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Bovine Metabolome Database

Showing metabocard for Cytidine (BMDB00089)

Legend: metabolite field enzyme field

Version 1.0
Creation Date 2005-11-16 15:48:42
Update Date 2009-06-15 10:43:47
Accession Number BMDB00089
Common Name Cytidine
Description Cytidine 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)
  1. 1-(b-D-Ribofuranosyl)-2-oxo-4-amino-1,2-dihydro-1,3-diazine
  2. 1-b-D-Ribofuranosylcytosine
  3. 1-b-D-ribosyl-Cytosine
  4. 1-beta-D-Ribofuranosylcytosine
  5. 1-beta-D-ribofuranosyl-Cytosine
  6. 1beta-D-Ribofuranosylcytosine
  7. 1beta-Ribofuranosylcytosine
  8. 4-Amino-1-b-D-ribofuranosyl-2(1H)-pyrimidinone
  9. Cytidine
  10. Cytosine riboside
  11. cytosine-1b-D-Ribofuranoside
  12. cytosine-1beta-D-Ribofuranoside
  13. 1-(b-delta-Ribofuranosyl)-2-oxo-4-amino-1,2-dihydro-1,3-diazine
  14. 1-beta-delta-Ribofuranosylcytosine
  15. 1-beta-delta-ribosyl-Cytosine
  16. 1-beta-delta-ribofuranosyl-Cytosine
  17. 1beta-delta-Ribofuranosylcytosine
  18. 4-Amino-1-beta-delta-ribofuranosyl-2(1H)-pyrimidinone
  19. cytosine-1b-delta-Ribofuranoside
  20. cytosine-1beta-delta-Ribofuranoside
Chemical IUPAC Name 4-amino-1-[3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-pyrimidin-2-one
Chemical Formula C9H13N3O5
Chemical Structure Structure
Chemical Taxonomy
  • Organic
Super Class
  • Nucleosides and Nucleoside conjugates
  • Nucleoside Analogues
Sub Class
  • Miscellaneous nucleosides
  • Mammalian_Metabolite
  • primary alcohol; secondary alcohol; 1,2-diol; primary amine; primary aromatic amine; oxo(het)arene; aromatic compound; heterocyclic compound
  • Protein component; Component of Pyrimidine metabolism
  • Endogenous
Average Molecular Weight 243.217
Monoisotopic Molecular Weight 243.085526
Isomeric SMILES NC1=NC(=O)N(C=C1)[C@@H]1O[C@H](CO)[C@@H](O)[C@H]1O
Canonical SMILES NC1=NC(=O)N(C=C1)C1OC(CO)C(O)C1O
KEGG Compound ID C00475 Link Image
BioCyc ID CYTIDINE Link Image
BiGG ID 35089 Link Image
Wikipedia Link Cytidine Link Image
METLIN ID 3376 Link Image
PubChem Compound 6175 Link Image
PubChem Substance 3132638 Link Image
ChEBI ID 17562 Link Image
CAS Registry Number 65-46-3
InChI Identifier InChI=1/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
Synthesis Reference Qu, Guirong; Yang, Xining; Shen, Yanhong; Dong, Chunhong; Guo, Haiming; Wang, Xiuqiang; Wang, Dongchao. Synthesis of cytidine. Faming Zhuanli Shenqing Gongkai Shuomingshu (2007), 11pp.
Melting Point (Experimental) 230.5 oC
Experimental Water Solubility Not Available Source: PhysProp
Predicted Water Solubility 176.0 mg/mL [MEYLAN,WM et al. (1996)]; 43.800003 mg/mL [Predicted by ALOGPS] Calculated using ALOGPS
Physiological Charge 0
State Solid
Experimental LogP/Hydrophobicity -2.51 [HANSCH,C ET AL. (1995)] Source: PhysProp
Predicted LogP/Hydrophobicity -2.18 [Predicted by ALOGPS]; -2.8 [Predicted by PubChem via XLOGP] Calculated using ALOGPS
Material Safety Data Sheet (MSDS)
MOL File Show
SDF File Show
PDB File Show
2D Structure
3D Structure
Experimental PDB ID Not Available
Experimental 1H NMR Spectrum Download Spectrum
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Experimental 13C NMR Spectrum Not Available
Experimental 13C HSQC Spectrum Download Spectrum
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Predicted 1H NMR Spectrum Show Image
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Predicted 13C NMR Spectrum Show Image
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Mass Spectrum
Low Energy
Download File
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Medium Energy
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High Energy
Download File
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Simplified TOCSY Spectrum Show Image
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BMRB Spectrum Show Image
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Cellular Location
  • Cytoplasm (Predicted from LogP)
  • Extracellular
  • lysosome
  • mitochondria
  • nucleus
Biofluid Location
  • Breast_Milk
Tissue Location
Tissue References
All Tissues
Concentrations (Normal)
Biofluid Breast_Milk
Value 5.800 uM
Age N/A
Sex N/A
Condition Normal
Comments Raw. whole.
Biofluid Breast_Milk
Value 2.440 +/- 0.780 uM
Age N/A
Sex N/A
Condition Normal
Comments Raw. raw.
Biofluid Breast_Milk
Value 2.400 uM
Age N/A
Sex N/A
Condition Normal
Comments Raw.
Biofluid Breast_Milk
Value NA NA
Age NA
Sex NA
Condition Normal
Comments Detected but not quantified in conventional whole milk
Concentrations (Abnormal) Not Available
Pathway Names
  • Pyrimidine Metabolism
HMDB Pathways
Name Pyrimidine Metabolism
Image Show Link Image
KEGG Pathways
Name Pyrimidine Metabolism
Image Show Link Image
SimCell Pathways
Name Pyrimidine Metabolism
Image Show Link Image
General References
  1. Wikipedia Link Image
Metabolic Enzymes
  1. Activation-induced cytidine deaminase
  2. Uridine-cytidine kinase 1
Enzyme 1 [top]
Enzyme 1 ID 580
Enzyme 1 Name Activation-induced cytidine deaminase
Enzyme 1 Synonyms
  1. Cytidine aminohydrolase
Enzyme 1 Gene Name AICDA
Enzyme 1 Protein Sequence >Activation-induced cytidine deaminase
Enzyme 1 Number of Residues 199
Enzyme 1 Molecular Weight 24051.4
Enzyme 1 Theoretical pI 9.65
Enzyme 1 GO Classification
Enzyme 1 General Function Involved in cytidine deaminase activity
Enzyme 1 Specific Function RNA-editing deaminase involved in somatic hypermutation, gene conversion, and class-switch recombination. Required for several crucial steps of B-cell terminal differentiation necessary for efficient antibody responses
Enzyme 1 Pathways Not Available
Enzyme 1 Reactions Not Available
Enzyme 1 Pfam Domain Function
Enzyme 1 Signals
  • None
Enzyme 1 Transmembrane Regions
  • None
Enzyme 1 Essentiality Not Available
Enzyme 1 GenBank ID Protein 83755095 Link Image
Enzyme 1 UniProtKB/Swiss-Prot ID Q2PT36 Link Image
Enzyme 1 UniProtKB/Swiss-Prot Entry Name AICDA_BOVIN Link Image
Enzyme 1 PDB ID Not Available
Enzyme 1 Cellular Location Not Available
Enzyme 1 Gene Sequence Not Available
Enzyme 1 GenBank Gene ID DQ303466 Link Image
Enzyme 1 GeneCard ID AICDA Link Image
Enzyme 1 GenAtlas ID Not Available
Enzyme 1 HGNC ID Not Available
Enzyme 1 Chromosome Location Chromosome:1
Enzyme 1 Locus 12p13
Enzyme 1 SNPs SNPJam Report Link Image
Enzyme 1 General References Not Available
Enzyme 1 Metabolite References Not Available
Enzyme 2 [top]
Enzyme 2 ID 583
Enzyme 2 Name Uridine-cytidine kinase 1
Enzyme 2 Synonyms
  1. UCK 1
  2. Uridine monophosphokinase 1
  3. Cytidine monophosphokinase 1
Enzyme 2 Gene Name UCK1
Enzyme 2 Protein Sequence >Uridine-cytidine kinase 1
Enzyme 2 Number of Residues 277
Enzyme 2 Molecular Weight 31195.2
Enzyme 2 Theoretical pI 7.40
Enzyme 2 GO Classification
Enzyme 2 General Function Nucleotide transport and metabolism
Enzyme 2 Specific Function Phosphorylates uridine and cytidine to uridine monophosphate and cytidine monophosphate. Does not phosphorylate deoxyribonucleosides or purine ribonucleosides. Can use ATP or GTP as a phosphate donor
Enzyme 2 Pathways
  • Pyrimidine metabolism
  • UMP biosynthesis via salvage pathway
  • UMP from uridine:step 1/1
Enzyme 2 Reactions Not Available
Enzyme 2 Pfam Domain Function
Enzyme 2 Signals
  • None
Enzyme 2 Transmembrane Regions
  • None
Enzyme 2 Essentiality Not Available
Enzyme 2 GenBank ID Protein 112362124 Link Image
Enzyme 2 UniProtKB/Swiss-Prot ID Q0P5A4 Link Image
Enzyme 2 UniProtKB/Swiss-Prot Entry Name UCK1_BOVIN Link Image
Enzyme 2 PDB ID Not Available
Enzyme 2 Cellular Location Not Available
Enzyme 2 Gene Sequence >834 bp
Enzyme 2 GenBank Gene ID BC120304 Link Image
Enzyme 2 GeneCard ID UCK1 Link Image
Enzyme 2 GenAtlas ID Not Available
Enzyme 2 HGNC ID Not Available
Enzyme 2 Chromosome Location Chromosome:9
Enzyme 2 Locus 9q34.13
Enzyme 2 SNPs SNPJam Report Link Image
Enzyme 2 General References Not Available
Enzyme 2 Metabolite References Not Available