5-(Hydroxymethyl)-2'-deoxycytidine - ≥95% , CAS No.7226-77-9

CAS: 7226-77-9 Cat. No.: H276536 Molecular Weight: 257.25

GRADE & PURITY ≥95%

Synonyms

Cytidine, 2'-deoxy-5-(hydroxymethyl)- | HY-131394 | 2'-deoxy-5-(hydroxymethyl)cytidine | 4-Amino-1-(4-hydroxy-5-hydroxymethyl-tetrahydro-furan-2-yl)-5-hydroxymethyl-1H-pyrimidin-2-one | 5-Hydroxymethyldeoxycytidine monophosphate | PD017712 | 4-Amino-1-((2

Storage

Store at -20°C

Shipped In

Ice chest + Ice pads

Overview

Product description：

5-Hydroxymethyl-2’-deoxycytidine (5hmdC) is an oxidation derivative of 5-methyl-2'-deoxycytidine (5-mdC) in DNA. 5-Hydroxymethyl-2’-deoxycytidine may serve as a marker of irreversibly damaged cells.

Specifications

Synonyms

Cytidine, 2'-deoxy-5-(hydroxymethyl)- | HY-131394 | 2'-deoxy-5-(hydroxymethyl)cytidine | 4-Amino-1-(4-hydroxy-5-hydroxymethyl-tetrahydro-furan-2-yl)-5-hydroxymethyl-1H-pyrimidin-2-one | 5-Hydroxymethyldeoxycytidine monophosphate | PD017712 | 4-Amino-1-((2

Specifications & Purity

≥95%

Biochemical and Physiological Mechanisms

Modified pyrimidine capable of producing interstrand cross-links in double-stranded DNA. Used to quantify DNA hydroxymethylation levels in biological samples.

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.

Note

Wherever possible, you should prepare and use solutions on the same day. However, if you need to make up stock solutions in advance, we recommend that you store the solution as aliquots in tightly sealed vials at -20°C. Generally, these will be useable for up to one month. Before use, and prior to opening the vial we recommend that you allow your product to equilibrate to room temperature for at least 1 hour. Need more advice on solubility, usage and handling? Please visit our frequently asked questions (FAQ) page for more details.

Purity

≥95%

Names and Identifiers

• Canonical Smiles: C1C(C(OC1N2C=C(C(=NC2=O)N)CO)CO)O
• IUPAC Name: 4-amino-1-[(2R,4S,5R)-4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]-5-(hydroxymethyl)pyrimidin-2-one
• InChIKey: HMUOMFLFUUHUPE-XLPZGREQSA-N
• INCHI: 1S/C10H15N3O5/c11-9-5(3-14)2-13(10(17)12-9)8-1-6(16)7(4-15)18-8/h2,6-8,14-16H,1,3-4H2,(H2,11,12,17)/t6-,7+,8+/m0/s1
• Isomeric SMILES: C1[C@@H]([C@H](O[C@H]1N2C=C(C(=NC2=O)N)CO)CO)O
• Molecular Weight: 257.25
• Reaxy-Rn: 62050958
• Reaxys-RN_link_address: https://www.reaxys.com/reaxys/secured/hopinto.do?context=S&query=IDE.XRN=62050958&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 Aromatic alcohols
• Molecular Framework: Aromatic heteromonocyclic compounds
• Substituents: Pyrimidine 2'-deoxyribonucleoside - Aminopyrimidine - Pyrimidone - Hydropyrimidine - Pyrimidine - Imidolactam - Heteroaromatic compound - Tetrahydrofuran - Secondary alcohol - Oxacycle - Azacycle - Organoheterocyclic compound - Alcohol - Hydrocarbon derivative - Organic oxide - Organopnictogen compound - Primary amine - Primary alcohol - Organooxygen compound - Organonitrogen compound - Organic oxygen compound - Amine - Aromatic alcohol - Organic nitrogen compound - 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: Not available

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)

CEM-SS (2428 Activities)

Explore this target

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

Associated Targets(non-human)

Human immunodeficiency virus 1 (70413 Activities)

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

Mechanisms of Action

Chemical and Physical Properties

• Melt Point(°C): 205 °C
• Molecular Weight: 257.240 g/mol
• XLogP3: -2.100
• Hydrogen Bond Donor Count: 4
• Hydrogen Bond Acceptor Count: 5
• Rotatable Bond Count: 3
• 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: 408.000
• 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