65996-50-1|1H-Pyrrolo[3,2-d]pyrimidine-2,4(3H,5H)-dione| Ambeed

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Quality Control of [ 65996-50-1 ] Purity: 97% SDS Specification

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Product Details of [ 65996-50-1 ]

CAS No. :	65996-50-1
Formula :	C₆H₅N₃O₂
M.W :	151.12
SMILES Code :	O=C1NC2=C(NC=C2)C(N1)=O
MDL No. :	MFCD08059275
InChI Key :	BSRITDQWGPSXPQ-UHFFFAOYSA-N
Pubchem ID :	592097

Safety of [ 65996-50-1 ]

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

Computational Chemistry of [ 65996-50-1 ] Show Less

Physicochemical Properties

Num. heavy atoms	11
Num. arom. heavy atoms	9
Fraction Csp3	0.0
Num. rotatable bonds	0
Num. H-bond acceptors	2.0
Num. H-bond donors	3.0
Molar Refractivity	39.54
TPSA ? Topological Polar Surface Area: Calculated from Ertl P. et al. 2000 J. Med. Chem.	81.51 Å²

Lipophilicity

Log P_o/w (iLOGP)? iLOGP: in-house physics-based method implemented from Daina A et al. 2014 J. Chem. Inf. Model.	0.49
Log P_o/w (XLOGP3)? XLOGP3: Atomistic and knowledge-based method calculated by XLOGP program, version 3.2.2, courtesy of CCBG, Shanghai Institute of Organic Chemistry	-0.43
Log P_o/w (WLOGP)? WLOGP: Atomistic method implemented from Wildman SA and Crippen GM. 1999 J. Chem. Inf. Model.	-0.46
Log P_o/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.	-0.47
Log P_o/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	1.86
Consensus Log P_o/w? Consensus Log P_o/w: Average of all five predictions	0.2

Water Solubility

Log S (ESOL):? ESOL: Topological method implemented from Delaney JS. 2004 J. Chem. Inf. Model.	-1.11
Solubility	11.7 mg/ml ; 0.0774 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.	-0.82
Solubility	23.0 mg/ml ; 0.153 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	-2.33
Solubility	0.699 mg/ml ; 0.00462 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.	-7.53 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)	1.84

Application In Synthesis of [ 65996-50-1 ]

* 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.

Downstream synthetic route of [ 65996-50-1 ]

[ 65996-50-1 ] Synthesis Path-Downstream 1~41

1
[ 65996-50-1 ]
[ 63200-54-4 ]

Yield	Reaction Conditions	Operation in experiment
70%		A suspension of lH-pyrrolo[3,2-d]pyrimidine-2,4(3H,5H)-dione (0.38 g, 2.52 mmol) in phosphorus oxychloride (30 mL) was heated to 120 for 6 h during which the mixture became clear and homogeneous. The mixture was allowed to cool to room temperature and the excess phosphorus oxychloride was removed in vacuo. The residue was cooled in ice, cold ammonium hydroxide (30 mL, pH=8) was added and the mixture stirred for 30 min. The precipitate was collected and washed with cold water. The solid was dried in vacuo to afford 2,4-dichloro-5H-pyrrolo[3,2-d]pyrimidine (0.33 g, 70%).
60%		To <strong>[65996-50-1]pyrrolo[3,2-d]pyrimidin-2,4-dione</strong> 18 (2.00 g, 13.2 mmol), 1N NaOH (15 mL), and 0.60 g NaOH in 15 mL H2O was added and the mixture stirred at 40 C until a solution was formed. The solution was then cooled to room temperature (21-25 C) and then placed in an ice bath to obtain thick slurry. The slurry was then filtered to obtain a pale yellow solid. The solid was dissolved in 1N NaOH (15 mL), and heated to 40 C to obtain a clear solution that upon cooling provided white crystals. The crystals were washed with MeOH (20 mL) and acetone (20 mL), and then dried under vacuum. The dry solids were taken in phenylphosphonic dichloride (10 mL) and heated to 170-175 C for 5 h during which the reaction mixture became a brown-black solution. After 5 h the hot reaction mixture was poured onto ice, extracted with EtOAc (200 mL) and the organic layer washed with sat. NaHCO3 solution (3×100 mL) till all effervescence subsided. The organic layer was then washed with brine and dried over MgSO4. The organic layer was concentrated in vacuo and loaded onto silica. The product was purified using column chromatography eluting with 9:1 then 3:1 hexanes/EtOAc to obtain 18 as an off-white solid (1.50 g, 7.9 mmol, 60 %). Rf 0.5 in 3:1 hexanes/EtOAc. Mp 228.3-232.0 C. 1H NMR (400 MHz, DMSO-d6): δ 6.71 (d, 1H, J=3.2Hz), 8.09 (d, 1H, J=2.8Hz), 12.75 (s, 1H, NH). 13C NMR (100 MHz, DMSO-d6): δ 103.2, 124.3, 138.0, 143.5, 149.6, 153.9. ESI-MS m/z for C6H3Cl2N3 calculated [M+H]+ 187.9776, found 187.9777.
60%	With P,P-dichlorophenylphosphine oxide; at 170 - 175℃; for 5h;	5.1.1.2 2,4-Dichloropyrrolo[3,2-d]pyrimidine (1) To <strong>[65996-50-1]pyrrolo[3,2-d]pyrimidin-2,4-dione</strong> 5 (2.00 g, 13.2 mmol), 1 N NaOH (15 mL), and 0.60 g NaOH in 15 mL H2O was added and the mixture stirred at 40 C until a clear solution was obtained. The solution was cooled to room temperature (21-25 C) and then placed in an ice bath to obtain thick slurry. The slurry was then filtered to obtain a pale yellow solid. The solid was dissolved in 1 N NaOH (15 mL), and heated to 40 C to obtain a clear solution that upon cooling provided white crystals. The crystals were washed with MeOH (20 mL) and acetone (20 mL), and then dried under vacuum. The dry solids were taken in phenylphosphonic dichloride (10 mL) and heated to 170-175 C for 5 h during which the reaction mixture became a brown-black solution. After 5 h the hot reaction mixture was poured onto ice, extracted with EtOAc (200 mL) and the organic layer washed with satd NaHCO3 solution (3* 100 mL) till all effervescence subsided. The organic layer was then washed with brine and dried over MgSO4. The organic layer was concentrated in vacuo and loaded onto silica. The product was purified using column chromatography eluting with 9:1 then 3:1 hexanes/EtOAc to obtain 1 as an off-white solid (1.50 g, 7.9 mmol, 60%). Rf 0.5 in 3:1 hexanes/EtOAc. Mp 228.3-232.0 C. 1H NMR (400 MHz, DMSO-d6): δ 6.71 (d, 1H, J = 3.2 Hz), 8.09 (d, 1H, J = 2.8 Hz), 12.75 (s, 1H, NH). 13C NMR (100 MHz, DMSO-d6): δ 103.2, 124.3, 138.0, 143.5, 149.6, 153.9. ESI-MS m/z for C6H3Cl2N3 calculated [M+H]+ 187.9776, found 187.9777.

60%		To <strong>[65996-50-1]pyrrolo[3,2-d]pyrimidin-2,4-dione</strong> 18 (2.00 g, 13.2 mmol), 1 N NaOH (15 mL), and 0.60 g NaOH in 15 mL H2O was added and the mixture stirred at 40 C. until a solution was formed. The solution was then cooled to room temperature (21-25 C.) and then placed in an ice bath to obtain thick slurry. The slurry was then filtered to obtain a pale yellow solid. The solid was dissolved in 1 N NaOH (15 mL), and heated to 40 C. to obtain a clear solution that upon cooling provided white crystals. The crystals were washed with MeOH (20 mL) and acetone (20 mL), and then dried under vacuum. The dry solids were taken in phenylphosphonic dichloride (10 mL) and heated to 170-175 C. for 5 h during which the reaction mixture became a brown-black solution. After 5 h the hot reaction mixture was poured onto ice, extracted with EtOAc (200 mL) and the organic layer washed with sat. NaHCO3 solution (3×100 mL) till all effervescence subsided. The organic layer was then washed with brine and dried over MgSO4. The organic layer was concentrated in vacuo and loaded onto silica. The product was purified using column chromatography eluting with 9:1 then 3:1 hexanes/EtOAc to obtain compound 19 as an off-white solid (1.50 g, 7.9 mmol, 60%). Rf 0.5 in 3:1 hexanes/EtOAc. Mp 228.3-232.0 C. 1H NMR (400 MHz, DMSO-d6): δ 6.71 (d, 1H, J=3.2 Hz), 8.09 (d, 1H, J=2.8 Hz), 12.75 (s, 1H, NH). 13C NMR (100 MHz, DMSO-d6): δ 103.2, 124.3, 138.0, 143.5, 149.6, 153.9. ESI-MS m/z for C6H3Cl2N3 calculated [M+H]+ 187.9776. found 187.9777.
60%		Parent compound 5 was synthesized starting from commercially available 6-methyluracil (1),shown in Scheme 1. Nitration at C5 was accomplished by adding 6-methyluracil to a solution ofconcentrated sulfuric and nitric acids at 0 C, followed by quenching in ice water to give 2 as apale yellow solid [24]. This was followed by a modified Batcho-Leimgruber indole synthesis tofirst prepare enamine 3 [52,53]. Ring cyclization is accomplished by reduction of the nitro moietyto an amino group, with subsequent nucleophilic attack at C8 by the amino lone pair with loss of dimethylamine. The reduction of the nitro group is accomplished by stirring 3 in acetic acid and zincdust overnight at 80 C, followed by filtration, formation of the N5 sodium salt via NaOH dissolution,then re-acidification and collection of solid 4 [23,24]
		(4) To 1,5-dihydro-pyrrolo[3,2-d]pyrimidine-2,4-dione (35.0g) was added aqueous 1N sodium hydroxide solution (231ml) and after stirring for a while, the mixture was concentrated in vacuo. The residue was subjected to azeotropic distillation with toluene. To the residue was gradually added phenylphosphonic dichloride (239g) and then the temperature of the mixture was raised to 180C, followed by stirring for 3 hours. Thereto was further gradually added phenylphosphoric dichloride (100g) and the mixture was stirred overnight. The reaction mixture was gradually poured into ice-water under stirring and the mixture was extracted with ethyl acetate. The organic layer was washed with aqueous sodium bicarbonate solution, dried and concentrated in vacuo. To the residue was added ethyl acetate/ diisopropyl ether to give 2,4-dichloro-5H-pyrrolo[3,2-d]pyrimidine as crystals (19.96g). APCI-MS (m/e): 188/190 (M+H)+
		(4) A 1N aqueous sodium hydroxide solution (231 mL) was added to 1,5-dihydro-<strong>[65996-50-1]pyrrolo[3,2-d]pyrimidin-2,4-dione</strong>(35.0 g) and the mixture was stirred for a while, then it was concentrated under reduced pressure and the residue was azeotropically distilled after adding toluene. Phenyl phosphonic dichloride(239 g) was slowly added to the residue and the mixture was heated to 180C and stirred for 3 hours after exothermic reaction was over. Further phenyl phosphonic dichloride(100 g) was slowly added and the mixture was stirred overnight. The reaction solution was poured into ice water slowly with stirring, and it was extracted with ethyl acetate. The organic layer was washed with a sodium bicarbonate solution and dried. The residue was crystallized with ethyl acetate and diisopropyl ether to give 2,4-dichloro-5H-pyrrolo[3,2-d]pyrimidine(19.96 g). APCI-MS(m/e):188/190[M+H]+ .
	With trichlorophosphate; at 120℃; for 6h;	To 100 ml eggplant vials were added 0.38 g of compound 1-3 and30ml of phosphorus oxychloride,The oil bath was heated at 120 C for 6 hours,Cooled to room temperature,The phosphorus oxychloride was distilled off under reduced pressure,The residue was added dropwise with 30 mL of cold ammonia to pH 8 under ice-cooling. Plus,Continue to stir for 30min, filter, filter cake washed by cold water after vacuum drying to get the target 1-4.

References: [1]Journal of Heterocyclic Chemistry,1987,vol. 24,p. 821 - 827.
[2]Patent: WO2009/62258,2009,A1 .Location in patent: Page/Page column 98.
[3]Bioorganic and Medicinal Chemistry,2014,vol. 22,p. 2113 - 2122.
[4]Bioorganic and Medicinal Chemistry,2015,vol. 23,p. 4354 - 4363.
[5]Patent: US2016/257696,2016,A1 .Location in patent: Paragraph 0069-0070.
[6]ChemMedChem,2018,vol. 13,p. 178 - 185.
[7]Molecules,2019,vol. 24.
[8]Pharmaceutical Chemistry Journal,1988,vol. 22,p. 135 - 141.
Khimiko-Farmatsevticheskii Zhurnal,1988,vol. 22,p. 185 - 191.
[9]Patent: EP1956009,2008,A1 .Location in patent: Page/Page column 38.
[10]Patent: EP1970373,2008,A1 .Location in patent: Page/Page column 94.
[11]European Journal of Medicinal Chemistry,2012,vol. 52,p. 205 - 212.
[12]Bioorganic and Medicinal Chemistry,2013,vol. 21,p. 1749 - 1755.
[13]Patent: CN106866678,2017,A .Location in patent: Paragraph 0114; 0116; 0117; 0127; 0128; 0129.

2
[ 65996-50-1 ]
[ 114684-93-4 ]
[ 63200-54-4 ]

References: [1]Pharmaceutical Chemistry Journal,1988,vol. 22,p. 135 - 141.
Khimiko-Farmatsevticheskii Zhurnal,1988,vol. 22,p. 185 - 191.
[2]Pharmaceutical Chemistry Journal,1988,vol. 22,p. 135 - 141.
Khimiko-Farmatsevticheskii Zhurnal,1988,vol. 22,p. 185 - 191.

3
5-Nitro-2,4-dioxo-6-(β-dimethylaminovinyl)-1,2,3,4-tetrahydropyrimidine [ No CAS ]
[ 65996-50-1 ]

Yield	Reaction Conditions	Operation in experiment
	With acetic acid; zinc; at 80℃; for 1h;	In a 100 mL eggplant flask was added 1.43 g of compound 1-2 and 23 ml of acetic acid,The oil bath was heated to 80 C and 2 g of zinc powder was added in portions.After heating for 1 hour, the reaction solution was cooled to room temperature,Solid precipitation. Filter, filter cake by acetic acid,Washed with 10ml 5% sodium hydroxide solution dissolved.The solution was stirred at 70 C for 30 min,Add acetic acid to pH 5-6. Filter, filter cake by cold water,Wash the ethanol and then dry to get the target 1-3.

References: [1]Pharmaceutical Chemistry Journal,1988,vol. 22,p. 135 - 141.
Khimiko-Farmatsevticheskii Zhurnal,1988,vol. 22,p. 185 - 191.
[2]Molecules,2019,vol. 24.
[3]European Journal of Medicinal Chemistry,2012,vol. 52,p. 205 - 212.
[4]Bioorganic and Medicinal Chemistry,2013,vol. 21,p. 1749 - 1755.
[5]Patent: CN106866678,2017,A .Location in patent: Paragraph 0114; 0116; 0117; 0124; 0125; 0126.

4
[ 1560-54-9 ]
6-azido-2,4(1H,3H)pyrimidinedione [ No CAS ]
[ 873-83-6 ]
[ 65996-50-1 ]

References: [1]Heteroatom Chemistry,2002,vol. 13,p. 357 - 365.

5
[ 16632-21-6 ]
[ 65996-50-1 ]

References: [1]Pharmaceutical Chemistry Journal,1988,vol. 22,p. 135 - 141.
Khimiko-Farmatsevticheskii Zhurnal,1988,vol. 22,p. 185 - 191.
[2]European Journal of Medicinal Chemistry,2012,vol. 52,p. 205 - 212.
[3]Bioorganic and Medicinal Chemistry,2013,vol. 21,p. 1749 - 1755.
[4]Patent: CN106866678,2017,A .
[5]ChemMedChem,2018,vol. 13,p. 178 - 185.
[6]Molecules,2019,vol. 24.

6
[ 65996-50-1 ]
[ 114684-99-0 ]

7
[ 65996-50-1 ]
[ 114684-95-6 ]

8
[ 65996-50-1 ]
[ 114685-00-6 ]

9
[ 65996-50-1 ]
[ 114684-97-8 ]

10
[ 65996-50-1 ]
[ 114684-98-9 ]

11
[ 65996-50-1 ]
[ 114684-94-5 ]

12
[ 65996-50-1 ]
2,4-Bis-(dimethylamino)pyrrolo<3,2-d>pyrimidine hydrochloride [ No CAS ]

13
[ 65996-50-1 ]
[ 114684-96-7 ]

14
[ 65996-50-1 ]
[ 114685-04-0 ]

15
[ 65996-50-1 ]
[ 114685-02-8 ]

16
[ 65996-50-1 ]
[ 114685-01-7 ]

17
[ 65996-50-1 ]
[ 142545-07-1 ]

References: [1]Journal of Heterocyclic Chemistry,1992,vol. 29,p. 343 - 354.

18
[ 65996-50-1 ]
[ 142545-01-5 ]

References: [1]Journal of Heterocyclic Chemistry,1992,vol. 29,p. 343 - 354.

19
[ 65996-50-1 ]
[ 142545-05-9 ]

References: [1]Journal of Heterocyclic Chemistry,1992,vol. 29,p. 343 - 354.

20
[ 65996-50-1 ]
[ 142545-03-7 ]

References: [1]Journal of Heterocyclic Chemistry,1992,vol. 29,p. 343 - 354.

21
[ 65996-50-1 ]
[ 142545-06-0 ]

References: [1]Journal of Heterocyclic Chemistry,1992,vol. 29,p. 343 - 354.

22
[ 65996-50-1 ]
C₃₂H₂₅N₃O₈S [ No CAS ]

References: [1]Journal of Heterocyclic Chemistry,1992,vol. 29,p. 343 - 354.

23
[ 65996-50-1 ]
[ 142545-08-2 ]

References: [1]Journal of Heterocyclic Chemistry,1992,vol. 29,p. 343 - 354.

24
[ 65996-50-1 ]
[ 142545-04-8 ]

References: [1]Journal of Heterocyclic Chemistry,1992,vol. 29,p. 343 - 354.

25
[ 65996-50-1 ]
[ 113544-41-5 ]