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Chemical Structure| 38696-21-8
Chemical Structure| 38696-21-8
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Product Details of [ 38696-21-8 ]

CAS No. :38696-21-8 MDL No. :MFCD07368228
Formula : C6H8BrN3 Boiling Point : -
Linear Structure Formula :- InChI Key :NYMYGNLCILQUMT-UHFFFAOYSA-N
M.W : 202.05 Pubchem ID :12735315
Synonyms :

Calculated chemistry of [ 38696-21-8 ]

Physicochemical Properties

Num. heavy atoms : 10
Num. arom. heavy atoms : 6
Fraction Csp3 : 0.33
Num. rotatable bonds : 1
Num. H-bond acceptors : 2.0
Num. H-bond donors : 0.0
Molar Refractivity : 43.94
TPSA : 29.02 Ų

Pharmacokinetics

GI absorption : High
BBB permeant : Yes
P-gp substrate : No
CYP1A2 inhibitor : Yes
CYP2C19 inhibitor : No
CYP2C9 inhibitor : No
CYP2D6 inhibitor : No
CYP3A4 inhibitor : No
Log Kp (skin permeation) : -6.57 cm/s

Lipophilicity

Log Po/w (iLOGP) : 1.93
Log Po/w (XLOGP3) : 1.35
Log Po/w (WLOGP) : 1.31
Log Po/w (MLOGP) : 0.85
Log Po/w (SILICOS-IT) : 1.09
Consensus Log Po/w : 1.31

Druglikeness

Lipinski : 0.0
Ghose : None
Veber : 0.0
Egan : 0.0
Muegge : 0.0
Bioavailability Score : 0.55

Water Solubility

Log S (ESOL) : -2.32
Solubility : 0.964 mg/ml ; 0.00477 mol/l
Class : Soluble
Log S (Ali) : -1.56
Solubility : 5.55 mg/ml ; 0.0274 mol/l
Class : Very soluble
Log S (SILICOS-IT) : -2.62
Solubility : 0.484 mg/ml ; 0.00239 mol/l
Class : Soluble

Medicinal Chemistry

PAINS : 0.0 alert
Brenk : 0.0 alert
Leadlikeness : 1.0
Synthetic accessibility : 1.82

Safety of [ 38696-21-8 ]

Signal Word:Warning Class:N/A
Precautionary Statements:P261-P305+P351+P338 UN#:N/A
Hazard Statements:H302-H315-H319-H335 Packing Group:N/A
GHS Pictogram:

Application In Synthesis of [ 38696-21-8 ]

* 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.

  • Upstream synthesis route of [ 38696-21-8 ]
  • Downstream synthetic route of [ 38696-21-8 ]

[ 38696-21-8 ] Synthesis Path-Upstream   1~9

  • 1
  • [ 7752-82-1 ]
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  • [ 31402-54-7 ]
  • [ 38696-21-8 ]
YieldReaction ConditionsOperation in experiment
20%
Stage #1: With sodium hydride In N,N-dimethyl-formamide; mineral oil at 0℃; for 0.25 h;
Stage #2: at 0 - 20℃; for 4.5 h;
Step 39a: 5-Bromo-N-methylpyrimidin-2-amine (compound 0601-116) and 5-bromo-N,N- dimethylpyrimidin-2-amine (compound 0601-117)A mixture of 5-bromopyrimidin-2-amine (3.48 g, 20 mmol) and DMF (20 mL) was cooled to 0°C. To the mixture NaH (60percent, 1.44 g, 36 mmol) was added. After 15 minutes, iodomethane (5 mL, 80 mmol) was added and stirred at 0°C for 0.5 h and the mixture was warmed to room temperature for additional 4 hours. Water (30 mL) was added and extracted with ethyl acetate (3 x 30 mL). The combined organic layers was washed with brine, dried over Na2S04, concentrated and purified by column chromatograph on silica gel (ethyl acetate in petroleum ether, 10percent v/v) to give two compounds: compound 0601-116 (0.76 g, 20percent) as a white solid, LCMS: 190 [M+2]+; 1HNMR (400 MHz, DMSO-<3/4) δ 2.75 (d, J= 4.8 Hz, 3H), 7.35 (d, J= 4.0 Hz, 1H), 8.34 (s, 2H); compound 0601-117 (1.96 g, 49percent) as a yellow solid, LCMS: 202 [M+l]+; 1HNMR (400 MHz, DMSO-<3/4) δ 3.12 (s, 6H), 8.43 (s, 2H).
20%
Stage #1: With sodium hydride In N,N-dimethyl-formamide; mineral oil at 0℃; for 0.25 h;
Stage #2: at 0 - 20℃; for 4.5 h;
Step 39a: 5-Bromo-N-methylpyrimidin-2-amine (compound 0601-116) and 5-bromo-N,N-dimethylpyrimidin-2-amine (compound 0601-117)[0353]A mixture of 5-bromopyrimidin-2-amine (3.48 g, 20 mmol) and DMF (20 mL) was cooled to 0° C. To the mixture NaH (60percent, 1.44 g, 36 mmol) was added. After 15 minutes, iodomethane (5 mL, 80 mmol) was added and stirred at 0° C. for 0.5 h and the mixture was warmed to room temperature for additional 4 hours. Water (30 mL) was added and extracted with ethyl acetate (3×30 mL). The combined organic layers was washed with brine, dried over Na2SO4, concentrated and purified by column chromatograph on silica gel (ethyl acetate in petroleum ether, 10percent v/v) to give two compounds: compound 0601-116 (0.76 g, 20percent) as a white solid, LCMS: 190 [M+2]+; 1HNMR (400 MHz, DMSO-d6) δ 2.75 (d, J=4.8 Hz, 3H), 7.35 (d, J=4.0 Hz, 1H), 8.34 (s, 2H); compound 0601-117 (1.96 g, 49percent) as a yellow solid, LCMS: 202 [M+1]+; 1HNMR (400 MHz, DMSO-d6) δ 3.12 (s, 6H), 8.43 (s, 2H).
20%
Stage #1: With sodium hydride In N,N-dimethyl-formamide at 0℃; for 0.25 h;
Stage #2: at 0 - 20℃; for 4.5 h;
5-bromo-pyrimidine-2-amine (3.48g, 20mmol) and a mixture of DMF (20mL) was cooled to 0 . NaH (60percent, 1.44g, 36mmol) to the mixture was added. After 15 minutes, then 0.5 hours with stirring at O ° C. was added iodoethane (5 mL, 80 mmol), the mixture was further warmed to room temperature for 4 hours. With the addition of water (30mL) and extracted with ethyl acetate (3x30mL). The combined organic layers were washed with brine, dried over Na2SO4, and concentrated and purified by column chromatography (petroleum ether in ethyl acetate, 10percent v / v) on silica gel to give the two compounds: Compound 0601 the -116 as a white solid (0.76g, 20percent)
Reference: [1] Patent: WO2011/130628, 2011, A1, . Location in patent: Page/Page column 173
[2] Patent: US2013/102595, 2013, A1, . Location in patent: Paragraph 0352; 0353
[3] Patent: JP2015/187145, 2015, A, . Location in patent: Paragraph 0310
  • 2
  • [ 7752-82-1 ]
  • [ 74-88-4 ]
  • [ 38696-21-8 ]
YieldReaction ConditionsOperation in experiment
85% With sodium hydride In tetrahydrofuran at 20℃; [00159] Scheme 1. Preparation of relevant pyri(mi)dyl halides A-H. Key: (a) NBS, NH4OAc, MeCN, rt, 5 min, pyr: 85-90percent; pym: quant; (b) pyr: RCHO, Na(CN)BH3, MeCN, reflux, 1-12h (82percent, R = C5Hn); pym: NaH, Rl, THF, rt, overnight (85percent, R = Me); (c) Me3(Bn)NBr, f-BuONO, CH2Br2, rt, overnight, pyr: 77-83percent; pym: 30- 40percent; (d) pym: HI, CH2CI2, 0°C, 80-85percent; (e) i. NaOH, Br2, H20, rt, 50-60percent, ii. POCI3, PhNEt2, reflux, 4h, 75-85percent, iii. HI, CH2CI2, 0°C, 80-85percent; (f) ROH, Na, rt, 1-12 h, quant.; (g) RZnl, CI2Pd(PPh3)2, DMF/THF, rt, overnight, pyr (Br): 72percent (R = C6H13), pym (I) 81 percent, (R = C6H13); (h) alkyne, Cul, CI2Pd(PPh3)2, Et3N, MeCN, rt, 1-12 h, quant. [00161] The pyrimidyl bromides were prepared in a similar manner, beginning with bromination of 2-aminopyrimidine. N-Alkylation could not be achieved by reductive amination (presumably due to the decreased nucleophilicity of the amine) and was instead accomplished using NaH and an appropriate alkyl halide to give (B). Nonaqueous diazotization/halo-dediazoniation was used to prepare 5-bromo-2- halopyrimidines, but in diminished yield relative to the analogous reaction with the 2- aminopyridine (again, presumably due to the decreased nucleophilicity of the amine group). Alternatively, 2-pyrimidinone could serve as a precursor to 5-bromo-2- halopyrimidines (Lutz, F.; Kawasaki, T.; Soai, K. Tetrahedron-Asymmetry 2006, 17, 486.) or as a substrate for alkylation to generate 5-bromo-2-alkoxypyrimidines (D) (Kokatla, H. P.; Lakshman, M. K. Org. Lett. 2010, 12, 4478.) Introduction of an alkyne substituent at the 2-position to give ( proceeded satisfactorily under Sonogoshira conditions, but alkylation using Negishi conditions was unselective. Since reduction of the 2- alkynylpyrimidyl bromide (F) to the corresponding 2-alkyl pyrimidyl bromide (H) was complicated by competing removal of the bromine, we turned to 5-bromo-2- iodopyrimidine as a precursor for the cross coupling reactions and saw a dramatic improvement in selectivity and yields.
Reference: [1] Patent: WO2012/162818, 2012, A1, . Location in patent: Page/Page column 45-46
[2] Journal of Organic Chemistry, 2008, vol. 73, # 23, p. 9326 - 9333
  • 3
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YieldReaction ConditionsOperation in experiment
86% at 20℃; Inert atmosphere To a solution of 5-bromo-2-chloropyrimidine (2 g, 10.34 mmol) and dimethylamine (5 ml, 10.00 mmol) in tetrahydrofuran (2 ml_) was stirred at room temperature overnight. The solvent was removed and the residue was purified by silica gel chromatography 5percentEtOAc/PE) to give 5-bromo-N,N-dimethylpyrimidin-2-amine (1 .9 g, 8.93 mmol, 86 percent yield) as a white solid. LCMS: [M+H] 202.
3.2 g at 20℃; for 1 h; A mixture of 22.5 ml (45.5 mmol) solution of dimethylamine in THF, 3.0 g (15.5 mmol) 2-chloro-5-bromo-pyrimidine and ACN are stirred at RT for 1 h. The solvent is evaporated, water is added and the mixture is extracted with EtOAc. The organic phases are pooled, dried and evaporated yielding 3.2 g 5-bromo-N,N-dimethyl- pyrimidin-2-amine .
Reference: [1] ACS Medicinal Chemistry Letters, 2011, vol. 2, # 1, p. 34 - 38
[2] Patent: WO2017/98440, 2017, A1, . Location in patent: Page/Page column 212
[3] Patent: WO2017/194453, 2017, A1, . Location in patent: Page/Page column 46
  • 4
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YieldReaction ConditionsOperation in experiment
90% at 20℃; for 5 h; 50 percent Aqueous solution of dimethylamine (30 ml) was added to 5-bromo-2-chloropyridine (1.79 g, 10 mmol) and the mixture was stirred at room temperature under argon atmosphere for 5 hrs. Saturated sodium bicarbonate solution (15 ml) was added to the reaction mixture and the mixture was extracted with ethyl acetate. The extract was washed with brine and dried. The solvent was distilled off under reduced pressure and the residue was dried at 40 °C under reduced pressure for 2 hrs. to give 5-bromo-2-dimethylaminopyrimidine (1.83 g, 90 percent) as colorless crystals. m.p.: 81 - 82°C; IR (Nujol): 1586, 1527 cm-1; APCI-MS m/z: 202/204 [M+H]+.
90% at 20℃; for 5 h; Inert atmosphere (Preparation 29) 1)
50percent Aqueous solution of dimethylamine (30 ml) was added to 5-bromo-2-chloropyridine (1.79 g, 10 mmol) and the mixture was stirred at room temperature under argon atmosphere for 5 hrs.
Saturated sodium bicarbonate solution (15 ml) was added to the reaction mixture and the mixture was extracted with ethyl acetate.
The extract was washed with brine and dried.
The solvent was distilled off under reduced pressure and the residue was dried at 40° C. under reduced pressure for 2 hrs. to give 5-bromo-2-dimethylaminopyrimidine (1.83 g, 90percent) as colorless crystals.
m.p. : 81-82° C.; IR (Nujol) : 1586, 1527 cm-1; APCI-MSm/z: 202/204 [M+H]
Reference: [1] Patent: EP1481965, 2004, A1, . Location in patent: Page 29-30
[2] Patent: EP2959918, 2015, A1, . Location in patent: Paragraph 0111
  • 5
  • [ 7752-82-1 ]
  • [ 74-88-4 ]
  • [ 31402-54-7 ]
  • [ 38696-21-8 ]
YieldReaction ConditionsOperation in experiment
20%
Stage #1: With sodium hydride In N,N-dimethyl-formamide; mineral oil at 0℃; for 0.25 h;
Stage #2: at 0 - 20℃; for 4.5 h;
Step 39a: 5-Bromo-N-methylpyrimidin-2-amine (compound 0601-116) and 5-bromo-N,N- dimethylpyrimidin-2-amine (compound 0601-117)A mixture of 5-bromopyrimidin-2-amine (3.48 g, 20 mmol) and DMF (20 mL) was cooled to 0°C. To the mixture NaH (60percent, 1.44 g, 36 mmol) was added. After 15 minutes, iodomethane (5 mL, 80 mmol) was added and stirred at 0°C for 0.5 h and the mixture was warmed to room temperature for additional 4 hours. Water (30 mL) was added and extracted with ethyl acetate (3 x 30 mL). The combined organic layers was washed with brine, dried over Na2S04, concentrated and purified by column chromatograph on silica gel (ethyl acetate in petroleum ether, 10percent v/v) to give two compounds: compound 0601-116 (0.76 g, 20percent) as a white solid, LCMS: 190 [M+2]+; 1HNMR (400 MHz, DMSO-<3/4) δ 2.75 (d, J= 4.8 Hz, 3H), 7.35 (d, J= 4.0 Hz, 1H), 8.34 (s, 2H); compound 0601-117 (1.96 g, 49percent) as a yellow solid, LCMS: 202 [M+l]+; 1HNMR (400 MHz, DMSO-<3/4) δ 3.12 (s, 6H), 8.43 (s, 2H).
20%
Stage #1: With sodium hydride In N,N-dimethyl-formamide; mineral oil at 0℃; for 0.25 h;
Stage #2: at 0 - 20℃; for 4.5 h;
Step 39a: 5-Bromo-N-methylpyrimidin-2-amine (compound 0601-116) and 5-bromo-N,N-dimethylpyrimidin-2-amine (compound 0601-117)[0353]A mixture of 5-bromopyrimidin-2-amine (3.48 g, 20 mmol) and DMF (20 mL) was cooled to 0° C. To the mixture NaH (60percent, 1.44 g, 36 mmol) was added. After 15 minutes, iodomethane (5 mL, 80 mmol) was added and stirred at 0° C. for 0.5 h and the mixture was warmed to room temperature for additional 4 hours. Water (30 mL) was added and extracted with ethyl acetate (3×30 mL). The combined organic layers was washed with brine, dried over Na2SO4, concentrated and purified by column chromatograph on silica gel (ethyl acetate in petroleum ether, 10percent v/v) to give two compounds: compound 0601-116 (0.76 g, 20percent) as a white solid, LCMS: 190 [M+2]+; 1HNMR (400 MHz, DMSO-d6) δ 2.75 (d, J=4.8 Hz, 3H), 7.35 (d, J=4.0 Hz, 1H), 8.34 (s, 2H); compound 0601-117 (1.96 g, 49percent) as a yellow solid, LCMS: 202 [M+1]+; 1HNMR (400 MHz, DMSO-d6) δ 3.12 (s, 6H), 8.43 (s, 2H).
20%
Stage #1: With sodium hydride In N,N-dimethyl-formamide at 0℃; for 0.25 h;
Stage #2: at 0 - 20℃; for 4.5 h;
5-bromo-pyrimidine-2-amine (3.48g, 20mmol) and a mixture of DMF (20mL) was cooled to 0 . NaH (60percent, 1.44g, 36mmol) to the mixture was added. After 15 minutes, then 0.5 hours with stirring at O ° C. was added iodoethane (5 mL, 80 mmol), the mixture was further warmed to room temperature for 4 hours. With the addition of water (30mL) and extracted with ethyl acetate (3x30mL). The combined organic layers were washed with brine, dried over Na2SO4, and concentrated and purified by column chromatography (petroleum ether in ethyl acetate, 10percent v / v) on silica gel to give the two compounds: Compound 0601 the -116 as a white solid (0.76g, 20percent)
Reference: [1] Patent: WO2011/130628, 2011, A1, . Location in patent: Page/Page column 173
[2] Patent: US2013/102595, 2013, A1, . Location in patent: Paragraph 0352; 0353
[3] Patent: JP2015/187145, 2015, A, . Location in patent: Paragraph 0310
  • 6
  • [ 506-59-2 ]
  • [ 32779-36-5 ]
  • [ 38696-21-8 ]
Reference: [1] Patent: US2004/82586, 2004, A1,
[2] Patent: WO2014/100695, 2014, A1, . Location in patent: Paragraph 00373
  • 7
  • [ 5621-02-3 ]
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Reference: [1] Bulletin of the Chemical Society of Japan, 1999, vol. 72, # 11, p. 2523 - 2535
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Reference: [1] Journal of Organic Chemistry, 2012, vol. 77, # 16, p. 6908 - 6916
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  • [ 38696-21-8 ]
  • [ 56621-99-9 ]
Reference: [1] Journal of Organic Chemistry, 2012, vol. 77, # 16, p. 6908 - 6916
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