Human Metabolome Database Version 3.5

Showing metabocard for Cytidine (HMDB00089)

Record Information
Version 3.5
Creation Date 2005-11-16 08:48:42 -0700
Update Date 2013-05-29 13:24:44 -0600
HMDB ID HMDB00089
Secondary Accession Numbers None
Metabolite Identification
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 Link_out, 15780864 Link_out, 16720547 Link_out).
Structure Thumb
Download: MOL | SDF | PDB | SMILES | InChI
Display: 2D Structure | 3D Structure
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 Formula C9H13N3O5
Average Molecular Weight 243.2166
Monoisotopic Molecular Weight 243.085520541
IUPAC Name 4-amino-1-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-1,2-dihydropyrimidin-2-one
Traditional IUPAC Name cytidine
CAS Registry Number 65-46-3
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 Key UHDGCWIWMRVCDJ-XVFCMESISA-N
Chemical Taxonomy
Kingdom Organic Compounds
Super Class Nucleosides, Nucleotides, and Analogues
Class Pyrimidine Nucleosides and Analogues
Sub Class N/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 Parent Pyrimidine Nucleosides and Analogues
Ontology
Status Detected and Quantified
Origin
  • Endogenous
Biofunction
  • Component of Pyrimidine metabolism
  • Protein component
Application Not Available
Cellular locations
  • Extracellular
  • Mitochondria
  • Nucleus
  • Lysosome
Physical Properties
State Solid
Experimental Properties
Property Value Reference
Melting Point 230.5 °C Not Available
Boiling Point Not Available Not Available
Water Solubility Not Available Not Available
LogP -2.51 HANSCH,C ET AL. (1995)
Predicted Properties
Property Value Source
Water Solubility 43.8 g/L ALOGPS
LogP -2.18 ALOGPS
LogP -2.8 ChemAxon
LogS -0.74 ALOGPS
pKa (strongest acidic) 12.55 ChemAxon
pKa (strongest basic) -0.55 ChemAxon
Hydrogen Acceptor Count 7 ChemAxon
Hydrogen Donor Count 4 ChemAxon
Polar Surface Area 128.61 A2 ChemAxon
Rotatable Bond Count 2 ChemAxon
Refractivity 54.54 ChemAxon
Polarizability 22.39 ChemAxon
Formal Charge 0 ChemAxon
Physiological Charge 0 ChemAxon
Spectra
1H NMR Spectrum
MS/MS Spectrum Quattro_QQQ 10
MS/MS Spectrum Quattro_QQQ 25
MS/MS Spectrum Quattro_QQQ 40
MS/MS Spectrum LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic)
MS/MS Spectrum LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic)
MS/MS Spectrum LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic)
MS/MS Spectrum LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic)
MS/MS Spectrum LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic)
MS/MS Spectrum LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic)
MS/MS Spectrum LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic)
MS/MS Spectrum LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic)
MS/MS Spectrum LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic)
MS/MS Spectrum LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic)
MS/MS Spectrum LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic)
MS/MS Spectrum LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic)
[1H,1H] 2D NMR Spectrum
[1H,13C] 2D NMR Spectrum
Biological Properties
Cellular Locations
  • Extracellular
  • Mitochondria
  • Nucleus
  • Lysosome
Biofluid Locations
  • Blood
  • Cerebrospinal Fluid (CSF)
  • Urine
Tissue Location
  • All Tissues
  • Prostate
Pathways
Name SMPDB Link KEGG Link
Pyrimidine Metabolism SMP00046 map00240 Link_out
Normal Concentrations
Biofluid Status Value Age Sex Condition Reference
Blood Detected and Quantified
0.25 +/- 0.19 uM Adult (>18 years old) Both Normal
Blood Detected and Quantified
0.1 +/- 0.0 uM Adult (>18 years old) Both Normal
Cerebrospinal Fluid (CSF) Detected and Quantified
0.44 +/- 0.32 uM Infant (0-1 year old) Both Normal
Urine Detected and Quantified
0.78 (0.00-1.6) umol/mmol creatinine Adult (>18 years old) Both Normal
Urine Detected and Quantified
0.07 +/- 0.05 umol/mmol creatinine Adult (>18 years old) Female Normal
Urine Detected and Quantified
0.08 +/- 0.06 umol/mmol creatinine Adult (>18 years old) Male Normal
Urine Detected and Quantified
0.07 +/- 0.05 umol/mmol creatinine Adult (>18 years old) Both Normal
Urine Detected and Quantified
1.50 +/- 1.34 umol/mmol creatinine Children (1-13 year old) Both Normal
Urine Detected and Quantified
1.12 +/- 0.69 umol/mmol creatinine Adolescent (13-18 years old) Both Normal
Urine Detected and Quantified
0.33 +/- 0.17 umol/mmol creatinine Adult (>18 years old) Both Normal
Abnormal Concentrations
Biofluid Status Value Age Sex Condition Reference
Blood Detected and Quantified 0.26 +/- 0.13 uM Adult (>18 years old) Both Canavan disease
Urine Detected and Quantified 4.03 +/- 1.77 umol/mmol creatinine Adult (>18 years old) Both Canavan 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 Link_out
      Associated OMIM IDs
      DrugBank ID Not Available
      DrugBank Metabolite ID Not Available
      Phenol Explorer Compound ID Not Available
      Phenol Explorer Metabolite ID Not Available
      FoodDB ID FDB021809
      KNApSAcK ID Not Available
      Chemspider ID 5940 Link_out
      KEGG Compound ID C00475 Link_out
      BioCyc ID CYTIDINE Link_out
      BiGG ID 35089 Link_out
      Wikipedia Link Cytidine Link_out
      NuGOwiki Link HMDB00089 Link_out
      Metagene Link HMDB00089 Link_out
      METLIN ID 3376 Link_out
      PubChem Compound 6175 Link_out
      PDB ID CTN Link_out
      ChEBI ID 17562 Link_out
      References
      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.
      Material Safety Data Sheet (MSDS) Download (PDF)
      General References
      1. 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 Link_out
      2. 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 Link_out
      3. 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 Link_out
      4. 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 Link_out
      5. Min IM, Selsing E: Antibody class switch recombination: roles for switch sequences and mismatch repair proteins. Adv Immunol. 2005;87:297-328. Pubmed: 16102577 Link_out
      6. 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 Link_out
      7. Barbour JD, Grant RM: The role of viral fitness in HIV pathogenesis. Curr HIV/AIDS Rep. 2005 Feb;2(1):29-34. Pubmed: 16091246 Link_out
      8. 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 Link_out
      9. Cansev M: Uridine and cytidine in the brain: their transport and utilization. Brain Res Rev. 2006 Sep;52(2):389-97. Pubmed: 16769123 Link_out
      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 Link_out
      11. Navaratnam N, Sarwar R: An overview of cytidine deaminases. Int J Hematol. 2006 Apr;83(3):195-200. Pubmed: 16720547 Link_out

      Enzymes
      Name: 5'-nucleotidase
      Reactions:
      Cytidine monophosphate + Water unknown Cytidine + Phosphoric acid details
      Gene Name: NT5E
      Uniprot ID: P21589 Link_out
      Protein Sequence: FASTA
      Gene Sequence: FASTA
      Name: Cytosolic 5'-nucleotidase 1B
      Reactions:
      Cytidine monophosphate + Water unknown Cytidine + Phosphoric acid details
      Gene Name: NT5C1B
      Uniprot ID: Q96P26 Link_out
      Protein Sequence: FASTA
      Gene Sequence: FASTA
      Name: Cytosolic 5'-nucleotidase 1A
      Reactions:
      Cytidine monophosphate + Water unknown Cytidine + Phosphoric acid details
      Gene Name: NT5C1A
      Uniprot ID: Q9BXI3 Link_out
      Protein Sequence: FASTA
      Gene Sequence: FASTA
      Name: 5'(3')-deoxyribonucleotidase, cytosolic type
      Reactions:
      Cytidine monophosphate + Water unknown Cytidine + Phosphoric acid details
      Gene Name: NT5C
      Uniprot ID: Q8TCD5 Link_out
      Protein Sequence: FASTA
      Gene Sequence: FASTA
      Name: 5'(3')-deoxyribonucleotidase, mitochondrial
      Reactions:
      Cytidine monophosphate + Water unknown Cytidine + Phosphoric acid details
      Gene Name: NT5M
      Uniprot ID: Q9NPB1 Link_out
      Protein Sequence: FASTA
      Gene Sequence: FASTA
      Name: Uridine-cytidine kinase 1
      Reactions:
      Adenosine triphosphate + Cytidine unknown ADP + Cytidine monophosphate details
      Uridine triphosphate + Cytidine unknown Uridine 5'-diphosphate + Cytidine monophosphate details
      Guanosine triphosphate + Cytidine unknown Guanosine diphosphate + Cytidine monophosphate details
      Inosine triphosphate + Cytidine unknown IDP + Cytidine monophosphate details
      Deoxyadenosine triphosphate + Cytidine unknown dADP + Cytidine monophosphate details
      dGTP + Cytidine unknown dGDP + Cytidine monophosphate details
      Thymidine 5'-triphosphate + Cytidine unknown dTDP + Cytidine monophosphate details
      dCTP + Cytidine unknown dCDP + Cytidine monophosphate details
      Deoxyuridine triphosphate + Cytidine unknown dUDP + Cytidine monophosphate details
      Gene Name: UCK1
      Uniprot ID: Q9HA47 Link_out
      Protein Sequence: FASTA
      Gene Sequence: FASTA
      Name: Bifunctional UDP-N-acetylglucosamine 2-epimerase/N-acetylmannosamine kinase
      Reactions: Not Available
      Gene Name: GNE
      Uniprot ID: Q9Y223 Link_out
      Protein Sequence: FASTA
      Gene Sequence: FASTA
      Name: Uridine-cytidine kinase 2
      Reactions:
      Adenosine triphosphate + Cytidine unknown ADP + Cytidine monophosphate details
      Uridine triphosphate + Cytidine unknown Uridine 5'-diphosphate + Cytidine monophosphate details
      Guanosine triphosphate + Cytidine unknown Guanosine diphosphate + Cytidine monophosphate details
      Inosine triphosphate + Cytidine unknown IDP + Cytidine monophosphate details
      Deoxyadenosine triphosphate + Cytidine unknown dADP + Cytidine monophosphate details
      dGTP + Cytidine unknown dGDP + Cytidine monophosphate details
      Thymidine 5'-triphosphate + Cytidine unknown dTDP + Cytidine monophosphate details
      dCTP + Cytidine unknown dCDP + Cytidine monophosphate details
      Deoxyuridine triphosphate + Cytidine unknown dUDP + Cytidine monophosphate details
      Gene Name: UCK2
      Uniprot ID: Q9BZX2 Link_out
      Protein Sequence: FASTA
      Gene Sequence: FASTA
      Name: AID
      Reactions: Not Available
      Gene Name: AID
      Uniprot ID: Q546Y9 Link_out
      Protein Sequence: FASTA
      Gene Sequence: FASTA
      Name: Cytosolic 5'-nucleotidase 3
      Reactions:
      Cytidine monophosphate + Water unknown Cytidine + Phosphoric acid details
      Gene Name: NT5C3
      Uniprot ID: Q9H0P0 Link_out
      Protein Sequence: FASTA
      Gene Sequence: FASTA
      Name: Cytosolic purine 5'-nucleotidase
      Reactions:
      Cytidine monophosphate + Water unknown Cytidine + Phosphoric acid details
      Gene Name: NT5C2
      Uniprot ID: P49902 Link_out
      Protein Sequence: FASTA
      Gene Sequence: FASTA
      Name: Cytidine deaminase
      Reactions:
      Cytidine + Water unknown Uridine + Ammonia details
      Gene Name: CDA
      Uniprot ID: P32320 Link_out
      Protein Sequence: FASTA
      Gene Sequence: FASTA
      Name: Uridine-cytidine kinase-like 1
      Reactions:
      Adenosine triphosphate + Cytidine unknown ADP + Cytidine monophosphate details
      Uridine triphosphate + Cytidine unknown Uridine 5'-diphosphate + Cytidine monophosphate details
      Guanosine triphosphate + Cytidine unknown Guanosine diphosphate + Cytidine monophosphate details
      Inosine triphosphate + Cytidine unknown IDP + Cytidine monophosphate details
      Deoxyadenosine triphosphate + Cytidine unknown dADP + Cytidine monophosphate details
      dGTP + Cytidine unknown dGDP + Cytidine monophosphate details
      Thymidine 5'-triphosphate + Cytidine unknown dTDP + Cytidine monophosphate details
      dCTP + Cytidine unknown dCDP + Cytidine monophosphate details
      Deoxyuridine triphosphate + Cytidine unknown dUDP + Cytidine monophosphate details
      Gene Name: UCKL1
      Uniprot ID: Q9NWZ5 Link_out
      Protein Sequence: FASTA
      Gene Sequence: FASTA
      Name: DNA dC->dU-editing enzyme APOBEC-3H
      Reactions:
      Cytidine + Water unknown Uridine + Ammonia details
      Gene Name: APOBEC3H
      Uniprot ID: Q6NTF7 Link_out
      Protein Sequence: FASTA
      Gene Sequence: FASTA
      Name: Zinc finger protein 638
      Reactions: Not Available
      Gene Name: ZNF638
      Uniprot ID: Q14966 Link_out
      Protein Sequence: FASTA
      Gene Sequence: FASTA
      Name: CUGBP Elav-like family member 2
      Reactions: Not Available
      Gene Name: CELF2
      Uniprot ID: O95319 Link_out
      Protein Sequence: FASTA
      Gene Sequence: FASTA
      Name: Probable DNA dC->dU-editing enzyme APOBEC-3A
      Reactions:
      Cytidine + Water unknown Uridine + Ammonia details
      Gene Name: APOBEC3A
      Uniprot ID: P31941 Link_out
      Protein Sequence: FASTA
      Name: Probable DNA dC->dU-editing enzyme APOBEC-3B
      Reactions:
      Cytidine + Water unknown Uridine + Ammonia details
      Gene Name: APOBEC3B
      Uniprot ID: Q9UH17 Link_out
      Protein Sequence: FASTA
      Name: Probable DNA dC->dU-editing enzyme APOBEC-3C
      Reactions:
      Cytidine + Water unknown Uridine + Ammonia details
      Gene Name: APOBEC3C
      Uniprot ID: Q9NRW3 Link_out
      Protein Sequence: FASTA
      Name: Probable DNA dC->dU-editing enzyme APOBEC-3D
      Reactions:
      Cytidine + Water unknown Uridine + Ammonia details
      Gene Name: APOBEC3D
      Uniprot ID: Q96AK3 Link_out
      Protein Sequence: FASTA
      Name: DNA dC->dU-editing enzyme APOBEC-3F
      Reactions:
      Cytidine + Water unknown Uridine + Ammonia details
      Gene Name: APOBEC3F
      Uniprot ID: Q8IUX4 Link_out
      Protein Sequence: FASTA
      Name: Activation-induced cytidine deaminase
      Reactions:
      Cytidine + Water unknown Uridine + Ammonia details
      Gene Name: AICDA
      Uniprot ID: Q9GZX7 Link_out
      Protein Sequence: FASTA