13009-95-5

Basic information

• Product Name: 5-hydroxymethyldeoxycytidylic acid
• Synonyms: 5-hydroxymethyldeoxycytidylic acid;2''-DEOXY-5-(HYDROXYMETHYL)-5''-CYTIDYLIC ACID;2(1H)-Pyrimidinone, 4-amino-1-(2-deoxy-5-o-phosphono-beta-D-erythro-pentofuranosyl)-5-(hydroxymethyl)-;2'-Deoxy-5-hydroxymethylcytidine-5'-phosphate;5'-Cytidylic acid, 2'-deoxy-5-(hydroxymethyl)-;5-Hydroxymethyl dcmp;5-Hydroxymethylcytosine deoxyribonucleotide;5-Hydroxymethyldeoxycytidylate
• CAS NO: 13009-95-5
• Molecular Formula: C₁₀H₁₆N₃O₈P
• Molecular Weight: 337.223
• Mol File: 13009-95-5.mol
• Article Data: 4

Chemical Properties

• Boiling Point: 702.6°Cat760mmHg
• Flash Point: 378.7°C
• Appearance: /
• Density: 2.03g/cm³
• Vapor Pressure: 8.05E-23mmHg at 25°C
• Refractive Index: 1.743
• CAS DataBase Reference: 5-hydroxymethyldeoxycytidylic acid(CAS DataBase Reference)
• NIST Chemistry Reference: 5-hydroxymethyldeoxycytidylic acid(13009-95-5)
• EPA Substance Registry System: 5-hydroxymethyldeoxycytidylic acid(13009-95-5)

Safety Data

• Hazardous Substances Data: 13009-95-5(Hazardous Substances Data)

Usage

Definition

ChEBI: A 2'-deoxycytidine phosphate compound having the phosphate group at the 5'-position and a hydroxymethyl substituent at the 5-position.

InChI:InChI=1/C10H16N3O8P/c11-9-5(3-14)2-13(10(16)12-9)8-1-6(15)7(21-8)4-20-22(17,18)19/h2,6-8,14-15H,1,3-4H2,(H2,11,12,16)(H2,17,18,19)/t6-,7+,8+/m0/s1

Synthetic route

formaldehyd (50-00-0) + cytidine 5'-(dihydrogen phosphate) (1032-65-1) → 5-hydroxymethyl-2'-deoxycytidine 5'-monophosphate (13009-95-5)

Conditions	Yield
in Gegenwart eines Enzympraeparats aus virusinfizierten Escherichiacoli-Zellen;

5-methyl-2′-deoxycytidine 5′-monophosphate (2498-41-1) → 5-hydroxymethyl-2'-deoxycytidine 5'-monophosphate (13009-95-5) + 5-formyl-2'-deoxycytidine 5'-monophosphate (137017-46-0)

Conditions	Yield
With sodium persulfate In water at 75℃; for 3h; sodium phosphate buffer pH 7.0;	A 15 % Spectr. B 10 % Spectr.
With sodium persulfate; buffer pH=7.0 In water at 75℃; for 4h;	A 12 % Spectr. B 8 % Spectr.

5-acetoxymethyl-3',5'-di-O-tert-butyldimethylsilyl-2'-deoxycytidine (354581-54-7) → 5-hydroxymethyl-2'-deoxycytidine 5'-monophosphate (13009-95-5)

Conditions	Yield
Multi-step reaction with 3 steps 1: trichlorophosphate; trimethyl phosphite / 2 h / 0 °C 2: trifluoroacetic acid / water / 1 h / 20 °C 3: potassium carbonate; water / methanol / 1 h / 20 °C View Scheme

3',5'-O-di(tert-butyldimethylsilyl)thymidine (40733-26-4) → 5-hydroxymethyl-2'-deoxycytidine 5'-monophosphate (13009-95-5)

Conditions

Yield

Multi-step reaction with 6 steps 1.1: N-Bromosuccinimide; 2,2'-azobis(isobutyronitrile) / tetrachloromethane / 1.5 h / 80 °C 2.1: 0.5 h / 40 °C 3.1: p-toluenesulfonyl chloride; N-methylcyclohexylamine; triethylamine / 4 h 3.2: 0.5 h 4.1: trichlorophosphate; trimethyl phosphite / 2 h / 0 °C 5.1: trifluoroacetic acid / water / 1 h / 20 °C 6.1: potassium carbonate; water / methanol / 1 h / 20 °C View Scheme

C18H32N3O9PSi → 5-hydroxymethyl-2'-deoxycytidine 5'-monophosphate (13009-95-5)

Conditions	Yield
Multi-step reaction with 2 steps 1: trifluoroacetic acid / water / 1 h / 20 °C 2: potassium carbonate; water / methanol / 1 h / 20 °C View Scheme

C12H18N3O9P → 5-hydroxymethyl-2'-deoxycytidine 5'-monophosphate (13009-95-5)

Conditions	Yield
With water; potassium carbonate In methanol at 20℃; for 1h;

3′,5′-bis-O-(tert-butyldimethylsilyl)-5-bromomethyl-2'-deoxyuridine (291525-17-2) → 5-hydroxymethyl-2'-deoxycytidine 5'-monophosphate (13009-95-5)

Conditions	Yield
Multi-step reaction with 5 steps 1.1: 0.5 h / 40 °C 2.1: p-toluenesulfonyl chloride; N-methylcyclohexylamine; triethylamine / 4 h 2.2: 0.5 h 3.1: trichlorophosphate; trimethyl phosphite / 2 h / 0 °C 4.1: trifluoroacetic acid / water / 1 h / 20 °C 5.1: potassium carbonate; water / methanol / 1 h / 20 °C View Scheme

5-acetoxymethyl-3',5'-di-O-tert-butyldimethylsilyl-2'-deoxyuridine (354581-52-5) → 5-hydroxymethyl-2'-deoxycytidine 5'-monophosphate (13009-95-5)

Conditions	Yield
Multi-step reaction with 4 steps 1.1: p-toluenesulfonyl chloride; N-methylcyclohexylamine; triethylamine / 4 h 1.2: 0.5 h 2.1: trichlorophosphate; trimethyl phosphite / 2 h / 0 °C 3.1: trifluoroacetic acid / water / 1 h / 20 °C 4.1: potassium carbonate; water / methanol / 1 h / 20 °C View Scheme

piperidine (110-89-4) + 5-hydroxymethyl-2'-deoxycytidine 5'-monophosphate (13009-95-5) → C15H25N4O7P

Conditions	Yield
With triphenylphosphine; 2-Aminophenyl disulfide In dimethyl sulfoxide at 20℃; for 8h;	94%

5-hydroxymethyl-2'-deoxycytidine 5'-monophosphate (13009-95-5) → 5-hydroxymethyl-2'-deoxycytidine-5’-triphosphate (10097-59-3)

Conditions	Yield
Multi-step reaction with 2 steps 1: 2-Aminophenyl disulfide; triphenylphosphine / dimethyl sulfoxide / 8 h / 20 °C 2: tris(tetra-n-butylammonium) hydrogen pyrophosphate; 4,5-dicyano-1H-imidazole / 6 h / 20 °C View Scheme

5-hydroxymethyl-2'-deoxycytidine 5'-monophosphate (13009-95-5) → 5-carboxy-deoxycytidine triphosphate

Conditions	Yield
Multi-step reaction with 3 steps 1: 2-Aminophenyl disulfide; triphenylphosphine / dimethyl sulfoxide / 8 h / 20 °C 2: tris(tetra-n-butylammonium) hydrogen pyrophosphate; 4,5-dicyano-1H-imidazole / 6 h / 20 °C 3: 2,2,6,6-Tetramethyl-1-piperidinyloxy free radical; [bis(acetoxy)iodo]benzene / dichloromethane; water; tert-butyl alcohol / 48 h / 20 °C View Scheme

5-hydroxymethyl-2'-deoxycytidine 5'-monophosphate (13009-95-5) → 5-formyl-2’-deoxycytidine-5’-triphosphate

Conditions	Yield
Multi-step reaction with 3 steps 1: 2-Aminophenyl disulfide; triphenylphosphine / dimethyl sulfoxide / 8 h / 20 °C 2: manganese(IV) oxide / methanol / 24 h / 50 °C 3: tris(tetra-n-butylammonium) hydrogen pyrophosphate; 4,5-dicyano-1H-imidazole / 6 h / 20 °C View Scheme

5-hydroxymethyl-2'-deoxycytidine 5'-monophosphate (13009-95-5) → C15H23N4O7P

Conditions	Yield
Multi-step reaction with 2 steps 1: 2-Aminophenyl disulfide; triphenylphosphine / dimethyl sulfoxide / 8 h / 20 °C 2: manganese(IV) oxide / methanol / 24 h / 50 °C View Scheme

Upstream product

• 50-00-0 formaldehyd 
• 1032-65-1 cytidine 5'-(dihydrogen phosphate) 
• 354581-54-7 5-acetoxymethyl-3',5'-di-O-tert-butyldimethylsilyl-2'-deoxycytidine 
• 40733-26-4 3',5'-O-di(tert-butyldimethylsilyl)thymidine 
• 291525-17-2 3′,5′-bis-O-(tert-butyldimethylsilyl)-5-bromomethyl-2'-deoxyuridine 
• 354581-52-5 5-acetoxymethyl-3',5'-di-O-tert-butyldimethylsilyl-2'-deoxyuridine 
• 2498-41-1 5-methyl-2′-deoxycytidine 5′-monophosphate 

Relevant articles and documents

Efficient synthesis of 5-hydroxymethyl-, 5-formyl-, and 5-carboxyl-2′-deoxycytidine and their triphosphates

An efficient P(V)-N activation strategy for the preparation of high-quality 5-hydroxymethyl-, 5-formyl-, and 5-carboxyl-2′-deoxycytidine triphosphates has been developed. The method was also optimized for gram-scale synthesis of the corresponding parent n

Oxidation of Cytosine and 5-Methylcytosine Nucleosides and 5-Methyl-2'-deoxycytidine 5'-Monophosphate with Peroxosulfate Ions

Reaction of 5-methylcytosine nucleosides and nucleotide with Na2S2O8 resulted in an oxidation of the 5-methyl group, while treatment of them and cytosine nucleosides with KHSO5 gave the corresponding N3-oxides.