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Chemical Structure| 38696-21-8 Chemical Structure| 38696-21-8

Structure of 38696-21-8

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

CAS No. :38696-21-8
Formula : C6H8BrN3
M.W : 202.05
SMILES Code : CN(C1=NC=C(Br)C=N1)C
MDL No. :MFCD07368228
InChI Key :NYMYGNLCILQUMT-UHFFFAOYSA-N
Pubchem ID :12735315

Safety of [ 38696-21-8 ]

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

Computational Chemistry of [ 38696-21-8 ] Show Less

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 ?

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

29.02 Ų

Lipophilicity

Log Po/w (iLOGP)?

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

1.93
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

1.35
Log Po/w (WLOGP)?

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

1.31
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.

0.85
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

1.09
Consensus Log Po/w?

Consensus Log Po/w: Average of all five predictions

1.31

Water Solubility

Log S (ESOL):?

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

-2.32
Solubility 0.964 mg/ml ; 0.00477 mol/l
Class?

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

Soluble
Log S (Ali)?

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

-1.56
Solubility 5.55 mg/ml ; 0.0274 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

-2.62
Solubility 0.484 mg/ml ; 0.00239 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

Yes
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.

-6.57 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

0.0
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)

1.82

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.

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

[ 38696-21-8 ] Synthesis Path-Downstream   1~2

  • 1
  • [ 557-21-1 ]
  • [ 38696-21-8 ]
  • [ 55338-76-6 ]
YieldReaction ConditionsOperation in experiment
53% tetrakis(triphenylphosphine) palladium(0); In N,N-dimethyl-formamide; at 86.0℃; for 4.0h; Step B. 2-(dimethylamino)pyrimidine-5-carbonitrile <n="77"/>The compound (5-Bromo-pyrimidin-2-yl)-dimethyl-amine (202 mg, 1.0 mmol), Zn(CN)2 (82 mg, 0.7 mmol) and Pd(PPh3)4 (58 mg, 0.05 mmol) in anhydrous DMF (1.0 ml) was heated to 86C (oil bath temperature) for 4 hours, then cooled to room temperature, diluted with toluene (5 ml), washed twice with diluted NH4OH solution, brine and dried over Na2SO4, then filtered and concentrated. The residue was separated by flash chromatography (CH2CI2ZTHF = 40:1) to give 79 mg (53%) of the desired product as a white solid. 2-(dimethylamino)pyrimidine-5-carbonitrile, MS: m/z 149 (M + H)
  • 2
  • [ 38696-21-8 ]
  • [ 73183-34-3 ]
  • [ 1032759-30-0 ]
YieldReaction ConditionsOperation in experiment
60% With dichloro(1,1'-bis(diphenylphosphanyl)ferrocene)palladium(II)*CH2Cl2; potassium acetate; In 1,4-dioxane; 1,2-dimethoxyethane; at 150.0℃; for 0.25h;Inert atmosphere; Microwave irradiation; A mixture of 5-bromo-N,N-dimethylpyrimidin-2-amine (0.966 g, 4.78 mmol), 4,4,4',4',5,5,5',5'-octamethyl-2,2'-bi(1,3,2-dioxaborolane) (1.46 g, 5.74 mmol), PdCl2dppf(DCM) (0.114 g, 0.14 mmol) and KOAc (1.407 g, 14.34 mmol) were placed under Ar in a 20 mL microwave flask. Anhydrous 1,2-dimethoxyethane (16 mL) was added and the flask was irradiated at 150 oC for 15 minutes. The reaction was filtered through celite, concentrated and slurried in EtOAc. The reaction was filtered through celite again and the organics were concentrated and purified by column chromatography 0 to 30 % EtOAC in Hexanes. The material was isolated as a light teal solid (0.718 g, 60 % yield). 1H NMR (400 MHz, CDCl3) delta 8.59 (s, 2H), 3.21 (s, 6H), 1.31 (s, 12H).13C NMR (100 MHz, CDCl3) delta 164.1, 83.7, 77.4, 37.2, 25.2, 24.9. HRMS (EI+) m/z calculated for C12H12BN3O2 [M+H]+: 250.1721, found: 250.17189.
With dichloro(1,1'-bis(diphenylphosphanyl)ferrocene)palladium(II)*CH2Cl2; potassium acetate; In 1,4-dioxane; at 100.0℃; for 12h;Inert atmosphere; PdCl2(dppf)-CH2Cl2 adduct (323 mg, 0.396 mmol) was added to a solution of 4,4,4',4',5,5,5',5'-octamethyl-2,2'-bi(1 ,3,2-dioxaborolane) (1207 mg, 4.75 mmol), 5-bromo- N,N-dimethylpyrimidin-2-amine (800 mg, 3.96 mmol) and potassium acetate (1 166 mg, 1 1 .88 mmol) in 1 ,4-dioxane (10 ml_) at room temperature under an atmosphere of nitrogen. The resulting solution was stirred at 100 C for 12 hr. The reaction was filtered and the filtrate was concentrated to afford crude product.
0.6 g With dichloro(1,1'-bis(diphenylphosphanyl)ferrocene)palladium(II)*CH2Cl2; potassium acetate; In 1,4-dioxane; at 100.0℃; for 4.5h; A mixture of 0.5 g (2.48 mmol) 5-bromo-N,N-dimethyl-pyrimidin-2-amine, 0.8 g (3.24 mmol) bis(pinacolato)diborone, 0.6 g (6.38 mmol) KOAc, 0.2 g (0.25 mmol) (0358) Pd(dppf)CI2 * DCM and dioxane is heated to 100C for 4.5 h. After cooling to RT, the reaction mixture is filtered through a pad of Celite and evorated, water is added and the mixture is extracted with EtOAc. The organic phases are pooled, dried and evaporated The crude product is purified by FC. (0359) Yield: 0.6 g (96%), ESI-MS: m/z = 250 (M+H)+, Rt(HPLC): 0.22 min (HPLC-A)
 

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