Np mrd loader

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Record Information
Version1.0
Created at2005-11-16 15:48:42 UTC
Updated at2021-12-24 16:04:36 UTC
NP-MRD IDNP0001193
Secondary Accession NumbersNone
Natural Product Identification
Common NameCytidine
DescriptionCytidine is a nucleoside that is composed of the base cytosine linked to the five-carbon sugar D-ribose. Cytidine is a pyrimidine that besides being incorporated into nucleic acids, can serve as a substrate for the salvage pathway of pyrimidine nucleotide synthesis. It is a precursor of cytidine triphosphate (CTP) needed in the phosphatidylcholine (PC) and phosphatidylethanolamine (PE) biosynthetic pathways. These variations probably reflect the species differences in cytidine deaminase, the enzyme that converts cytidine to uridine in the body. The transport of cytidine into the brain's extracellular fluid, and then into neurons and glia, are essential prerequisites for cytidine to be utilized in the brain. An efficient mechanism mediating the brain uptake of circulating cytidine has not yet been demonstrated. The biosynthesis of PC, the most abundant phosphatide in the brain, via the Kennedy pathway requires phosphocholine and cytidine triphosphate (CTP), a cytidine nucleotide involved in the rate-limiting step. The enzyme that converts CTP to endogenous CDP-choline (CTP:Phosphocholine cytidylyltransferase) is unsaturated at physiological brain CTP levels. APOBEC is a family of enzymes that has been discovered with the ability to deaminate cytidines on RNA or DNA. The human apolipoprotein B mRNA-editing enzyme, catalytic polypeptide-like 3G protein (APOBEC3G, or hA3G), provides cells with an intracellular antiretroviral activity that is associated with the hypermutation of viral DNA through cytidine deamination. Indeed, hA3G belongs to a family of vertebrate proteins that contains one or two copies of a signature sequence motif unique to cytidine deaminases (CTDAs) (PMID: 16769123 , 15780864 , 16720547 ).
Structure
Thumb
Synonyms
ValueSource
1-beta-D-RibofuranosylcytosineChEBI
1beta-D-RibofuranosylcytosineChEBI
4-AMINO-1-BETA-D-ribofuranosyl-2(1H)-pyrimidinoneChEBI
4-Amino-1-beta-D-ribofuranosylpyrimidin-2(1H)-oneChEBI
4-Amino-1beta-D-ribofuranosyl-2(1H)-pyrimidinoneChEBI
CydChEBI
CytidinChEBI
Cytosine ribosideChEBI
Cytosine-1beta-D-ribofuranosideChEBI
ZytidinChEBI
PosilentKegg
1-b-D-RibofuranosylcytosineGenerator
1-Β-D-ribofuranosylcytosineGenerator
1b-D-RibofuranosylcytosineGenerator
1Β-D-ribofuranosylcytosineGenerator
4-AMINO-1-b-D-ribofuranosyl-2(1H)-pyrimidinoneGenerator
4-AMINO-1-β-D-ribofuranosyl-2(1H)-pyrimidinoneGenerator
4-Amino-1-b-D-ribofuranosylpyrimidin-2(1H)-oneGenerator
4-Amino-1-β-D-ribofuranosylpyrimidin-2(1H)-oneGenerator
4-Amino-1b-D-ribofuranosyl-2(1H)-pyrimidinoneGenerator
4-Amino-1β-D-ribofuranosyl-2(1H)-pyrimidinoneGenerator
Cytosine-1b-D-ribofuranosideGenerator
Cytosine-1β-D-ribofuranosideGenerator
1-(b-D-Ribofuranosyl)-2-oxo-4-amino-1,2-dihydro-1,3-diazineHMDB
1-(b-delta-Ribofuranosyl)-2-oxo-4-amino-1,2-dihydro-1,3-diazineHMDB
1-b-D-Ribosyl-cytosineHMDB
1-beta-D-Ribofuranosyl-cytosineHMDB
1-beta-delta-Ribofuranosyl-cytosineHMDB
1-beta-delta-RibofuranosylcytosineHMDB
1-beta-delta-Ribosyl-cytosineHMDB
1beta-delta-RibofuranosylcytosineHMDB
1beta-RibofuranosylcytosineHMDB
4-Amino-1-beta-delta-ribofuranosyl-2(1H)-pyrimidinoneHMDB
Cytosine-1b-delta-ribofuranosideHMDB
Cytosine-1beta-delta-ribofuranosideHMDB
Cytosine ribonucleosideHMDB
Ribonucleoside, cytosineHMDB
Riboside, cytosineHMDB
1-(beta-D-Ribofuranosyl)-2-oxo-4-amino-1,2-dihydro-1,3-diazineHMDB
1-(Β-D-ribofuranosyl)-2-oxo-4-amino-1,2-dihydro-1,3-diazineHMDB
Chemical FormulaC9H13N3O5
Average Mass243.2166 Da
Monoisotopic Mass243.08552 Da
IUPAC Name4-amino-1-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-1,2-dihydropyrimidin-2-one
Traditional Namecytidine
CAS Registry Number65-46-3
SMILES
NC1=NC(=O)N(C=C1)[C@@H]1O[C@H](CO)[C@@H](O)[C@H]1O
InChI Identifier
InChI=1S/C9H13N3O5/c10-5-1-2-12(9(16)11-5)8-7(15)6(14)4(3-13)17-8/h1-2,4,6-8,13-15H,3H2,(H2,10,11,16)/t4-,6-,7-,8-/m1/s1
InChI KeyUHDGCWIWMRVCDJ-XVFCMESISA-N
Spectra
Spectrum TypeDescriptionDepositor IDDeposition DateView
1D NMR1H NMR Spectrum (1D, 500 MHz, H2O, experimental)Wishart Lab2021-06-20View Spectrum
2D NMR[1H, 13C]-HSQC NMR Spectrum (2D, 600 MHz, H2O, experimental)Wishart Lab2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 700 MHz, H2O, simulated)Ahselim2021-12-24View Spectrum
1D NMR1H NMR Spectrum (1D, 700 MHz, H2O, experimental)Ahselim2021-12-24View Spectrum
Species
Species of Origin
Species NameSourceReference
Cannabis sativaCannabisDB
      Not Available
Capsicum annuumKNApSAcK Database
Fritillaria cirrhosaKNApSAcK Database
Morinda citrifoliaKNApSAcK Database
Chemical Taxonomy
Description Belongs to the class of organic compounds known as pyrimidine nucleosides. Pyrimidine nucleosides are compounds comprising a pyrimidine base attached to a ribosyl or deoxyribosyl moiety.
KingdomOrganic compounds
Super ClassNucleosides, nucleotides, and analogues
ClassPyrimidine nucleosides
Sub ClassNot Available
Direct ParentPyrimidine nucleosides
Alternative Parents
Substituents
  • Pyrimidine nucleoside
  • Glycosyl compound
  • N-glycosyl compound
  • Pentose monosaccharide
  • Aminopyrimidine
  • Pyrimidone
  • Hydropyrimidine
  • Monosaccharide
  • Pyrimidine
  • Imidolactam
  • Tetrahydrofuran
  • Heteroaromatic compound
  • Secondary alcohol
  • Oxacycle
  • Azacycle
  • Organoheterocyclic compound
  • Organic nitrogen compound
  • Primary alcohol
  • Organic oxide
  • Organooxygen compound
  • Organonitrogen compound
  • Amine
  • Alcohol
  • Organopnictogen compound
  • Organic oxygen compound
  • Primary amine
  • Hydrocarbon derivative
  • Aromatic heteromonocyclic compound
Molecular FrameworkAromatic heteromonocyclic compounds
External Descriptors
Physical Properties
StateSolid
Experimental Properties
PropertyValueReference
Melting Point230.5 °CNot Available
Boiling Point545.68 °C. @ 760.00 mm Hg (est)The Good Scents Company Information System
Water Solubility175700 mg/L @ 25 °C (est)The Good Scents Company Information System
LogP-2.51Hansch CH, Leo A and Hoekman DH. "Exploring QSAR: Hydrophobic, Electronic, and Steric Constraints. Volume 1" ACS Publications (1995).
Predicted Properties
PropertyValueSource
Water Solubility43.8 g/LALOGPS
logP10(-2.2) g/LALOGPS
logP10(-2.8) g/LChemAxon
logS10(-0.74) g/LALOGPS
pKa (Strongest Acidic)12.55ChemAxon
pKa (Strongest Basic)-0.062ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count7ChemAxon
Hydrogen Donor Count4ChemAxon
Polar Surface Area128.61 ŲChemAxon
Rotatable Bond Count2ChemAxon
Refractivity54.54 m³·mol⁻¹ChemAxon
Polarizability22.4 ųChemAxon
Number of Rings2ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDHMDB0000089
DrugBank IDDB02097
Phenol Explorer Compound IDNot Available
FoodDB IDFDB021809
KNApSAcK IDC00042440
Chemspider ID5940
KEGG Compound IDC00475
BioCyc IDCYTIDINE
BiGG ID35089
Wikipedia LinkCytidine
METLIN ID3376
PubChem Compound6175
PDB IDNot Available
ChEBI ID17562
Good Scents IDrw1233441
References
General References
  1. Sreekumar A, Poisson LM, Rajendiran TM, Khan AP, Cao Q, Yu J, Laxman B, Mehra R, Lonigro RJ, Li Y, Nyati MK, Ahsan A, Kalyana-Sundaram S, Han B, Cao X, Byun J, Omenn GS, Ghosh D, Pennathur S, Alexander DC, Berger A, Shuster JR, Wei JT, Varambally S, Beecher C, Chinnaiyan AM: Metabolomic profiles delineate potential role for sarcosine in prostate cancer progression. Nature. 2009 Feb 12;457(7231):910-4. doi: 10.1038/nature07762. [PubMed:19212411 ]
  2. Eells JT, Spector R: Purine and pyrimidine base and nucleoside concentrations in human cerebrospinal fluid and plasma. Neurochem Res. 1983 Nov;8(11):1451-7. [PubMed:6656991 ]
  3. Lee SH, Jung BH, Kim SY, Chung BC: A rapid and sensitive method for quantitation of nucleosides in human urine using liquid chromatography/mass spectrometry with direct urine injection. Rapid Commun Mass Spectrom. 2004;18(9):973-7. [PubMed:15116424 ]
  4. Mahieux R, Suspene R, Delebecque F, Henry M, Schwartz O, Wain-Hobson S, Vartanian JP: Extensive editing of a small fraction of human T-cell leukemia virus type 1 genomes by four APOBEC3 cytidine deaminases. J Gen Virol. 2005 Sep;86(Pt 9):2489-94. [PubMed:16099907 ]
  5. Schrofelbauer B, Yu Q, Zeitlin SG, Landau NR: Human immunodeficiency virus type 1 Vpr induces the degradation of the UNG and SMUG uracil-DNA glycosylases. J Virol. 2005 Sep;79(17):10978-87. [PubMed:16103149 ]
  6. Min IM, Selsing E: Antibody class switch recombination: roles for switch sequences and mismatch repair proteins. Adv Immunol. 2005;87:297-328. [PubMed:16102577 ]
  7. Zhong SQ, Sun LJ, Yan YZ, Sun YQ, Zhong YY: Effect of Xuesaitong soft capsule on hemorrheology and in auxiliarily treating patients with acute cerebral infarction. Chin J Integr Med. 2005 Jun;11(2):128-31. [PubMed:16150200 ]
  8. Barbour JD, Grant RM: The role of viral fitness in HIV pathogenesis. Curr HIV/AIDS Rep. 2005 Feb;2(1):29-34. [PubMed:16091246 ]
  9. Cansev M: Uridine and cytidine in the brain: their transport and utilization. Brain Res Rev. 2006 Sep;52(2):389-97. [PubMed:16769123 ]
  10. Huthoff H, Malim MH: Cytidine deamination and resistance to retroviral infection: towards a structural understanding of the APOBEC proteins. Virology. 2005 Apr 10;334(2):147-53. [PubMed:15780864 ]
  11. Navaratnam N, Sarwar R: An overview of cytidine deaminases. Int J Hematol. 2006 Apr;83(3):195-200. [PubMed:16720547 ]
  12. Reina J: [Plitidepsin, an inhibitor of the cell elongation factor eEF1a, and molnupiravir an analogue of the ribonucleoside cytidine, two new chemical compounds with intense activity against SARS-CoV-2]. Rev Esp Quimioter. 2021 Oct;34(5):402-407. doi: 10.37201/req/042.2021. Epub 2021 Apr 27. [PubMed:33902254 ]