5-Methylcytidine - 10mM in DMSO , CAS No.2140-61-6

CAS: 2140-61-6 Cat. No.: M422586 Molecular Weight: 257.24

GRADE & PURITY 10mM in DMSO

Synonyms

NSC-363933 | M1931 | s6138 | 5-Methylcytidine | 5-methyl-cytidine | DTXSID401016977 | 4-amino-1-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-5-methyl-1,2-dihydropyrimidin-2-one | AC-32357 | AM83948 | EINECS 218-390-8 | Adenosine receptor ago

Storage

Store at -80°C

Shipped In

Dry ice packs + Cold packs

Specifications

Synonyms

NSC-363933 | M1931 | s6138 | 5-Methylcytidine | 5-methyl-cytidine | DTXSID401016977 | 4-amino-1-[(2R, 3R, 4S, 5R)-3, 4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-5-methyl-1, 2-dihydropyrimidin-2-one | AC-32357 | AM83948 | EINECS 218-390-8 | Adenosine receptor ago

Specifications & Purity

10mM in DMSO

Biochemical and Physiological Mechanisms

Endogenous modified nucleoside. DNA methylation marker. 5-methylcytosine derivative. 5-methyltransferase Trm4 substrate. Accumulates in uncharged histone tRNA molecules when 5-methyltransferase Trm4 is depleted.

Storage

Store at -80°C

Shipped In

Dry ice packs + Cold packs

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

Names and Identifiers

• Canonical Smiles: CC1=CN(C(=O)N=C1N)C2C(C(C(O2)CO)O)O
• IUPAC Name: 4-amino-1-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-5-methylpyrimidin-2-one
• InChIKey: ZAYHVCMSTBRABG-JXOAFFINSA-N
• INCHI: 1S/C10H15N3O5/c1-4-2-13(10(17)12-8(4)11)9-7(16)6(15)5(3-14)18-9/h2,5-7,9,14-16H,3H2,1H3,(H2,11,12,17)/t5-,6-,7-,9-/m1/s1
• Isomeric SMILES: CC1=CN(C(=O)N=C1N)[C@H]2[C@@H]([C@@H]([C@H](O2)CO)O)O
• Molecular Weight: 257.24
• Reaxy-Rn: 25358540
• Reaxys-RN_link_address: https://www.reaxys.com/reaxys/secured/hopinto.do?context=S&query=IDE.XRN=25358540&ln=

Taxonomic Classification

Taxonomy Tree

• Kingdom Organic compounds
  • Superclass Nucleosides, nucleotides, and analogues
    • Class Pyrimidine nucleosides

• Kingdom: Organic compounds
• Superclass: Nucleosides, nucleotides, and analogues
• Class: Pyrimidine nucleosides
• Subclass: Not available
• Intermediate Tree Nodes: Not available
• Direct Parent: Pyrimidine nucleosides
• Alternative Parents: Glycosylamines Pentoses Hydroxypyrimidines Hydropyrimidines Tetrahydrofurans Heteroaromatic compounds Secondary alcohols Oxacyclic compounds Azacyclic compounds Primary alcohols Organopnictogen compounds Organonitrogen compounds Hydrocarbon derivatives
• Molecular Framework: Aromatic heteromonocyclic compounds
• Substituents: Pyrimidine nucleoside - Glycosyl compound - N-glycosyl compound - Pentose monosaccharide - Hydroxypyrimidine - Hydropyrimidine - Monosaccharide - Pyrimidine - Tetrahydrofuran - Heteroaromatic compound - Secondary alcohol - Organoheterocyclic compound - Azacycle - Oxacycle - Organic nitrogen compound - Hydrocarbon derivative - Primary alcohol - Organopnictogen compound - Organooxygen compound - Organonitrogen compound - Alcohol - Organic oxygen compound - Aromatic heteromonocyclic compound
• Description: This compound belongs to the class of organic compounds known as pyrimidine nucleosides. These are compounds comprising a pyrimidine base attached to a ribosyl or deoxyribosyl moiety.
• External Descriptors: methylcytidine

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(non-human)

L1210 (27553 Activities)

Explore this target

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

L1210/ara C (6 Activities)

Explore this target

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

Mechanisms of Action

Chemical and Physical Properties

• Specific Rotation[α]: 15° (C=2,H2O)
• Melt Point(°C): 211 °C(dec.)
• Molecular Weight: 257.240 g/mol
• XLogP3: -2.000
• Hydrogen Bond Donor Count: 4
• Hydrogen Bond Acceptor Count: 5
• Rotatable Bond Count: 2
• Exact Mass: 257.101 Da
• Monoisotopic Mass: 257.101 Da
• Topological Polar Surface Area: 129.000 Ų
• Heavy Atom Count: 18
• Formal Charge: 0
• Complexity: 422.000
• Isotope Atom Count: 0
• Defined Atom Stereocenter Count: 4
• 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. Deng Dehai, Qin Yichao, Lin Xiuying, Chu Meng, Lv Daizhu, Lin Huan.  (2025)  Unveiling transfer RNA modifications of oil palm and their dynamic changes during fruit ripening.  BMC PLANT BIOLOGY,  25  (1): (1-17).  [PMID:40155815] [10.1186/s12870-025-06426-9]

2. Sirui Zhu, Yuanyuan Li, You Wu, Yanan Shen, Ying Wang, Yujie Yan, Weijun Chen, Qiong Fu, Yirong Wang, Xiang Yu, Feng Yu.  (2023)  The FERONIA-YUELAO module participates in translational control by modulating the abundance of tRNA fragments in Arabidopsis.  DEVELOPMENTAL CELL,      [PMID:37977150] [10.1016/j.devcel.2023.10.014]