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Chemical Structure| 56-45-1
Chemical Structure| 56-45-1

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CAS No.: 56-45-1

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L-Serine is a non-essential amino acid that plays a critical role in cell proliferation and metabolism. It is suitable for biological research and studies on amino acid metabolism-related diseases.

Synonyms: Serine;(S)-Serine;L-Serine

4.5 *For research use only!

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Product Details of [ 56-45-1 ]

CAS No. :56-45-1
Formula : C3H7NO3
Linear Structure Formula :NH3CH(CH2OH)CO2
M.W : 105.09
Synonyms :
Serine;(S)-Serine;L-Serine
MDL No. :MFCD00064224
InChI Key :MTCFGRXMJLQNBG-REOHCLBHSA-N
Pubchem ID :5951

Safety of [ 56-45-1 ]

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

Calculated chemistry of [ 56-45-1 ] Show Less

Physicochemical Properties

Num. heavy atoms 7
Num. arom. heavy atoms 0
Fraction Csp3 0.67
Num. rotatable bonds 2
Num. H-bond acceptors 4.0
Num. H-bond donors 3.0
Molar Refractivity 22.18
TPSA ?

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

83.55 ?2

Lipophilicity

Log Po/w (iLOGP)?

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

0.18
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

-3.07
Log Po/w (WLOGP)?

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

-1.61
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.

-3.91
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

-1.45
Consensus Log Po/w?

Consensus Log Po/w: Average of all five predictions

-1.97

Water Solubility

Log S (ESOL):?

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

1.57
Solubility 3950.0 mg/ml ; 37.5 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.

1.88
Solubility 7970.0 mg/ml ; 75.9 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

1.3
Solubility 2080.0 mg/ml ; 19.8 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.

-9.12 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

3.0
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)

1.51

Application In Synthesis [ 56-45-1 ]

* 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 [ 56-45-1 ]
  • Downstream synthetic route of [ 56-45-1 ]

[ 56-45-1 ] Synthesis Path-Upstream   1~2

  • 1
  • [ 67-56-1 ]
  • [ 56-45-1 ]
  • [ 7691-28-3 ]
YieldReaction ConditionsOperation in experiment
65%
Stage #1: With bromic acid; potassium bromide; sodium nitrite In water at -10 - 20℃;
Stage #2: With bromic acid In water at 65℃; for 48 h;
[1496] Step 2: methyl 2-bromo-3-hydroxypropanoate[1497] To a solution of L-serine (5.0 g, 47.6 mmol), a 48 w/wpercent bromic acid solution (13.0 mL, 109.5 mmol), and potassium bromide (20.0 g, 157.1 mmol) in water (44.0 mL) was added portionwise sodium nitrite (6.0 g, 80.9 mmol) at -10 ℃. The reaction mixture was stirred at room temperature overnight. The reaction mixture was saturated with sodium chloride and then extracted with ethyl acetate. The organic layer was dried over anhydrous magnesium sulfate, filtered, and then evaporated. The residue was dissolved in methanol (50.0 mL) and then 48 w/wpercent bromic acid (0.2 mL) was added thereto. The reaction mixture was stirred at 65 ℃ for 2 days and then concentrated under reduced pressure to discard excess methanol. The resulting dark yellow residue was dissolved in dichloromethane (100.0 mL) and then washed with a saturated sodium hydrogen carbonate solution (50.0 mL) and brine. The organic layer was dried over anhydrous sodium sulfate, filtered, and then evaporated. The residue was dried under reduced pressure to give 5.7 g of the titled compound (Yield: 65percent).[1498] 1H NMR (CDCl3, 400 MHz) δ 4.36(t, 1H), 4.01-4.08(m, 1H), 3.93-3.97(m, 1H), 3.82(s, 3H), 2.56(t, 1H)
65%
Stage #1: With bromic acid; potassium bromide; sodium nitrite In water at -10 - 20℃;
Stage #2: at 65℃; for 48 h;
Step 2:
methyl 2-bromo-3-hydroxypropanoate
To a solution of L-serine (5.0 g, 47.6 mmol), a 48 w/w percent bromic acid solution (13.0 mL, 109.5 mmol), and potassium bromide (20.0 g, 157.1 mmol) in water (44.0 mL) was added portionwise sodium nitrite (6.0 g, 80.9 mmol) at -10° C.
The reaction mixture was stirred at room temperature overnight.
The reaction mixture was saturated with sodium chloride and then extracted with ethyl acetate.
The organic layer was dried over anhydrous magnesium sulfate, filtered, and then evaporated.
The residue was dissolved in methanol (50.0 mL) and then 48 w/w percent bromic acid (0.2 mL) was added thereto.
The reaction mixture was stirred at 65° C. for 2 days and then concentrated under reduced pressure to discard excess methanol.
The resulting dark yellow residue was dissolved in dichloromethane (100.0 mL) and then washed with a saturated sodium hydrogen carbonate solution (50.0 mL) and brine.
The organic layer was dried over anhydrous sodium sulfate, filtered, and then evaporated.
The residue was dried under reduced pressure to give 5.7 g of the titled compound (Yield: 65percent).
1H NMR (CDCl3, 400 MHz) δ 4.36 (t, 1H), 4.01-4.08 (m, 1H), 3.93-3.97 (m, 1H), 3.82 (s, 3H), 2.56 (t, 1H)
Reference: [1] Patent: WO2013/43001, 2013, A1, . Location in patent: Paragraph 1496; 1497; 1498
[2] Patent: US2015/11528, 2015, A1, . Location in patent: Paragraph 0818-0819
  • 2
  • [ 56-45-1 ]
  • [ 108-98-5 ]
  • [ 34317-61-8 ]
Reference: [1] Journal of the American Chemical Society, 1993, vol. 115, # 4, p. 1264 - 1270
 

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