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Chemical Structure| 108-13-4 Chemical Structure| 108-13-4

Structure of 108-13-4

Chemical Structure| 108-13-4

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CAS No.: 108-13-4

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Product Details of [ 108-13-4 ]

CAS No. :108-13-4
Formula : C3H6N2O2
M.W : 102.09
SMILES Code : O=C(N)CC(N)=O
MDL No. :MFCD00008034
InChI Key :WRIRWRKPLXCTFD-UHFFFAOYSA-N
Pubchem ID :7911

Safety of [ 108-13-4 ]

GHS Pictogram:
Signal Word:Warning
Hazard Statements:H302-H315-H319-H332-H335
Precautionary Statements:P261-P280-P305+P351+P338

Computational Chemistry of [ 108-13-4 ] Show Less

Physicochemical Properties

Num. heavy atoms 7
Num. arom. heavy atoms 0
Fraction Csp3 0.33
Num. rotatable bonds 2
Num. H-bond acceptors 2.0
Num. H-bond donors 2.0
Molar Refractivity 22.35
TPSA ?

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

86.18 ?2

Lipophilicity

Log Po/w (iLOGP)?

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

-0.33
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

-1.82
Log Po/w (WLOGP)?

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

-1.65
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.

-1.81
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

-1.37
Consensus Log Po/w?

Consensus Log Po/w: Average of all five predictions

-1.4

Water Solubility

Log S (ESOL):?

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

0.81
Solubility 653.0 mg/ml ; 6.39 mol/l
Class?

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

Highly soluble
Log S (Ali)?

Ali: Topological method implemented from
Ali J. et al. 2012 J. Chem. Inf. Model.

0.53
Solubility 344.0 mg/ml ; 3.37 mol/l
Class?

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

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

0.61
Solubility 417.0 mg/ml ; 4.08 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.

-8.21 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

 2.0
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

1.0 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)

 1.0

Application In Synthesis of [ 108-13-4 ]

* 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 [ 108-13-4 ]

[ 108-13-4 ] Synthesis Path-Downstream   1~9

  • 1
  • [ 50743-32-3 ]
  • [ 108-13-4 ]
  • [ 86443-28-9 ]
  • 2
  • [ 108-13-4 ]
  • [ 2345-56-4 ]
  • 3
  • [ 71-33-0 ]
  • [ 108-13-4 ]
  • 1,2,3,4,5,6-hexahydro-6-(dicarbamoylmethyl)-1,3,5-triazine-2,4-dione [ No CAS ]
  • 4
  • [ 108-13-4 ]
  • [ 383-63-1 ]
  • [ 672-47-9 ]
YieldReaction ConditionsOperation in experiment
44.4% With NaH; In toluene; mineral oil; butan-1-ol; EXAMPLE 3 4,6-Dihydroxy-2-trifluoromethylpyrimidine, Compound VI, starting material for Step 2 Sodium hydride (900 g, 57.5% dispersion in mineral oil; 518 g active NaH; 22.5M) was stirred with 7.5 L toluene in a 22 L round-bottomed flask. Butanol was added over 5 hr. so that the pot temperature was maintained at 40. The mixture was stirred an additional 16 hr. Malonamide (765 g; 7.5 M) was added, followed by ethyl trifluoroacetate (1065 g; 7.5 M). The ensuing reaction was exothermic; the mixture was then heated on a steam-bath for 3.5 hrs. It was then stirred at 23-25 for an additional 16 hrs. The mixture was extracted with water (1*4 L and 1*2 L). The combined aqueous extracts were treated with activated charcoal and filtered. The filtrate was maintained at 10-15 as it was acidified to pH 1-2 with 37% hydrochloric acid. The mixture was chilled to 5. The solid was isolated by filtration and dried at 50 in vacuo to give 600 g (44.4% yield) VI m.p. 255-256 (Lit. 265).
To a suspension of 60% NaH in oil (11.7 g) in toluene (98 mL) was added BuOH (21. 8 g). The mixture was stirred at ambient temperature for 16 hr. To the mixture were added malonamide (10.0 g) and trifluoro-acetic acid ethyl ester (13.9 g). The mixture was stirred at 100C for 3.5 hr and ambient temperature for 16 hr. The organic layer was extracted with water (two times) and the aqueous layer was filtrated through activated carbon. To the aqueous layer was added conc. HCI (pH 1) and the suspension was stirred at 4C for 2 hr. The precipitate was collected by filtration and dried at 80C under reduced pressure to give 2-trifluoromethyl-pyrimidine-4, 6-diol (3.25 g). ESI MS m/e 178, M-H+ ;'H NMR (300 MHz, CDC13) 8 6.00 (s, 1 H), 12.48 (brs, 2 H).
  • 5
  • [ 349-43-9 ]
  • [ 108-13-4 ]
  • [ 1313546-74-5 ]
  • 6
  • [ 108-13-4 ]
  • [ 109-94-4 ]
  • [ 1193-24-4 ]
  • 7
  • [ 108-13-4 ]
  • [ 431-47-0 ]
  • [ 672-47-9 ]
YieldReaction ConditionsOperation in experiment
-(Trifluoromethyl)pyrimidine-4,6-diol (15) Sodium hydride (57 g of a 60% dispersion in mineral oil, 1430 mmol) was stirred in toluene under nitrogen and cooled with a wet ice bath. Butanol (130 mL, 1430 mmol) was added drop-wise and mixture was stirred for 30 min.Malonamide (50 g, 480 mmol) was added in one portion followed by the drop-wise addition of methyl trifluoroacetate (14) (67.5 g, 475 mmol), which led to an immediate exotherm. When the addition was complete, the reaction mixture was stirred at 40 C overnight and then cooled to RT. The reaction was diluted with 1 N HCI (300 mL) and then concentrated HCI was added until pH = 2. The layers were separated and the aqueous layer was extracted with ethyl acetate (3X), dried over magnesium sulfate, and concentrated. The resulting orange solid was triturated with 2:1 heptane: DCM (2 x 100 mL), collected by filtration, and dried under vacuum overnight to provide 28.1 g of 15 as a light orange solid. LCMS m/z 181.1 (M+1 ). H NMR (400 MHz, CD3OD) δ 5.90 (s, 1 H).
To the reaction flask was added 500 mL methanol, cooled to 0 ~ 5 C, 118.6 g sodium methoxide was added,Stirring until substantially clear, adding 102.1g malonamide, stirring, warmed to 35 ,153.7 g of methyl trifluoroacetate was added, and after completion of the addition, the mixture was stirred for 30 minutes,The temperature was raised to 65 to 70 C and refluxed for 15 hours. After the reaction, cooling to 25 ~ 35 ,100 mL methyl tertiary ether was added dropwise and the temperature dropped to 5 ~ 10 C. After stirring, the filter cake was rinsed with ruthenium ether. After filtration, the solid was transferred to a single-necked flask and concentrated under reduced pressure. Add water, stir until clear, add concentrated hydrochloric acid to adjust pH = 1 ~ 2, filter to obtain filter cake 95g. The filter cake was added with 250 mL of ethyl acetate, heated to reflux, stirred, filtered and concentrated under reduced pressure to constant weight to give 118.4 g of an off-white solid in a yield of 65.8% and HPLC of 94.3%.
  • 8
  • [ 108-13-4 ]
  • [ 155377-05-2 ]
  • 2-(6-trifluoromethyl-pyridin-2-yl)-1H-pyrimidine-4,6-dione [ No CAS ]
YieldReaction ConditionsOperation in experiment
With sodium; In ethanol; for 1h;Reflux; Step 1: Preparation of 2-(6-Trifluoromethyl-pyridin-2-yl)-1H-pyrimidine-4, 6-dione To a solution of sodium (32 g, 0.16 mol) in ethanol (500 mL) was added 6-trifluoro- methylpyridine-2-carboxylic acid methyl ester (6.15 g, 3 mmol) and malonamide (1.02 g, 1 mmol). The mixture was heated to reflux for 1 hour, then concentrated to give a residue which was poured to water (100 mL). Saturated NaHCO3 solution was added to adjust to pH 7, the mixture was filtered, and then added iN HC1 solution to adjust pH to 3. DCM (20 mL) was added, and the precipitated solid was collected by filtration and dried to give 2-(6-trifluoromethyl-pyridin-2-yl)- 1 H-pyrimidine-4,6-dione. LCMS: [M+ 1] = 257.9
  • 9
  • [ 108-13-4 ]
  • [ 126712-07-0 ]
  • 5-methoxy-2-oxo-1,2-dihydroquinoline-3-carboxamide [ No CAS ]
 

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