5-Ethynyl-2'-deoxycytidine

Base Information

• Chemical Name: 5-Ethynyl-2'-deoxycytidine
• CAS No.: 69075-47-4
• Molecular Formula: C11H13N3O4
• Molecular Weight: 251.242
• DSSTox Substance ID: DTXSID10567311
• Nikkaji Number: J1.924.855K
• Wikidata: Q82453159
• Mol file: 69075-47-4.mol

Synonyms:5-ethynyl-2'-deoxycytidine

Chemical Property of 5-Ethynyl-2'-deoxycytidine

Chemical Property:

• Melting Point: 191 °C (decomp)(Solv: dichloromethane (75-09-2); methanol (67-56-1))
• Boiling Point: 475.7±55.0 °C(Predicted)
• PKA: 14.03±0.60(Predicted)
• PSA: 111.59000
• Density: 1.54±0.1 g/cm3(Predicted)
• LogP: -1.21010
• XLogP3: -1.5
• Hydrogen Bond Donor Count: 3
• Hydrogen Bond Acceptor Count: 4
• Rotatable Bond Count: 3
• Exact Mass: 251.09060590
• Heavy Atom Count: 18
• Complexity: 476

Purity/Quality:

98%min ^*data from raw suppliers

5-Ethynyl-2’-deoxycytidine ^*data from reagent suppliers

Safty Information:

• Pictogram(s):  
• Hazard Codes: 

MSDS Files:

SDS file from LookChem

Useful:

• Canonical SMILES: C#CC1=CN(C(=O)N=C1N)C2CC(C(O2)CO)O
• Isomeric SMILES: C#CC1=CN(C(=O)N=C1N)[C@H]2C[C@@H]([C@H](O2)CO)O
• Description: 5''-Ethynyl-2''-deoxycytidine (EdC) is a nucleoside analog that inhibits replication of the herpes simplex virus-1 (HSV-1) KOS strain (ID50 = 0.2 μg/mL). It also reduces virus-induced cytopathogenicity of HSV-1, HSV-2, and vaccinia virus strains in PRK cells (MICs = 0.2-0.4, 1-2, and 5 μg/ml, respectively). EdC is an inhibitor of thymidylate synthetase, selectively reducing DNA incorporation of [1'',2''-3H]deoxyuridine over [CH3-3H]deoxythymidine in PRK cells (ID50s = 3 and 120 μg/ml, respectively). It inhibits thymidine synthetase in and reduces proliferation of L1210 cells, an effect which is reversed by addition of deoxythymidine (ID50s = 4.4 and 1,000 μg/ml, respectively). EdC has been used to monitor DNA synthesis and cellular replication via click chemistry conjugation of the ethynyl group to an azido group of various fluorochromes.
• Uses: 5-Ethynyl-2’-deoxycytidine is an lower toxicity analog of 2’-deoxycytidine, a metabolic labeling probe for DNA synthesis. 5-Ethynyl-2’-deoxycytidine is most commonly used when thymidine analogs is undesirable. A relatively nontoxic 2′-deoxycytidine analog for metabolic labeling of newly synthesized DNA in vivo. Especially suitable if the use of thymidine analogs is undesirable.

Technology Process of 5-Ethynyl-2'-deoxycytidine

There total 8 articles about 5-Ethynyl-2'-deoxycytidine which guide to synthetic route it. The literature collected by LookChem mainly comes from the sharing of users and the free literature resources found by Internet computing technology. We keep the original model of the professional version of literature to make it easier and faster for users to retrieve and use. At the same time, we analyze and calculate the most feasible synthesis route with the highest yield for your reference as below:

synthetic route:

Reference yield: 98.0%

5-trimethylsilylethynyl-2′-deoxycytidine (1279719-43-5) → 4-amino-1-(2-deoxy-β-D-erythro-pentofuranosyl)-5-ethynylpyrimidin-2(1H)-one (69075-47-4)

Guidance literature:

With potassium fluoride; In 1,4-dioxane; methanol; at 20 ℃; for 1.5h;

DOI:10.1002/chem.201502209

Reference yield: 91.0%

5-trimethylsilylethynyl-3',5'-diacetyl-2'-deoxycytidine (1211548-81-0) → 4-amino-1-(2-deoxy-β-D-erythro-pentofuranosyl)-5-ethynylpyrimidin-2(1H)-one (69075-47-4)

Guidance literature:

With methanol; potassium carbonate; at 0 ℃; for 2h;

DOI:10.1039/b919921g

Reference yield: 40.0%

2-Chloroethanesulfonyl chloride (1622-32-8) + 3-azidopropylamine (88192-19-2) → 4-amino-1-(2-deoxy-β-D-erythro-pentofuranosyl)-5-ethynylpyrimidin-2(1H)-one (69075-47-4)

Guidance literature:

3-azidopropylamine; With N-ethyl-N,N-diisopropylamine; In dichloromethane; at 0 ℃; for 1h; Inert atmosphere;

2-Chloroethanesulfonyl chloride; In dichloromethane; at 0 ℃; for 1h; Inert atmosphere;

DOI:10.1002/chem.201502209

upstream raw materials:

5-trimethylsilylethynyl-3',5'-diacetyl-2'-deoxycytidine

5-trimethylsilylethynyl-2′-deoxycytidine

5-Iodo-2'-deoxycytidine

2-Chloroethanesulfonyl chloride

Downstream raw materials:

2'-Deoxy-5-(1-(2,2'-bithiophen-3-yl)-1H-1,2,3-triazol-4-yl)cytidine

2'-deoxy-5-(1-(thiophen-3-yl)-1H-1,2,3-triazol-4-yl)cytidine

2'-deoxy-5-(1-(phenyl)-1H-1,2,3-triazol-4-yl)cytidine

4-N-acetyl-5-(1-phenyl-1H-1,2,3-triazol-4-yl)-2'-deoxycytidine

Refernces

• 1、 Ghanty, Uday,Denizio, Jamie E.,Liu, Monica Yun,Kohli, Rahul M.. "Exploiting Substrate Promiscuity to Develop Activity-Based Probes for Ten-Eleven Translocation Family Enzymes". supporting information. p. 17329 - 17332. Retrieved 2019/01/04.
• 2、 Ingale, Sachin A.,Mei, Hui,Leonard, Peter,Seela, Frank. "Ethynyl side chain hydration during synthesis and workup of "clickable" oligonucleotides: Bypassing acetyl group formation by triisopropylsilyl protection". . p. 11271 - 11282. Retrieved 2013/12/04.