2′-Deoxycytidine - ≥99% , CAS No.951-77-9

CAS: 951-77-9 Cat. No.: D104773 Formula: C₉H₁₃N₃O₄ Molecular Weight: 227.22 Beilstein Registry Number: 87567 EC Number: 213-454-1

GRADE & PURITY ≥99%

Synonyms

CYTIDINE, 2'-DEOXY- | Desoxycytidin [German] | MFCD00006547 | Doxecitine | 4-amino-1-[(2R,4S,5R)-4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]-1,2-dihydropyrimidin-2-one | C00881 | 1-(2-Deoxy-b-D-ribofuranosyl)cytosine | Deoxyribose cytidine | Cytidine, 2'-deox

Storage

Store at -20°C

Shipped In

Ice chest + Ice pads

Overview

application：

2′-Deoxycytidine (deoxyC) is one of the deoxynucleosides which after phosphorylation to dCTP is used to synthesis DNA via various DNA polymerases or reverse transcriptases. 2′-Deoxycytidine (deoxyC) is the substrate for deoxycytidine deaminase (EC 3.5.4.14) which converts it into 2′-deoxyuridine. 2′-Deoxycytidine is phosphorylated to the nucleotide dCMP by the enzyme deoxycytidine kinase (DCK).

product description：

2′-Deoxycytidine (deoxyC) is one of the deoxynucleosides containing cytosine as the nucleobase. It is found in the blood, feces, and urine.

application：

2′-Deoxycytidine has been used:

as a substrate for Trypanosoma brucei cytidine deaminase (TbCDA) to measure its activity

as a standard in the isolation and quantification of metabolite levels in murine tumor interstitial fluid by liquid chromatography-mass spectrometry (LC–MS)

to study the role of autophagy in response to oncogenes and DNA replication stress 

Specifications

Synonyms

CYTIDINE, 2'-DEOXY- | Desoxycytidin [German] | MFCD00006547 | Doxecitine | 4-amino-1-[(2R,4S,5R)-4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]-1,2-dihydropyrimidin-2-one | C00881 | 1-(2-Deoxy-b-D-ribofuranosyl)cytosine | Deoxyribose cytidine | Cytidine, 2'-deox

Specifications & Purity

≥99%

Biochemical and Physiological Mechanisms

2′-Deoxycytidine (deoxyC) forms dCTP upon phosphorylation which is used to synthesis DNA via various DNA polymerases or reverse transcriptases. DeoxyC is the substrate for deoxycytidine deaminase (EC 3.5.4.14) which converts it into 2′-deoxyuridine. Deoxy

Storage

Store at -20°C

Shipped In

Ice chest + Ice pads

This product requires cold chain shipping. Ground and other economy services are not available.

Purity

≥99%

Names and Identifiers

• Pubchem Sid: 504752485
• Pubchem Sid Url: https://pubchem.ncbi.nlm.nih.gov/substance/504752485
• Canonical Smiles: C1C(C(OC1N2C=CC(=NC2=O)N)CO)O
• IUPAC Name: 4-amino-1-[(2R,4S,5R)-4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]pyrimidin-2-one
• InChIKey: CKTSBUTUHBMZGZ-SHYZEUOFSA-N
• INCHI: 1S/C9H13N3O4/c10-7-1-2-12(9(15)11-7)8-3-5(14)6(4-13)16-8/h1-2,5-6,8,13-14H,3-4H2,(H2,10,11,15)/t5-,6+,8+/m0/s1
• Isomeric SMILES: C1[C@@H]([C@H](O[C@H]1N2C=CC(=NC2=O)N)CO)O
• WGK Germany: 3
• RTECS: HA3800000
• Alternate CAS: 652157-52-3
• Molecular Weight: 227.22
• Beilstein: 87567
• Reaxy-Rn: 14609546
• Reaxys-RN_link_address: https://www.reaxys.com/reaxys/secured/hopinto.do?context=S&query=IDE.XRN=14609546&ln=

Taxonomic Classification

Taxonomy Tree

• Kingdom Organic compounds
  • Superclass Nucleosides, nucleotides, and analogues
    • Class Pyrimidine nucleosides
      • Subclass Pyrimidine 2'-deoxyribonucleosides

• Kingdom: Organic compounds
• Superclass: Nucleosides, nucleotides, and analogues
• Class: Pyrimidine nucleosides
• Subclass: Pyrimidine 2'-deoxyribonucleosides
• Intermediate Tree Nodes: Not available
• Direct Parent: Pyrimidine 2'-deoxyribonucleosides
• Alternative Parents: Pyrimidones Aminopyrimidines and derivatives Imidolactams Hydropyrimidines Tetrahydrofurans Heteroaromatic compounds Secondary alcohols Oxacyclic compounds Azacyclic compounds Primary amines Primary alcohols Organopnictogen compounds Organic oxides Hydrocarbon derivatives
• Molecular Framework: Aromatic heteromonocyclic compounds
• Substituents: Pyrimidine 2'-deoxyribonucleoside - Aminopyrimidine - Pyrimidone - Hydropyrimidine - Pyrimidine - Imidolactam - Heteroaromatic compound - Tetrahydrofuran - Secondary alcohol - Azacycle - Oxacycle - Organoheterocyclic compound - Alcohol - Hydrocarbon derivative - Organic oxide - Organopnictogen compound - Primary amine - Primary alcohol - Organooxygen compound - Organonitrogen compound - Organic oxygen compound - Organic nitrogen compound - Amine - Aromatic heteromonocyclic compound
• Description: This compound belongs to the class of organic compounds known as pyrimidine 2'-deoxyribonucleosides. These are compounds consisting of a pyrimidine linked to a ribose which lacks a hydroxyl group at position 2.
• External Descriptors: Deoxyribonucleosides

Data sources

1. Djoumbou Feunang Y, Eisner R, Knox C, Chepelev L, Hastings J, Owen G, Fahy E, Steinbeck C, Subramanian S, Bolton E, Greiner R, and Wishart DS. ClassyFire: Automated Chemical Classification With A Comprehensive, Computable Taxonomy. Journal of Cheminformatics, 2016, 8:61.

DOI: 10.1186/s13321-016-0174-y

Associated Targets(Human)

DCK Tchem Deoxycytidine kinase (530 Activities)

Discover Target: DCK

Activity Type	Relation	Activity value	Units	Action Type	Journal	PubMed Id	doi	Assay Aladdin ID

TK1 Tchem Thymidine kinase, cytosolic (627 Activities)

Discover Target: TK1

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CCRF-CEM (65223 Activities)

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DU-145 (51482 Activities)

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MCF7 (126967 Activities)

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MT4 (17854 Activities)

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ATH-8 cell line (300 Activities)

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HaCaT (4069 Activities)

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HCT-116 (91556 Activities)

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MEN1 Tchem Menin/Histone-lysine N-methyltransferase MLL (48157 Activities)

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Associated Targets(non-human)

TK Thymidine kinase (276 Activities)

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pol Human immunodeficiency virus type 1 reverse transcriptase (18245 Activities)

Discover Target: pol

Activity Type	Relation	Activity value	Units	Action Type	Journal	PubMed Id	doi	Assay Aladdin ID

Deoxycytidylate deaminase (6 Activities)

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Activity Type	Relation	Activity value	Units	Action Type	Journal	PubMed Id	doi	Assay Aladdin ID

Cda Cytidine deaminase (37 Activities)

Discover Target: Cda

Activity Type	Relation	Activity value	Units	Action Type	Journal	PubMed Id	doi	Assay Aladdin ID

dnk Deoxynucleoside kinase (95 Activities)

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deoA Thymidine phosphorylase (531 Activities)

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Uck1 Uridine-cytidine kinase 1 (5 Activities)

Discover Target: Uck1

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Hdac6 Histone deacetylase 6 (222 Activities)

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Tk2 Thymidine kinase 2 (53 Activities)

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Enterococcus faecium (13803 Activities)

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Human immunodeficiency virus (3636 Activities)

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L1210 (27553 Activities)

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C6 (2371 Activities)

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L6 (7924 Activities)

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LM (36 Activities)

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dak Deoxyadenosine kinase (12 Activities)

Discover Target: dak

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Perknaster fuscus (7 Activities)

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Woodchuck hepatitis virus (122 Activities)

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Ileum (29 Activities)

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Mechanisms of Action

Chemical and Physical Properties

• Solubility: Soluble in water, DMSO.
• Specific Rotation[α]: 59 ° (C=1, H2O)
• Melt Point(°C): 209-211°C
• Molecular Weight: 227.220 g/mol
• XLogP3: -1.800
• Hydrogen Bond Donor Count: 3
• Hydrogen Bond Acceptor Count: 4
• Rotatable Bond Count: 2
• Exact Mass: 227.091 Da
• Monoisotopic Mass: 227.091 Da
• Topological Polar Surface Area: 108.000 Ų
• Heavy Atom Count: 16
• Formal Charge: 0
• Complexity: 355.000
• Isotope Atom Count: 0
• Defined Atom Stereocenter Count: 3
• Undefined Atom Stereocenter Count: 0
• Defined Bond Stereocenter Count: 0
• Undefined Bond Stereocenter Count: 0
• The total count of all stereochemical bonds: 0
• Covalently-Bonded Unit Count: 1

References

1. Wenqing Wang, Hao Li, Meiyao Li, Huiling Lu, Jianming Pan.  (2023)  Layer-by-layer assembled magnetic molecularly imprinted nanoparticles for highly specific separation of adenosine 5′-monophosphate: Relations between adsorption properties and imprinted layers.  SEPARATION AND PURIFICATION TECHNOLOGY,      [PMID:] [10.1016/j.seppur.2023.125346]

2. Meiyao Li, Pan Wang, Shunshun Luo, Yu Wu, Xiaohua Tian, Jianming Pan.  (2023)  Construction of anti-biofouling imprinted sorbents based on anisotropic polydopamine nanotubes for fast and selective capture of 2′-deoxyadenosine.  SEPARATION AND PURIFICATION TECHNOLOGY,      [PMID:] [10.1016/j.seppur.2023.123384]

3. Pan Wang, Mengdei Zhou, Zhuangxin Wei, Lu Liu, Tao Cheng, Xiaohua Tian, Jianming Pan.  (2023)  Preparation of bowl-shaped polydopamine surface imprinted polymer composite adsorbent for specific separation of 2′-deoxyadenosine.  CHINESE JOURNAL OF CHEMICAL ENGINEERING,      [PMID:] [10.1016/j.cjche.2023.01.009]

4. Zhuangxin Wei, Pan Wang, Xiaohua Tian, Wei sun, Jianming Pan.  (2022)  Imprinted polymer beads featuring both predefined multiple-point interaction and accessible binding sites for precise recognition of 2′-deoxyadenosine.  SEPARATION AND PURIFICATION TECHNOLOGY,      [PMID:] [10.1016/j.seppur.2022.122048]

5. Chang Xiangwei, Zhang Zhenyu, Yan Hui, Su Shulan, Wei Dandan, Guo Sheng, Shang Erxin, Sun Xiaodong, Gui Shuangying, Duan Jinao.  (2021)  Discovery of Quality Markers of Nucleobases, Nucleosides, Nucleotides and Amino Acids for Chrysanthemi Flos From Different Geographical Origins Using UPLC–MS/MS Combined With Multivariate Statistical Analysis.  Frontiers in Chemistry,      [PMID:34422760] [10.3389/fchem.2021.689254]

6. Jia Ding, Fei Liu, Chunling Qi, Yunlei Zhou, Huanshun Yin, Shiyun Ai.  (2021)  Enhanced photoactivity of perovskite Bi4NbO8Cl/PTC-NH2 heterojunction and its application for photoelectrochemical sensing of DNA hydroxymethylation.  SENSORS AND ACTUATORS B-CHEMICAL,      [PMID:] [10.1016/j.snb.2021.130211]

7. Yang Hongmei, Su Rui, Wishnok John S., Liu Ning, Chen Changbao, Liu Shuying, Tannenbaum Steven R..  (2019)  Magnetic silica nanoparticles for use in matrix-assisted laser desorption ionization mass spectrometry of labile biomolecules such as oligosaccharides, amino acids, peptides and nucleosides.  MICROCHIMICA ACTA,  186  (2): (1-8).  [PMID:30637518] [10.1007/s00604-018-3208-5]

8. Yuanyuan Xu, Yue Yang, Aifang Xue, Hao Chen, Shengqing Li.  (2018)  In situ precipitation of hydrous titanium dioxide for dispersive micro solid-phase extraction of nucleosides and their separation.  NEW JOURNAL OF CHEMISTRY,  42  (7): (4909-4914).  [PMID:] [10.1039/C7NJ04590E]

9. Li-li Zhang, Yong-liang Bai, Shu-lan Shu, Da-wei Qian, Zhen Ou-yang, Li Liu, Jin-ao Duan.  (2014)  Simultaneous quantitation of nucleosides, nucleobases, amino acids, and alkaloids in mulberry leaf by ultra high performance liquid chromatography with triple quadrupole tandem mass spectrometry.  JOURNAL OF SEPARATION SCIENCE,  37  (11): (1265-1275).  [PMID:24616434] [10.1002/jssc.201301267]

10. Sheng Guo, Jin-ao Duan, Dawei Qian, Hanqing Wang, Yuping Tang, Yefei Qian, Dawei Wu, Shulan Su, Erxin Shang.  (2013)  Hydrophilic interaction ultra-high performance liquid chromatography coupled with triple quadrupole mass spectrometry for determination of nucleotides, nucleosides and nucleobases in Ziziphus plants.  JOURNAL OF CHROMATOGRAPHY A,      [PMID:23800804] [10.1016/j.chroma.2013.05.074]

11. Hongmei Yang, Debin Wan, Fengrui Song, Zhiqiang Liu, Shuying Liu.  (2013)  Argon Direct Analysis in Real Time Mass Spectrometry in Conjunction with Makeup Solvents: A Method for Analysis of Labile Compounds.  ANALYTICAL CHEMISTRY,      [PMID:23252884] [10.1021/ac3026543]

12. Pan Wang, Tao Cheng, Zhuangxin Wei, Lu Liu, Yue Wang, Xiaohua Tian, Jianming Pan.  (2024)  Bioinspired Surface Engineering with Dual Covalent Receptors Incorporated via Precise Post-Imprinting Modification to Enhance the Specific Identification of Adenosine 5′-Monophosphate.  Engineering,      [PMID:] [10.1016/j.eng.2024.11.015]

13. Yamin Liu, Xunjiang Wang, Jiaojiao Wei, Kangning Fu, Yilin Chen, Linnan Li, Zhengtao Wang, Li Yang.  (2024)  Comprehensive Profiling of Amino Acids and Derivatives in Biological Samples: A Robust UHPLC-MS/MS Method for Investigating Acute Lung Injury.  JOURNAL OF CHROMATOGRAPHY A,      [PMID:38537486] [10.1016/j.chroma.2024.464816]

14. Pan Wang, Jiahui Chen, Lu Liu, Xiaohua Tian, Jianming Pan.  (2024)  Construction of dual receptors imprinted polymers by precise control of sequential assembly efficiency in confined sites to enhance specific separation of adenosine 5′-monophosphate.  SEPARATION AND PURIFICATION TECHNOLOGY,      [PMID:] [10.1016/j.seppur.2024.126353]

15. Tong Ren, Zhen Feng, Fang Jiang, Xingtong Liu, Tingting Chen, Yanli Guo, Lei Tian, Xiao-Feng Kang, Fujun Yao.  (2024)  Nanopore detection of guanine derivatives based on vacancy G-quadruplex DNA.  MICROCHEMICAL JOURNAL,      [PMID:] [10.1016/j.microc.2024.112366]

16. Tao Cheng, Yaotao Cai, Yifan Su, JinTao Xu, Xiaohua Tian, Pan Wang, Jianming Pan.  (2024)  Selective separation of adenosine 5′-monophosphate by Dual-Receptor Post-Imprinted modified polymers using hydrophilic MOF nanosheets as substrates with active functional groups.  SEPARATION AND PURIFICATION TECHNOLOGY,      [PMID:] [10.1016/j.seppur.2024.128071]

17. Zhuangxin Wei, Pan Wang, Jiangnan Wang, Jianming Pan.  (2024)  Synergy of Post-Crosslinked imprinting strategy and silanol chemistry for the anisotropic construction of molecularly imprinted polymers onto Halloysite nanotubes.  CHEMICAL ENGINEERING JOURNAL,      [PMID:] [10.1016/j.cej.2024.150704]

18. Ruixue Meng, Yue Xiong, Meijiao Zhou, Mine Du, Lizhong Zhu, Wei Wang.  (2026)  Identification of Halophenol-Deoxyguanosine Adducts in SV-HUC-1 Cells Exposed to Halobenzoquinones via the Neutral Loss and Information-Dependent Acquisition Strategy.  ENVIRONMENTAL SCIENCE & TECHNOLOGY,      [PMID:41543259] [10.1021/acs.est.5c12092]

19. Zhuangxin Wei, Tao Wang, Pan Wang, Jianming Pan.  (2026)  Synergistic integration of oil-mediated adhesion and post-crosslinking imprinting technology for surface imprinted polymers to precision separation of 2′-deoxyadenosine.  CHEMICAL ENGINEERING JOURNAL,      [PMID:] [10.1016/j.cej.2026.173960]

Frequently Asked Questions

What are the CAS number, molecular formula and molecular weight?

The CAS Number is 951-77-9, the molecular formula is C9H13N3O4, and the molecular weight is 227.22 g/mol. InChIKey CKTSBUTUHBMZGZ-SHYZEUOFSA-N.

What is the purity of this product?

This product is supplied at ≥99% purity (chemical assay). Lot-specific values are stated on the Certificate of Analysis.

How should this product be stored?

Store at ?20 °C. Freezer storage is required to maintain the specified shelf life.

How is this product shipped?

This product ships in an insulated container with ice pads. Unpack on arrival and transfer it to the storage condition stated above.

What documentation is provided?

Available product documentation, including Certificates of Analysis (COA), Safety Data Sheets (SDS), and specification sheets, is shown in the product document area. Document availability and access follow the current site policy.