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Chemical Structure| 939412-86-9 Chemical Structure| 939412-86-9

Structure of 939412-86-9

Chemical Structure| 939412-86-9

*Storage: Inert atmosphere, room temperature.

(3-Chloropyrazin-2-yl)methanamine HCl

CAS No.: 939412-86-9

4.5 *For Research Use Only !

Cat. No.: A239564 Purity: 95%

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Product Details of [ 939412-86-9 ]

CAS No. :939412-86-9
Formula : C5H7Cl2N3
M.W : 180.04
SMILES Code : NCC1=NC=CN=C1Cl.[H]Cl
MDL No. :MFCD09910171
InChI Key :YYVVOYJKQZWKFS-UHFFFAOYSA-N
Pubchem ID :42614233

Safety of [ 939412-86-9 ]

GHS Pictogram:
Signal Word:Warning
Hazard Statements:H302-H315-H319-H335
Precautionary Statements:P261-P305+P351+P338

Computational Chemistry of [ 939412-86-9 ] 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 3.0
Num. H-bond donors 1.0
Molar Refractivity 41.68
TPSA ?

Topological Polar Surface Area: Calculated from
Ertl P. et al. 2000 J. Med. Chem.

51.8 Ų

Lipophilicity

Log Po/w (iLOGP)?

iLOGP: in-house physics-based method implemented from
Daina A et al. 2014 J. Chem. Inf. Model.

0.0
Log Po/w (XLOGP3)?

XLOGP3: Atomistic and knowledge-based method calculated by
XLOGP program, version 3.2.2, courtesy of CCBG, Shanghai Institute of Organic Chemistry

0.44
Log Po/w (WLOGP)?

WLOGP: Atomistic method implemented from
Wildman SA and Crippen GM. 1999 J. Chem. Inf. Model.

1.24
Log Po/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.

-0.39
Log Po/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

1.18
Consensus Log Po/w?

Consensus Log Po/w: Average of all five predictions

0.49

Water Solubility

Log S (ESOL):?

ESOL: Topological method implemented from
Delaney JS. 2004 J. Chem. Inf. Model.

-1.61
Solubility 4.4 mg/ml ; 0.0245 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.

-1.1
Solubility 14.4 mg/ml ; 0.0802 mol/l
Class?

Solubility class: Log S scale
Insoluble < -10 < Poorly < -6 < Moderately < -4 < Soluble < -2 Very < 0 < Highly

Very 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

-2.29
Solubility 0.923 mg/ml ; 0.00513 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

Yes
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.

-7.09 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)

1.96

Application In Synthesis of [ 939412-86-9 ]

* 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 [ 939412-86-9 ]

[ 939412-86-9 ] Synthesis Path-Downstream   1~2

  • 1
  • [ 939412-86-9 ]
  • [ 28697-11-2 ]
  • [ 1418307-23-9 ]
YieldReaction ConditionsOperation in experiment
84.4% To a mixture of (3-chloropyrazin-2-yl)methanamine hydrochloride (3.9 g, 21.8 mmol, leq) and (S)-l-((benzyloxy)carbonyl)piperidine-2-carboxylic acid (5.73 g, 21.8 mmol, 1.0 eq) in DCM (50 mL), was added TEA (12.1 mL, 87.2 mmol, 4.0 eq). The reaction mixture was cooled to 0 C. After 10 min, HATU (9.94 g, 26.2 mmol, 1.2 eq) was added, and the reaction mixture was stirred at 0 C for 1 h and then at room temperature overnight. The mixture was washed subsequently with 0.1 M HCl-solution, 5% NaHC0 ; water and brine. It was dried over anhydrous Na2S04, filtered and concentrated. The residue was purified by silica gel column chromatography (DCM/MeOH=200: l - 50: 1) to afford the desired product 1 (7.13 g, yield 84.4 %). LCMS: m/z = 389 [M+H]+.
73% With N-ethyl-N,N-diisopropylamine; N-[(dimethylamino)-3-oxo-1H-1,2,3-triazolo[4,5-b]pyridin-1-yl-methylene]-N-methylmethanaminium hexafluorophosphate; In dichloromethane; at 20℃; 2-Chloro-3-aminomethylpyrazine HCl (2 g; 11.1 minol), (5)-(-)-l-(carbobenzyloxy)-2- piperidine carboxylic acid (3.2 g; 12.2 minol) and N,N-diisopropylethylamine (7.7 mL; 44.4 minol) were dissolved in dichloromethane (100 mL). N-[(dimethylamino)-lH-l,2,3-triazolo- [4,5-6]pyridin-l -ylmethylene]-N-methylmethanaminium hexafluorophosphate N-oxide (HATU) (6.3 g; 16.7 minol) was added and the resulting mixture was stirred overnight at room temperature. The mixture was washed with aqueous sodium bicarbonate solution and water. The organic layer was then dried over sodium sulfate, filtered and evaporated to dryness. The crude material was chromatographed over S1O2 using a gradient of 20 -80% ethyl acetate in heptane to give 4.4 g; 11.3 minol of benzyl (2<S)-2-[(3-chloropyrazin-2-yl)methylcarbamoyl]piperidine-l- carboxylate (1-1) as a colorless oil (73%). Data: LCMS Rt = 5.85 min; m/z 389.2 (M+H)+; HPLC Rt = 8.30 min; NMR (400 MHz, CDCh, 300 K): delta = 8.35 (IH, d), 8.29 (IH, d), 7.35 (5H, bs), 5.20 (2H, s), 4.95 (IH, s), 4.76 (IH, d), 4.60 (IH, dd), 4.18 (IH, bs), 3.03 (IH, bs), 2.36 (IH, bd), 1.88 - 1.47 (6H, m).
54.6% With triethylamine; HATU; In dichloromethane; at 0 - 20℃; (S)-benzyl 2-((3-chloropyrazin-2-yl)methylcarbamoyl)piperidine-1-carboxylate To a solution of (3-chloropyrazin-2-yl)methanamine.HCI (3.60 g, 19.98 mmol, 40% wt) and (S)- 1-N-Cbz-pipecolinic acid (2.63 g, 9.99 mmol) in dichloromethane (40 mL) was added triethylamine (2.78 mL, 19.98 mmol) and the reaction mixture was cooled to 0C. After 15 min stirring at 0C, HATU (4.18 g, 10.99 mmol) was added. The mixture was stirred for 1 hour at 0C and then overnight at room temperature. The mixture was washed with 0.1 M HCI-solution, 5% NaHC03, water and brine, dried over sodium sulfate and concentrated in vacuo. The product was purified using silica gel chromatography (dichloromethane/methanol = 99/1 to 97/3 v/v% + triethylamine) to give 2.12 g of (S)-benzyl 2-((3-chloropyrazin-2- yl)methylcarbamoyl)piperidine-1-carboxylate (54.6%).
With N-ethyl-N,N-diisopropylamine; N-[(dimethylamino)-3-oxo-1H-1,2,3-triazolo[4,5-b]pyridin-1-yl-methylene]-N-methylmethanaminium hexafluorophosphate; In dichloromethane; at 20℃; 2-Chloro-3- aminomethylpyrazine.HCl (2 g; 11.1 mmol), <strong>[28697-11-2](S)-(-)-1-(carbobenzyloxy)-2-piperidine carboxylic acid</strong> (3.2 g; 12.2 mmol) and N,N-diisopropylethylamine (7.7 mL; 44.4 mmol) were dissolved in dichloromethane (100 mL). HATU (6.3 g; 16.7 mmol) was added and the resulting mixture was stirred overnight at room temperature. The mixture was washed with aqueous sodium bicarbonate solution and water. The organic layer was then dried over sodium sulfate, filtered and evaporated to dryness. The crude material was chromatographed over SiO2 using a gradient of 20-80% ethyl acetate in heptane to give 4.4 g; 11.3 mmol of benzyl (2S)-2-[(3-chloropyrazin-2-yl)methylcarbamoyl]piperidine- 1-carboxylate as a colorless oil (73%).

  • 2
  • [ 939412-86-9 ]
  • [ 219735-99-6 ]
  • [3-(2-chloro-4-methoxyphenyl)pyrazin-2-yl]methylamine [ No CAS ]
YieldReaction ConditionsOperation in experiment
64 mg With tetrakis(triphenylphosphine) palladium(0); potassium carbonate; In 1,2-dimethoxyethane; water; at 110℃; for 0.333333h;Microwave irradiation; (3-Chloropyrazin-2-yl)methanamine hydrochloride (157 mg, 0.873 mmol), 2-chloro-4- methoxyphenylboronic acid (325 mg, 1.75 mmol), potassium carbonate (482 mg, 3.49 mmol) and tetrakis(triphenylphosphine)palladium(0) (50 mg, 0.043 mmol) in water (1.5 mL) and DME (4.5 mL) was microwave irradiated at 110 C for 30 min. After organic solvent was removed in vacuo, the residue was extracted with EtOAc and washed successively with water and brine. The organic layer was dried over Na2S04and concentrated in vacuo. The residue was purified by flash chromatography on silica gel (MeOH/DCM) to obtain 64 mg of [3-(2-chloro-4-methoxy- phenyl)-pyrazin-2-yl]-methylamine.
 

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