stirred for 2 to 6 hours at 25-30°C, a second lot of 0.5m methyl chloride was fed in 1 to 2 hours and mass was stirred at 25-30°C for 6-8 hours. To this, 0.05m methyl chloride was fed and reaction mass was stirred for 2 to 6 hours. After the end of reaction HPLC indicated 85percent 2-methylthio- 4, 6- dihydroxypyrimidine and 5percent 2-methylthio-4-methoxy-6-hydroxypyrimidine. Yield of product was 75-80 mole percent. |
Yield | Reaction Conditions | Operation in experiment |
---|---|---|
61% | Stage #1: With trichlorophosphate In Trichloroethylene at 5 - 20℃; Stage #2: at 80℃; |
Example 1; 3-[2-r4-Amino-l-piperidinylV8-r2.6-difluorophenyl)-7-oxo-5,6.7,8- tetrahvdropyrimido[4,5- |
61% | Stage #1: With trichlorophosphate In N,N-dimethyl-formamide at 5 - 20℃; Stage #2: at 80℃; |
To the solution of phosphorus oxy chloride (65 mL, 0.70 mol) in trichloroethylene (46.5 mL) was added DMF (25 mL, 0.32 mol) slowly to keep the temperature between 5 0C to 10 0C. The solution was then warmed up to room temperature before 6-hydroxy-2-(methylthio)-4(lH)- pyrimidinone (25 g, 0.16 mol) was added in portions. The resultant reaction mixture was heated at 80 0C overnight followed by concentration under vacuum. The resulting slurry like residue was poured into ice, stirred for 2 hours then filtered to afford the crude product. The crude product was further purified by recrystalization with hexane to afford 4,6-dichloro-2-(methylthio)-5- pyrimidinecarbaldehyde (21.3 g , 61percent). 1H-NMR (CDCl3) δ 2.66 (s, 3 η), 10.4 (s, 1 η).To a solution of 4,6-dichloro-2-(methylthio)-5-pyrimidinecarbaldehyde (10.0 g, 44.8 mmol) in TηF (250 mL) was added 2,6-difluoroaniline (5.35 mL, 49.3 mmol, 1.1 eq) followed by Et3N (12.6 mL, 89.6 mmol, 2 eq). The reaction mixture was heated to 550C for about 22 h before <n="109"/>concentrated. The slurry was re-dissolved in DCM (250 mL) and washed with H2O (2 x 100 mL), then concentrated and further washed with acetone (2 x 10 mL) to give 9.87 g (70 percent) of pure 4- chloro-6-[(2,6-difluorophenyl)amino]-2-(methylthio)-5-pyrimidinecarbaldehyde. LC-MS m/z 316 (M+H)+.A solution of 4-chloro-6-[(2,6-difluorophenyl)amino]-2-(methylthio)-5- pyrimidinecarbaldehyde (200 mg, 0.63 mmol) in DMF (4.0 mL) and acetic anhydride (2.0 mL) was heated with a microwave (16O0C) for about 30 minutes. The resultant mixture was then concentrated. Flash chromatography (EtOAc / Hexane, 1 : 5) provided the title compound (109 mg, 51percent): LC-MS m/z 340 (M+H)+. |
Yield | Reaction Conditions | Operation in experiment |
---|---|---|
61% | With trichlorophosphate In Trichloroethylene at 5 - 80℃; | To the solution of phosphorus oxychloride (65 mL, 0.70 mol) in trichloroethylene(46.5 mL) was added DMF (25 mL, 0.32 mol) slowly to keep the temperature between 5 0C to 10 0C. The solution was then warmed up to room temperature before 6-hydroxy-2- (methylthio)-4(lH)-pyrimidinone (25 g, 0.16 mol) was added in portions. The resultant reaction mixture was heated at 80 0C overnight followed by concentration under vacuum.The resulting slurry like residue was poured into ice, stirred for about 2 hours then filtered to afford the crude product. The crude product was further purified by recrystalization with hexane to afford 4,6-dichloro-2-(methylthio)-5-pyrimidinecarbaldehyde (21.3 g , 61percent). 1H- NMR (CDCl3) δ 2.66 (s, 3 H), 10.4 (s, 1 H). To the mixture of hydroxylamine hydrochloride (139 mg, 2.0 mmol), HOAc (0.113 mL, 2.0 mmol) and EtOH (5 mL) was added 4,6-dichloro-2-(methylthio)-5- <n="80"/>pyrimidinecarbaldehyde (223 mg, 1.0 mol) to room temperature. The solution was then heated at 50 0C for about 1 hour, 60 0C for about 30 minutes and 70 0C for about 30 minutes before it was concentrated under vacuum and washed with H2O (10-20 mL) to afford 4,6- dichloro-2-(methylthio)-5-pyrimidinecarbaldehyde oxime (190 mg, 80percent). LC-MS m/z 238 (M + H)+ 1.57 minute, 1.65 minute; 1H-NMR (CDCl3) δ 2.62, 2.65 (3 H), 7.53, 8.30 (1 H). To 4,6-dichloro-2-(methylthio)-5-pyrimidinecarbaldehyde oxime (2.38 g, 10 mmol) was added SOCl2 (21.8 mL, 0.30 mol) slowly at room temperature. The solution was then heated at 75 0C for about 3 hours before it was concentrated under vacuum. The residue SOCl2 was removed by evaporation with toluene (5 mL) under vacuum. The resulting solid was washed with EtOH/H2O (1OmL, 1 : 1) to afford 4,6-dichloro-2-(methylthio)-5- pyrimidinecarbonitrile (2.04 g, 93percent). LC-MS m/z 220 (M + H)+1.99 minute; 1H-NMR (CDCl3) δ 2.64(3 H).To the solution of 4,6-dichloro-2-(methylthio)-5-pyrimidinecarbonitrile (2.20 g, 10.0 mmol) in DMF (10 mL) was added 2,6-difluoroaniline (2.17 mL, 20.0 mmol). The solution was stirred at 50 0C for about 60 minutes. The mixture was slowly added into a solution of MeOH (20 mL) and water (30 mL). The resultant solid was filtered and washed with MeOH / H2O (20 mL, 1 :1) to give 4-chloro-6-[(2,6-difluorophenyl)amino]-2-(methylthio)-5- pyrimidinecarbonitrile as a white solid (2.82 g, 90 percent). LC-MS m/z 313 (M + H)+; 1H-NMR (CDCl3) δ 2.33 (s, 3 H), 6.94 (s, 1 H), 7.04 (m, 2 H), 7.35 (m, 1 H). |
61% | With trichlorophosphate In Trichloroethylene at 5 - 80℃; | To the solution of phosphorus oxychloride (65 mL, 0.70 mol) in trichloroethylene(46.5 mL) was added DMF (25 mL, 0.32 mol) slowly to keep the temperature between 5 0C to 10 0C. The solution was then warmed up to room temperature before 6-hydroxy-2- (methylthio)-4(lH)-pyrimidinone (25 g, 0.16 mol) was added in portions. The resultant reaction mixture was heated at 80 0C overnight followed by concentration under vacuum. The resulting slurry like residue was poured into ice, stirred for about 2 hours then filtered to afford the crude product. The crude product was further purified by recrystalization with hexane to afford 4, 6-dichloro-2-(methylthio)-5-pyrimidinecarbaldehyde (21.3 g , 61percent). 1H- NMR (CDCl3) δ 2.66 (s, 3 H), 10.4 (s, 1 H).To the mixture of hydroxylamine hydrochloride (139 mg, 2.0 mmol), HOAc (0.113 rnL, 2.0 mmol) and EtOH (5 mL) was added 4,6-dichloro-2-(methylthio)-5- pyrimidinecarbaldehyde (223 mg, 1.0 mol) to room temperature. The solution was then heated at 50 0C for about 1 hour, 60 0C for about 30 minutes and 70 0C for about 30 minutes before it was concentrated under vacuum and washed with H2O (10-20 mL) to afford 4,6- dichloro-2-(methylthio)-5-pyrimidinecarbaldehyde oxime (190 mg, 80percent). LC-MS m/z 238 (M + H)+ 1.57 minute, 1.65 minute; 1H-NMR (CDCl3) δ 2.62, 2.65 (3 H), 7.53, 8.30 (1 H). To 4,6-dichloro-2-(methylthio)-5-pyrimidinecarbaldehyde oxime (2.38 g, 10 mmol) was added SOCl2 (21.8 mL, 0.30 mol) slowly at room temperature. The solution was then heated at 75 0C for about 3 hours before it was concentrated under vacuum. The residueSOCl2 was removed by evaporation with toluene (5 mL) under vacuum. The resulting solid was washed with EtOH/H2O (1OmL, 1 : 1) to afford 4,6-dichloro-2-(methylthio)-5- pyrimidinecarbonitrile (2.04 g, 93percent). LC-MS m/z 220 (M + H)+1.99 minute; 1H-NMR (CDCl3) δ 2.64(3 H). To the solution of 4,6-dichloro-2-(methylthio)-5-pyrimidinecarbonitrile (2.20 g, 10.0 mmol) in DMF (10 mL) was added 2,6-difluoroaniline (2.17 mL, 20.0 mmol). The solution was stirred at 50 0C for about 60 minutes. The mixture was slowly added into a solution of MeOH (20 mL) and water (30 mL). The resultant solid was filtered and washed with MeOH / H2O (20 mL, 1 :1) to give 4-chloro-6-[(2,6-difluorophenyl)amino]-2-(methylthio)-5- pyrimidinecarbonitrile as a white solid (2.82 g, 90 percent). LC-MS m/z 313 (M + H)+; 1H-NMR (CDCl3) δ 2.33 (s, 3 H), 6.94 (s, 1 H), 7.04 (m, 2 H), 7.35 (m, 1 H). |
Yield | Reaction Conditions | Operation in experiment |
---|---|---|
42% | Stage #1: at -5 - 20℃; for 1 h; Stage #2: at 20℃; for 3.5 h; Heating / reflux |
POCI3 (7OmL, 0.75mol) was cooled to -5°C and DMF (23mL, 0.3mol) was added slowly. The resultant mixture was allowed to stand at 2O0C for 1 hour. 4,6-dihydroxy-2-methyl- mercaptopyrimidine (15.8 g., 0.1 mol) was added using a solid addition funnel. The reaction mixture was first stirred at room temperature for 30 minutes and then heated at reflux for 3 hours. Following removal of excess POCI3 and DMF in vacuo, the residue was poured into <n="107"/>ice. The solid obtained was filtered and washed with cold water. After treating the solid with hexanes (sonication). the desired product was obtained as a white solid (9.3g, 42percent). 1H NMR (CDCl3, 300 MHz) δ 10.34 (s, IH), 2.64 (s, 3H); CHN Calc'd for C6H4Cl2N2OS: C, 32.30; H, 1.81; N, 12.56. Found: C, 32.44; H, 1.69; N, 12.51. |
13% | at 10 - 100℃; | Reference Example 69 Production of 4,6-dichloro-2-(methylsulfanyl)pyrimidine-5-carbaldehyde To ice-cooled phosphorus oxychloride (77.62 g, 506 mmol) was added dropwise DMF (9.29 mL, 120 mmol), and the mixture was stirred at room temperature for 1 hr. 2-(Methylsulfanyl)pyrimidine-4,6-diol (15.8 g, 100 mmol) was added thereto by small portions, and the mixture was stirred at room temperature for 1 hr, at 40-50°C for 1 hr, and then at 100°C overnight. After cooling, the reaction mixture was poured into ice, and the mixture was extracted twice with ethyl acetate. The extract was washed successively with water and brine, dried over magnesium sulfate, and concentrated under reduced pressure. The residue was purified by silica gel column chromatography (eluate, hexane:ethyl acetate=95:5-->85:15) to give the title compound (2.97 g, 13percent) as a pale-yellow solid. 1H NMR (300 MHz, CDCl3) δ:2.64 (3 H, s), 10.38 (1 H, s). |
Yield | Reaction Conditions | Operation in experiment |
---|---|---|
61% | Stage #1: With trichlorophosphate In Trichloroethylene at 5 - 20℃; Stage #2: at 20 - 80℃; Stage #3: With water In Trichloroethylene at 0℃; for 2 h; |
57a) 4-chloro-6-[(2,6-difluorophenyDamino]-2-(methylthio')-5- pyrimidinecarbonitrile; To the solution of phosphorus oxychloride (65 mL, 0.70 mol) in trichloroethylene (46.5 mL) was added DMF (25 mL, 0.32 mol) slowly to keep the temperature between 5 0C to 10 0C. The solution was then warmed up to room temperature before 6-hydroxy-2-(methylthio)-4(l/i)-pyrimidinone (25 g, 0.16 mol) was added in portions. The resultant reaction mixture was heated at 80 0C overnight followed by concentration under vacuum. The resulting slurry like residue was poured into ice, stirred for about 2 hours then filtered to afford the crude product. The crude product was further purified by recrystalization with hexane to afford 4,6- dichloro-2-(methylthio)-5-pyrimidinecarbaldehyde (21.3 g , 61percent). 1H-NMR (CDCl3) δ 2.66 (s, 3 H), 10.4 (s, I H). |
61% | Stage #1: With trichlorophosphate In Trichloroethylene at 5 - 10℃; Stage #2: at 20 - 80℃; |
Example 1; N-CcvclopropylmethylV3-r8-r2,6-difluoroρhenylV2-(r2-hvdroxy-l- rhvdroxymethvπethyl"|amino)-7-oxo-718-dihvdropyridor2,3-dlpyrimidin-4-yl)-4- methylbenzamidela) 4-chloro-8-(2.6-difluorophenyl)-2-('methylthio)pyridor2.3-^)pyrimidin-7r8Hr)- oneTo the solution of phosphorus oxychloride (65 mL, 0.70 mol) in trichloroethylene (46.5 mL) was added DMF (25 mL, 0.32 mol) slowly to keep the temperature between 5 0C to 10 0C. The solution was then warmed up to room temperature before 6-hydroxy-2- (methylthio)-4(lH)-pyrimidinone (25 g, 0.16 mol) was added in portions. The resultant reaction mixture was heated at 80 0C overnight followed by concentration under vacuum. The resulting slurry like residue was poured into ice, stirred for 2 hours then filtered to afford the crude product. The crude product was further purified by recrystalization with hexane to afford 4,6-dichloro-2-(methylthio)-5-pyrimidinecarbaldehyde (21.3 g , 61percent). 1H-NMR (CDCl3) δ 2.66 (s, 3 H), 10.4 (s, 1 H). |
Yield | Reaction Conditions | Operation in experiment |
---|---|---|
72% | at 0℃; for 2 h; | 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, 72percent) 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. |
65% | Stage #1: at 20℃; for 0.5 h; Stage #2: at 5 - 20℃; |
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 5°C then HNO3 fuming (19.5 mL, 426.73 mmol) was added drop wise at 5°C. The temperature was maintained at 10-15°C during the addition. The ice bath was removed and when the temperature reached 20°C, a violent exothermic event occurred (from 20°C to 45°C 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 50°C to give 42 g (65percent yield) of intermediate S2. This intermediate was directly used in the next step without any further purification. |
49% | at 50℃; for 3 h; | 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, 49percent). 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 3 h; | 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, 49percent). MS (ESI, negative mode): mass calcd. for C5H5N3O4S, 203.0; m/z found, 202.4 [M-H]. |
42 g | 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 5°C then HN03 fuming (19.5 mL, 426.73 mmol) was added drop wise at 5°C. The temperature was maintained at 10-15°C during the addition. The ice bath was removed and when the temperature reached 20°C, a violent exothermic event occurred (from 20°C to 45°C 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 50°C to give 42 g (65percent yield) of intermediate G-2. This intermediate was directly used in the next step without any further purification. |
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