Record Information
Version3.6
Creation Date2005-11-16 15:48:42 UTC
Update Date2013-05-29 19:24:44 UTC
HMDB IDHMDB00089
Secondary Accession NumbersNone
Metabolite 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 substrate for the salvage pathway of pyrimidine nucleotide synthesis; as precursor of the cytidine triphosphate (CTP) needed in the phosphatidylcholine (PC) and phosphatidylethanolamine (PE) biosynthetic pathway. These variations probably reflect the species differences in cytidine deaminase, the enzyme that converts cytidine to uridine in the body. The transports of cytidine into the brain's extracellular fluid, and then into neurons and glia, are essential prerequisites for cytidine to be utilized in 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, which is 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 has been discovered with the ability to deaminate cytidines on RNA or DNA. The human apolipoprotein B mRNA-editing enzyme, catalytic polypeptide-like 3G (APOBEC3G, or hA3G) protein, 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 contain one or two copies of a signature sequence motif unique to cytidine deaminases (CTDAs). (PMID: 16769123 , 15780864 , 16720547 ).
Structure
Thumb
Synonyms
  1. 1-(b-D-Ribofuranosyl)-2-oxo-4-amino-1,2-dihydro-1,3-diazine
  2. 1-(b-delta-Ribofuranosyl)-2-oxo-4-amino-1,2-dihydro-1,3-diazine
  3. 1-b-D-Ribofuranosylcytosine
  4. 1-b-D-Ribosyl-Cytosine
  5. 1-beta-D-Ribofuranosyl-Cytosine
  6. 1-beta-D-Ribofuranosylcytosine
  7. 1-beta-delta-Ribofuranosyl-Cytosine
  8. 1-beta-delta-Ribofuranosylcytosine
  9. 1-beta-delta-Ribosyl-Cytosine
  10. 1beta-D-Ribofuranosylcytosine
  11. 1beta-delta-Ribofuranosylcytosine
  12. 1beta-Ribofuranosylcytosine
  13. 4-Amino-1-b-D-ribofuranosyl-2(1H)-pyrimidinone
  14. 4-Amino-1-beta-delta-ribofuranosyl-2(1H)-pyrimidinone
  15. Cytidine
  16. Cytosine riboside
  17. Cytosine-1b-D-Ribofuranoside
  18. Cytosine-1b-delta-Ribofuranoside
  19. Cytosine-1beta-D-Ribofuranoside
  20. Cytosine-1beta-delta-Ribofuranoside
Chemical FormulaC9H13N3O5
Average Molecular Weight243.2166
Monoisotopic Molecular Weight243.085520541
IUPAC Name4-amino-1-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-1,2-dihydropyrimidin-2-one
Traditional IUPAC 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
Chemical Taxonomy
KingdomOrganic Compounds
Super ClassNucleosides, Nucleotides, and Analogues
ClassPyrimidine Nucleosides and Analogues
Sub ClassN/A
Other Descriptors
  • Aromatic Heteropolycyclic Compounds
  • a pyrimidine ribonucleoside(Cyc)
Substituents
  • 1,2 Diol
  • Aminopyrimidine
  • Glycosyl Compound
  • Hydropyrimidine
  • N Glycosyl Compound
  • Oxolane
  • Pentose Monosaccharide
  • Primary Alcohol
  • Pyrimidine
  • Pyrimidone
  • Saccharide
  • Secondary Alcohol
Direct ParentPyrimidine Nucleosides and Analogues
Ontology
StatusDetected and Quantified
Origin
  • Endogenous
Biofunction
  • Component of Pyrimidine metabolism
  • Protein component
ApplicationNot Available
Cellular locations
  • Extracellular
  • Mitochondria
  • Nucleus
  • Lysosome
Physical Properties
StateSolid
Experimental Properties
PropertyValueReference
Melting Point230.5 °CNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogP-2.51HANSCH,C ET AL. (1995)
Predicted Properties
PropertyValueSource
water solubility43.8 g/LALOGPS
logP-2.2ALOGPS
logP-2.8ChemAxon
logS-0.74ALOGPS
pKa (strongest acidic)12.55ChemAxon
pKa (strongest basic)-0.55ChemAxon
physiological charge0ChemAxon
hydrogen acceptor count7ChemAxon
hydrogen donor count4ChemAxon
polar surface area128.61ChemAxon
rotatable bond count2ChemAxon
refractivity54.54ChemAxon
polarizability22.39ChemAxon
Spectra
Spectra
Biological Properties
Cellular Locations
  • Extracellular
  • Mitochondria
  • Nucleus
  • Lysosome
Biofluid Locations
  • Blood
  • Cerebrospinal Fluid (CSF)
  • Urine
Tissue Location
  • All Tissues
  • Prostate
Pathways
NameSMPDB LinkKEGG Link
Pyrimidine MetabolismSMP00046map00240
Normal Concentrations
BiofluidStatusValueAgeSexConditionReference
BloodDetected and Quantified0.25 +/- 0.19 uMAdult (>18 years old)BothNormal
BloodDetected and Quantified0.1 +/- 0.0 uMAdult (>18 years old)BothNormal
Cerebrospinal Fluid (CSF)Detected and Quantified0.44 +/- 0.32 uMInfant (0-1 year old)BothNormal
UrineDetected and Quantified0.78 (0.00-1.6) umol/mmol creatinineAdult (>18 years old)BothNormal
UrineDetected and Quantified0.07 +/- 0.05 umol/mmol creatinineAdult (>18 years old)FemaleNormal
UrineDetected and Quantified0.08 +/- 0.06 umol/mmol creatinineAdult (>18 years old)MaleNormal
UrineDetected and Quantified0.07 +/- 0.05 umol/mmol creatinineAdult (>18 years old)BothNormal
UrineDetected and Quantified1.50 +/- 1.34 umol/mmol creatinineChildren (1-13 year old)BothNormal
UrineDetected and Quantified1.12 +/- 0.69 umol/mmol creatinineAdolescent (13-18 years old)BothNormal
UrineDetected and Quantified0.33 +/- 0.17 umol/mmol creatinineAdult (>18 years old)BothNormal
Abnormal Concentrations
BiofluidStatusValueAgeSexConditionReference
BloodDetected and Quantified0.26 +/- 0.13 uMAdult (>18 years old)BothCanavan disease
UrineDetected and Quantified4.03 +/- 1.77 umol/mmol creatinineAdult (>18 years old)BothCanavan disease
Associated Disorders and Diseases
Disease References
Canavan disease
  • Tavazzi B, Lazzarino G, Leone P, Amorini AM, Bellia F, Janson CG, Di Pietro V, Ceccarelli L, Donzelli S, Francis JS, Giardina B: Simultaneous high performance liquid chromatographic separation of purines, pyrimidines, N-acetylated amino acids, and dicarboxylic acids for the chemical diagnosis of inborn errors of metabolism. Clin Biochem. 2005 Nov;38(11):997-1008. Epub 2005 Sep 1. Pubmed: 16139832
Associated OMIM IDs
DrugBank IDNot Available
DrugBank Metabolite IDNot Available
Phenol Explorer Compound IDNot Available
Phenol Explorer Metabolite IDNot Available
FoodDB IDFDB021809
KNApSAcK IDNot Available
Chemspider ID5940
KEGG Compound IDC00475
BioCyc IDCYTIDINE
BiGG ID35089
Wikipedia LinkCytidine
NuGOwiki LinkHMDB00089
Metagene LinkHMDB00089
METLIN ID3376
PubChem Compound6175
PDB IDCTN
ChEBI ID17562
References
Synthesis ReferenceQu, Guirong; Yang, Xining; Shen, Yanhong; Dong, Chunhong; Guo, Haiming; Wang, Xiuqiang; Wang, Dongchao. Synthesis of cytidine. Faming Zhuanli Shenqing Gongkai Shuomingshu (2007), 11pp.
Material Safety Data Sheet (MSDS)Not Available
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. 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

Enzymes

Gene Name:
NT5E
Uniprot ID:
P21589
Reactions
Cytidine monophosphate + Water unknown Cytidine + Phosphoric aciddetails
Gene Name:
NT5C1B
Uniprot ID:
Q96P26
Reactions
Cytidine monophosphate + Water unknown Cytidine + Phosphoric aciddetails
Gene Name:
NT5C1A
Uniprot ID:
Q9BXI3
Reactions
Cytidine monophosphate + Water unknown Cytidine + Phosphoric aciddetails
Gene Name:
NT5C
Uniprot ID:
Q8TCD5
Reactions
Cytidine monophosphate + Water unknown Cytidine + Phosphoric aciddetails
Gene Name:
NT5M
Uniprot ID:
Q9NPB1
Reactions
Cytidine monophosphate + Water unknown Cytidine + Phosphoric aciddetails
Gene Name:
UCK1
Uniprot ID:
Q9HA47
Reactions
Adenosine triphosphate + Cytidine unknown ADP + Cytidine monophosphatedetails
Uridine triphosphate + Cytidine unknown Uridine 5'-diphosphate + Cytidine monophosphatedetails
Guanosine triphosphate + Cytidine unknown Guanosine diphosphate + Cytidine monophosphatedetails
Inosine triphosphate + Cytidine unknown IDP + Cytidine monophosphatedetails
Deoxyadenosine triphosphate + Cytidine unknown dADP + Cytidine monophosphatedetails
dGTP + Cytidine unknown dGDP + Cytidine monophosphatedetails
Thymidine 5'-triphosphate + Cytidine unknown dTDP + Cytidine monophosphatedetails
dCTP + Cytidine unknown dCDP + Cytidine monophosphatedetails
Deoxyuridine triphosphate + Cytidine unknown dUDP + Cytidine monophosphatedetails
Gene Name:
UCK2
Uniprot ID:
Q9BZX2
Reactions
Adenosine triphosphate + Cytidine unknown ADP + Cytidine monophosphatedetails
Uridine triphosphate + Cytidine unknown Uridine 5'-diphosphate + Cytidine monophosphatedetails
Guanosine triphosphate + Cytidine unknown Guanosine diphosphate + Cytidine monophosphatedetails
Inosine triphosphate + Cytidine unknown IDP + Cytidine monophosphatedetails
Deoxyadenosine triphosphate + Cytidine unknown dADP + Cytidine monophosphatedetails
dGTP + Cytidine unknown dGDP + Cytidine monophosphatedetails
Thymidine 5'-triphosphate + Cytidine unknown dTDP + Cytidine monophosphatedetails
dCTP + Cytidine unknown dCDP + Cytidine monophosphatedetails
Deoxyuridine triphosphate + Cytidine unknown dUDP + Cytidine monophosphatedetails
9. AID
Gene Name:
AID
Uniprot ID:
Q546Y9
Gene Name:
NT5C3
Uniprot ID:
Q9H0P0
Reactions
Cytidine monophosphate + Water unknown Cytidine + Phosphoric aciddetails
Gene Name:
NT5C2
Uniprot ID:
P49902
Reactions
Cytidine monophosphate + Water unknown Cytidine + Phosphoric aciddetails
Gene Name:
CDA
Uniprot ID:
P32320
Reactions
Cytidine + Water unknown Uridine + Ammoniadetails
Gene Name:
UCKL1
Uniprot ID:
Q9NWZ5
Reactions
Adenosine triphosphate + Cytidine unknown ADP + Cytidine monophosphatedetails
Uridine triphosphate + Cytidine unknown Uridine 5'-diphosphate + Cytidine monophosphatedetails
Guanosine triphosphate + Cytidine unknown Guanosine diphosphate + Cytidine monophosphatedetails
Inosine triphosphate + Cytidine unknown IDP + Cytidine monophosphatedetails
Deoxyadenosine triphosphate + Cytidine unknown dADP + Cytidine monophosphatedetails
dGTP + Cytidine unknown dGDP + Cytidine monophosphatedetails
Thymidine 5'-triphosphate + Cytidine unknown dTDP + Cytidine monophosphatedetails
dCTP + Cytidine unknown dCDP + Cytidine monophosphatedetails
Deoxyuridine triphosphate + Cytidine unknown dUDP + Cytidine monophosphatedetails
Gene Name:
APOBEC3H
Uniprot ID:
Q6NTF7
Reactions
Cytidine + Water unknown Uridine + Ammoniadetails
Gene Name:
ZNF638
Uniprot ID:
Q14966
Gene Name:
CELF2
Uniprot ID:
O95319
Gene Name:
APOBEC3A
Uniprot ID:
P31941
Reactions
Cytidine + Water unknown Uridine + Ammoniadetails
Gene Name:
APOBEC3B
Uniprot ID:
Q9UH17
Reactions
Cytidine + Water unknown Uridine + Ammoniadetails
Gene Name:
APOBEC3C
Uniprot ID:
Q9NRW3
Reactions
Cytidine + Water unknown Uridine + Ammoniadetails
Gene Name:
APOBEC3D
Uniprot ID:
Q96AK3
Reactions
Cytidine + Water unknown Uridine + Ammoniadetails
Gene Name:
APOBEC3F
Uniprot ID:
Q8IUX4
Reactions
Cytidine + Water unknown Uridine + Ammoniadetails
Gene Name:
AICDA
Uniprot ID:
Q9GZX7
Reactions
Cytidine + Water unknown Uridine + Ammoniadetails