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Human Metabolome Database Version 3.5

Showing metabocard for Cytidine (HMDB00089)

• Identification
• Taxonomy
• Ontology
• Physical properties
• Spectra
• Biological properties
• Concentrations
• Links
• References

enzymes (22)

• Blood
• Urine

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 , 15780864 , 16720547 ).
Structure	Download: MOL | SDF | SMILES | InChI Display: 2D Structure | 3D Structure
Synonyms	1-(b-D-Ribofuranosyl)-2-oxo-4-amino-1,2-dihydro-1,3-diazine 1-(b-delta-Ribofuranosyl)-2-oxo-4-amino-1,2-dihydro-1,3-diazine 1-b-D-Ribofuranosylcytosine 1-b-D-Ribosyl-Cytosine 1-beta-D-Ribofuranosyl-Cytosine 1-beta-D-Ribofuranosylcytosine 1-beta-delta-Ribofuranosyl-Cytosine 1-beta-delta-Ribofuranosylcytosine 1-beta-delta-Ribosyl-Cytosine 1beta-D-Ribofuranosylcytosine 1beta-delta-Ribofuranosylcytosine 1beta-Ribofuranosylcytosine 4-Amino-1-b-D-ribofuranosyl-2(1H)-pyrimidinone 4-Amino-1-beta-delta-ribofuranosyl-2(1H)-pyrimidinone Cytidine Cytosine riboside Cytosine-1b-D-Ribofuranoside Cytosine-1b-delta-Ribofuranoside Cytosine-1beta-D-Ribofuranoside 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
Normal Concentrations
	Biofluid Status Value Age Sex Condition Reference Blood Detected and Quantified 0.25 +/- 0.19 uM Adult (>18 years old) Both Normal 16139832 Blood Detected and Quantified 0.1 +/- 0.0 uM Adult (>18 years old) Both Normal 6656991 Cerebrospinal Fluid (CSF) Detected and Quantified 0.44 +/- 0.32 uM Infant (0-1 year old) Both Normal 3390913 Urine Detected and Quantified 0.78 (0.00-1.6) umol/mmol creatinine Adult (>18 years old) Both Normal 15116424 Urine Detected and Quantified 0.07 +/- 0.05 umol/mmol creatinine Adult (>18 years old) Female Normal 9129323 Urine Detected and Quantified 0.08 +/- 0.06 umol/mmol creatinine Adult (>18 years old) Male Normal 9129323 Urine Detected and Quantified 0.07 +/- 0.05 umol/mmol creatinine Adult (>18 years old) Both Normal 9129323 Urine Detected and Quantified 1.50 +/- 1.34 umol/mmol creatinine Children (1-13 year old) Both Normal 16139832 Urine Detected and Quantified 1.12 +/- 0.69 umol/mmol creatinine Adolescent (13-18 years old) Both Normal 16139832 Urine Detected and Quantified 0.33 +/- 0.17 umol/mmol creatinine Adult (>18 years old) Both Normal 16139832
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 16139832 Urine Detected and Quantified 4.03 +/- 1.77 umol/mmol creatinine Adult (>18 years old) Both Canavan disease 16139832
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	271900 (Canavan disease)
External Links
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
KEGG Compound ID	C00475
BioCyc ID	CYTIDINE
BiGG ID	35089
Wikipedia Link	Cytidine
NuGOwiki Link	HMDB00089
Metagene Link	HMDB00089
METLIN ID	3376
PubChem Compound	6175
PDB ID	CTN
ChEBI ID	17562
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	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 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 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 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 Min IM, Selsing E: Antibody class switch recombination: roles for switch sequences and mismatch repair proteins. Adv Immunol. 2005;87:297-328. Pubmed: 16102577 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 Barbour JD, Grant RM: The role of viral fitness in HIV pathogenesis. Curr HIV/AIDS Rep. 2005 Feb;2(1):29-34. Pubmed: 16091246 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 Cansev M: Uridine and cytidine in the brain: their transport and utilization. Brain Res Rev. 2006 Sep;52(2):389-97. Pubmed: 16769123 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 Navaratnam N, Sarwar R: An overview of cytidine deaminases. Int J Hematol. 2006 Apr;83(3):195-200. Pubmed: 16720547

---

Enzymes
Name: 5'-nucleotidase Reactions: Cytidine monophosphate + Water unknown Cytidine + Phosphoric acid details Gene Name: NT5E Uniprot ID: P21589 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 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 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 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 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 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 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 Protein Sequence: FASTA Gene Sequence: FASTA
Name: AID Reactions: Not Available Gene Name: AID Uniprot ID: Q546Y9 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 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 Protein Sequence: FASTA Gene Sequence: FASTA
Name: Cytidine deaminase Reactions: Cytidine + Water unknown Uridine + Ammonia details Gene Name: CDA Uniprot ID: P32320 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 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 Protein Sequence: FASTA Gene Sequence: FASTA
Name: Zinc finger protein 638 Reactions: Not Available Gene Name: ZNF638 Uniprot ID: Q14966 Protein Sequence: FASTA Gene Sequence: FASTA
Name: CUGBP Elav-like family member 2 Reactions: Not Available Gene Name: CELF2 Uniprot ID: O95319 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 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 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 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 Protein Sequence: FASTA
Name: DNA dC->dU-editing enzyme APOBEC-3F Reactions: Cytidine + Water unknown Uridine + Ammonia details Gene Name: APOBEC3F Uniprot ID: Q8IUX4 Protein Sequence: FASTA
Name: Activation-induced cytidine deaminase Reactions: Cytidine + Water unknown Uridine + Ammonia details Gene Name: AICDA Uniprot ID: Q9GZX7 Protein Sequence: FASTA

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