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Chemical Structure| 54568-12-6 Chemical Structure| 54568-12-6

Structure of 54568-12-6

Chemical Structure| 54568-12-6

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Product Details of [ 54568-12-6 ]

CAS No. :54568-12-6
Formula : C6H9N3
M.W : 123.16
SMILES Code : NC1=NC=NC(C)=C1C
MDL No. :MFCD09909808
InChI Key :SMPCNKPYFMZJMO-UHFFFAOYSA-N
Pubchem ID :643252

Safety of [ 54568-12-6 ]

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

Computational Chemistry of [ 54568-12-6 ] Show Less

Physicochemical Properties

Num. heavy atoms 9
Num. arom. heavy atoms 6
Fraction Csp3 0.33
Num. rotatable bonds 0
Num. H-bond acceptors 2.0
Num. H-bond donors 1.0
Molar Refractivity 36.37
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.

1.36
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

0.62
Log Po/w (WLOGP)?

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

0.68
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.

0.06
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

1.06
Consensus Log Po/w?

Consensus Log Po/w: Average of all five predictions

0.76

Water Solubility

Log S (ESOL):?

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

-1.49
Solubility 4.01 mg/ml ; 0.0325 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.

-1.28
Solubility 6.43 mg/ml ; 0.0522 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

-2.02
Solubility 1.17 mg/ml ; 0.00951 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.

-6.61 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)

1.49

Application In Synthesis of [ 54568-12-6 ]

* 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 [ 54568-12-6 ]

[ 54568-12-6 ] Synthesis Path-Downstream   1~8

  • 1
  • [ 67434-65-5 ]
  • [ 54568-12-6 ]
YieldReaction ConditionsOperation in experiment
42% To a solution of 4-chloro-5,6-dimethylpyrimidine D8 (0.18 g, 1.26 mmol) in dry toluene (4 ml) were added sodium t-butoxyde (0.17 g, 1.77 mmol), Pd2(dba)3 (0.12 g, 0.13 mmol), BINAP (0.24 g, 0.38 mmol) and benzophenone imine (0.25 ml, 1.51 mmol). The resulting mixture was degassed (3 x pump/N2) and then heated to 80 0C. After 1 h stirring, the mixture was cooled down to room temperature, diluted with Et2O (100 ml) and filtered through a celite pad. Volatiles were evaporated, the resulting oil was dissolved in THF (20 ml) and HCl (3 M aqueous solution, 0.63 ml, 1.89 mmol) was added. The mixture was stirred at room temperature for 3 h, concentrated under reduced pressure, neutralized with a saturated NaHCO3 aqueous solution and diluted with DCM (50 ml). The inorganic layer was back-extracted with DCM (2 x 50 ml). The collected organic layers were passed through a phase separator tube and evaporated. The orange solid residue was triturated several times with Et2O and dried to afford the title compound D9 (0.067 g, 0.54 mmol, 42% yield). 1H NMR (400 MHz, CDCl3) δ(ppm): 8.38 (s, 1 H), 4.78 (bs, 1 H), 2.43 (s, 3 H), 2.08 (s, 3 H).
  • 4
  • [ 67434-65-5 ]
  • [ 7664-41-7 ]
  • [ 54568-12-6 ]
  • 5
  • [ 14394-62-8 ]
  • [ 10034-85-2 ]
  • phosphorus [ No CAS ]
  • [ 54568-12-6 ]
  • 6
  • [ 14394-62-8 ]
  • [ 7732-18-5 ]
  • zinc dust [ No CAS ]
  • [ 54568-12-6 ]
  • 7
  • [ 1780-32-1 ]
  • [ 54568-12-6 ]
  • 8
  • [ 54568-12-6 ]
  • [ 1097180-24-9 ]
  • [ 1097180-31-8 ]
  • C19H28N4O2 [ No CAS ]
YieldReaction ConditionsOperation in experiment
In N,N-dimethyl-formamide; at 80℃; for 4h; A solution of 1,1-dimethylethyl (25)-2-(3-bromo-2-oxopropyl)-l-piperidinecarboxylate D2 (0.10 g, 0.31 mmol) and 5,6-dimethyl-4-pyrimidinamine D9 (0.042 g, 0.34 mmol) in DMF (1 ml) was stirred at 80 0C for 4 h. The solvent was evaporated under reduced pressure and the residue purified by flash chromatography on silica gel (from DCM 100 to DCM /MeOH 98/2) and then eluted through a SCX column to afford a crude material (0.018 g) containing the title compound DlO, the corresponding N-Boc protected derivative and some residual 5,6-dimethyl-4-pyrimidinamine. [N-Boc derivative data. UPLC: rt = 0.58 min, peak observed: 345 (M+l). C1QH2SN4O2 requires 344]. The crude was dissolved in DCM (2 ml), TFA (0.50 ml) was added drop wise and the reaction left under stirring for 1 h at room temperature. Volatiles were removed under reduced pressure and the residue eluted through a SCX cartridge to afford a crude material containing the title compound DlO (0.012 g) contaminated with some residual 5,6-dimethyl-4-pyrimidinamine. UPLC: rt = 0.36 min, peak observed: 245 (M+l). C14H20N4 requires 244.
 

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Technical Information

Categories

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