GRADE & PURITY ≥95%

Synonyms

4-amino-5-chloro-1-[(2R,4S,5R)-4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]pyrimidin-2-one | NSC 371331 | 2'-Deoxy-5-chlorocytidine | 5-cldc | 4-Amino-5-chloro-1-((2R,4S,5R)-4-hydroxy-5-(hydroxymethyl)tetrahydrofuran-2-yl)pyrimidin-2(1H)-one | 5-Chloro-2'-deox

Storage

Store at -20°C

Shipped In

Ice chest + Ice pads

Overview

5-Chloro-2'-deoxycytidine is of potential interest in research on chlorine-stressed DNA.

Specifications

Synonyms

4-amino-5-chloro-1-[(2R, 4S, 5R)-4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]pyrimidin-2-one | NSC 371331 | 2'-Deoxy-5-chlorocytidine | 5-cldc | 4-Amino-5-chloro-1-((2R, 4S, 5R)-4-hydroxy-5-(hydroxymethyl)tetrahydrofuran-2-yl)pyrimidin-2(1H)-one | 5-Chloro-2'-deox

Specifications & Purity

≥95%

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

≥95%

Names and Identifiers

• Pubchem Sid: 504756466
• Pubchem Sid Url: https://pubchem.ncbi.nlm.nih.gov/substance/504756466
• Canonical Smiles: C1C(C(OC1N2C=C(C(=NC2=O)N)Cl)CO)O
• IUPAC Name: 4-amino-5-chloro-1-[(2R,4S,5R)-4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]pyrimidin-2-one
• InChIKey: NGGRGTWYSXYVDK-RRKCRQDMSA-N
• INCHI: 1S/C9H12ClN3O4/c10-4-2-13(9(16)12-8(4)11)7-1-5(15)6(3-14)17-7/h2,5-7,14-15H,1,3H2,(H2,11,12,16)/t5-,6+,7+/m0/s1
• Isomeric SMILES: C1[C@@H]([C@H](O[C@H]1N2C=C(C(=NC2=O)N)Cl)CO)O
• Molecular Weight: 261.66
• Reaxy-Rn: 25081898
• Reaxys-RN_link_address: https://www.reaxys.com/reaxys/secured/hopinto.do?context=S&query=IDE.XRN=25081898&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 Halopyrimidines Aryl chlorides Imidolactams Hydropyrimidines Tetrahydrofurans Heteroaromatic compounds Secondary alcohols Oxacyclic compounds Azacyclic compounds Hydrocarbon derivatives Organic oxides Organochlorides Organopnictogen compounds Primary alcohols Primary amines
• Molecular Framework: Aromatic heteromonocyclic compounds
• Substituents: Pyrimidine 2'-deoxyribonucleoside - Aminopyrimidine - Halopyrimidine - Pyrimidone - Aryl chloride - Aryl halide - Hydropyrimidine - Pyrimidine - Imidolactam - Heteroaromatic compound - Tetrahydrofuran - Secondary alcohol - Oxacycle - Azacycle - Organoheterocyclic compound - Hydrocarbon derivative - Primary amine - Primary alcohol - Organooxygen compound - Organonitrogen compound - Organochloride - Organohalogen compound - Organic nitrogen compound - Organic oxygen compound - Amine - Organopnictogen compound - Organic oxide - Alcohol - 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(non-human)

Hdac6 Histone deacetylase 6 (222 Activities)

Discover Target: Hdac6

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

rep Replicase polyprotein 1ab (378 Activities)

Discover Target: rep

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

Mechanisms of Action

Chemical and Physical Properties

• Molecular Weight: 261.660 g/mol
• XLogP3: -0.900
• Hydrogen Bond Donor Count: 3
• Hydrogen Bond Acceptor Count: 4
• Rotatable Bond Count: 2
• Exact Mass: 261.052 Da
• Monoisotopic Mass: 261.052 Da
• Topological Polar Surface Area: 108.000 Ų
• Heavy Atom Count: 17
• Formal Charge: 0
• Complexity: 398.000
• 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