Cytidine (PAMDB000033)

IdentificationTaxonomyPhysical PropertiesBiological PropertiesSpectraConcentrationsLinksReferencesEnzymes Transporters
Proteins (3280)
Record Information
Version 1.0
Update Date 1/22/2018 11:54:54 AM
Metabolite IDPAMDB000033
Identification
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 biosynthesis of PC via the Kennedy pathway requires phosphocholine and cytidine triphosphate (CTP), a cytidine nucleotide, which is involved in the rate-limiting step. (PMID: 16769123, 15780864, 16720547)
Structure
Thumb
🔍MOLSDFPDBSMILESInChIView 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-δ-Ribofuranosyl)-2-oxo-4-amino-1,2-dihydro-1,3-diazine
  • 1-(beta-D-Ribofuranosyl)-2-oxo-4-amino-1,2-dihydro-1,3-diazine
  • 1-(beta-delta-Ribofuranosyl)-2-oxo-4-amino-1,2-dihydro-1,3-diazine
  • 1-(β-D-Ribofuranosyl)-2-oxo-4-amino-1,2-dihydro-1,3-diazine
  • 1-(β-δ-Ribofuranosyl)-2-oxo-4-amino-1,2-dihydro-1,3-diazine
  • 1-b-D-Ribofuranosyl-cytosine
  • 1-b-D-Ribofuranosylcytosine
  • 1-b-D-ribosyl-Cytosine
  • 1-b-delta-Ribofuranosyl-cytosine
  • 1-b-delta-Ribofuranosylcytosine
  • 1-b-delta-Ribosyl-cytosine
  • 1-b-δ-Ribofuranosyl-cytosine
  • 1-b-δ-Ribofuranosylcytosine
  • 1-b-δ-Ribosyl-cytosine
  • 1-beta-D-Ribofuranosyl-Cytosine
  • 1-beta-D-Ribofuranosylcytosine
  • 1-beta-D-Ribosyl-Cytosine
  • 1-beta-delta-Ribofuranosyl-Cytosine
  • 1-beta-delta-Ribofuranosylcytosine
  • 1-beta-delta-Ribosyl-Cytosine
  • 1-β-D-Ribofuranosyl-cytosine
  • 1-β-D-Ribofuranosylcytosine
  • 1-β-D-Ribosyl-cytosine
  • 1-β-δ-Ribofuranosyl-cytosine
  • 1-β-δ-Ribofuranosylcytosine
  • 1-β-δ-Ribosyl-cytosine
  • 1b-D-Ribofuranosylcytosine
  • 1b-delta-Ribofuranosylcytosine
  • 1b-Ribofuranosylcytosine
  • 1b-δ-Ribofuranosylcytosine
  • 1beta-D-Ribofuranosylcytosine
  • 1beta-delta-Ribofuranosylcytosine
  • 1beta-Ribofuranosylcytosine
  • 1β-D-Ribofuranosylcytosine
  • 1β-Ribofuranosylcytosine
  • 1β-δ-Ribofuranosylcytosine
  • 4-Amino-1-b-D-ribofuranosyl-2(1H)-pyrimidinone
  • 4-amino-1-b-delta-Ribofuranosyl-2(1H)-pyrimidinone
  • 4-amino-1-b-δ-Ribofuranosyl-2(1H)-pyrimidinone
  • 4-Amino-1-beta-delta-ribofuranosyl-2(1H)-pyrimidinone
  • 4-amino-1-β-δ-Ribofuranosyl-2(1H)-pyrimidinone
  • Cytidine
  • Cytosine riboside
  • Cytosine-1b-D-Ribofuranoside
  • Cytosine-1b-delta-Ribofuranoside
  • Cytosine-1b-δ-ribofuranoside
  • Cytosine-1beta-D-Ribofuranoside
  • Cytosine-1beta-delta-Ribofuranoside
  • Cytosine-1β-D-ribofuranoside
  • Cytosine-1β-δ-ribofuranoside
Chemical Formula: C9H13N3O5
Average Molecular Weight: 243.2166
Monoisotopic Molecular Weight: 243.085520541
InChI Key: UHDGCWIWMRVCDJ-XVFCMESISA-N
InChI: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
CAS number: 65-46-3
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
SMILES:NC1=NC(=O)N(C=C1)[C@@H]1O[C@H](CO)[C@@H](O)[C@H]1O
Chemical Taxonomy
Taxonomy DescriptionThis compound belongs to the class of organic compounds known as pyrimidine nucleosides. These are compounds comprising a pyrimidine base attached to a ribosyl or deoxyribosyl moiety.
Kingdom Organic compounds
Super ClassNucleosides, nucleotides, and analogues
Class Pyrimidine nucleosides
Sub ClassNot Available
Direct Parent Pyrimidine nucleosides
Alternative Parents
Substituents
  • Pyrimidine nucleoside
  • N-glycosyl compound
  • Glycosyl compound
  • Hydroxypyrimidine
  • Aminopyrimidine
  • Pyrimidine
  • Monosaccharide
  • Hydropyrimidine
  • Heteroaromatic compound
  • Oxolane
  • Secondary alcohol
  • 1,2-diol
  • Oxacycle
  • Azacycle
  • Organoheterocyclic compound
  • Hydrocarbon derivative
  • Primary alcohol
  • Organooxygen compound
  • Organonitrogen compound
  • Alcohol
  • Aromatic heteromonocyclic compound
Molecular Framework Aromatic heteromonocyclic compounds
External Descriptors
Physical Properties
State: Solid
Charge:0
Melting point: 230.5 °C
Experimental Properties:
PropertyValueSource
LogP:-2.51 [HANSCH,C ET AL. (1995)]PhysProp
Predicted Properties
PropertyValueSource
Water Solubility43.8 mg/mLALOGPS
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 Area128.61 Å2ChemAxon
Rotatable Bond Count2ChemAxon
Refractivity54.54 m3·mol-1ChemAxon
Polarizability22.39 Å3ChemAxon
Number of Rings2ChemAxon
Bioavailability1ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations: Cytoplasm
Reactions:
Cytidine monophosphate + Water > Cytidine + Phosphate
Cytidine + Water > Cytosine + Ribose
Cytidine + Guanosine triphosphate > Cytidine monophosphate + Guanosine diphosphate + Hydrogen ion
Cytidine + Hydrogen ion + Water > Ammonium + Uridine
3'-CMP + Water > Cytidine + Phosphate
Adenosine triphosphate + Cytidine <> ADP + Cytidine monophosphate
Uridine triphosphate + Cytidine <> Uridine 5'-diphosphate + Cytidine monophosphate
Guanosine triphosphate + Cytidine <> Guanosine diphosphate + Cytidine monophosphate
Inosine triphosphate + Cytidine <> IDP + Cytidine monophosphate
dATP + Cytidine <> dADP + Cytidine monophosphate
Cytidine + Water <> Uridine + Ammonia
dGTP + Cytidine <> dGDP + Cytidine monophosphate
Thymidine 5'-triphosphate + Cytidine <> dTDP + Cytidine monophosphate
dCTP + Cytidine <> dCDP + Cytidine monophosphate
Deoxyuridine triphosphate + Cytidine <> dUDP + Cytidine monophosphate
Cytidine + Water > D-ribose + Cytosine
Cytidine + Water + Deoxycytidine <> Uridine + Ammonia + Deoxyuridine
Pathways:
Spectra
Spectra:
Spectrum TypeDescriptionSplash Key
GC-MSGC-MS Spectrum - GC-MS (5 TMS)splash10-0zfr-2951000000-7baf0e1ea8b1a34362e2View in MoNA
GC-MSGC-MS Spectrum - GC-MS (4 TMS)splash10-0g4j-2980000000-9337623aef7fec22dd97View in MoNA
GC-MSGC-MS Spectrum - GC-MSNot Available
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 10V, Positive (Annotated)splash10-03di-0900000000-177050786fcbfaf2d270View in MoNA
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 25V, Positive (Annotated)splash10-03di-0900000000-1251248af66dca3401e2View in MoNA
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 40V, Positive (Annotated)splash10-03di-6900000000-c6b010a1d3e65a0942eeView in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Positivesplash10-0006-0590100000-94eb2baae24aa405b1baView in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Positivesplash10-0006-9000000000-8155621584c25975ffa1View in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Positivesplash10-03di-0900000000-5065bc83a32bee37d07cView in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Positivesplash10-0006-0590200000-4d5dc5376c40d083efbeView in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Positivesplash10-001i-0900000000-6ea86f62a48910b456a0View in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Positivesplash10-03di-0900000000-5c93b66b8899a4d3ce06View in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Positivesplash10-0006-0090000000-f0e6ac0bacdbef1206b0View in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Negativesplash10-000f-0090010000-1cf915fa4dfb86b5861bView in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Negativesplash10-0a4i-0900000000-6bb7990f165932decea7View in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Negativesplash10-0006-0090000000-0b7dc368d61ee31afb78View in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Negativesplash10-000l-0090020000-fa04fb11f98259c403b6View in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Negativesplash10-0006-0190172001-0671df3c315b8af9e13fView in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Negativesplash10-0a4i-0900000000-8aa3fec051a7d9807888View in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Negativesplash10-0006-0090000000-0563823e8f3a9def519aView in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Negativesplash10-004i-0028900000-f4b6c319a7e9fb17df2eView in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF (UPLC Q-Tof Premier, Waters) , Positivesplash10-01ox-0590000000-d5d20f84ab30e96c30f6View in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF (UPLC Q-Tof Premier, Waters) 30V, Positivesplash10-03di-0930000000-c4d3377790616b8b7869View in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF (UPLC Q-Tof Premier, Waters) , Negativesplash10-0a4i-1930000000-faec28788ea577988b82View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, PositiveNot Available
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, PositiveNot Available
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, PositiveNot Available
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, NegativeNot Available
1D NMR1H NMR SpectrumNot Available
2D NMR[1H,1H] 2D NMR SpectrumNot Available
2D NMR[1H,13C] 2D NMR SpectrumNot Available
References
References:
  • Barbour JD, Grant RM: The role of viral fitness in HIV pathogenesis. Curr HIV/AIDS Rep. 2005 Feb;2(1):29-34. Pubmed: 16091246
  • Bennett, B. D., Kimball, E. H., Gao, M., Osterhout, R., Van Dien, S. J., Rabinowitz, J. D. (2009). "Absolute metabolite concentrations and implied enzyme active site occupancy in Escherichia coli." Nat Chem Biol 5:593-599. Pubmed: 19561621
  • Cansev, M. (2006). "Uridine and cytidine in the brain: their transport and utilization." Brain Res Rev 52:389-397. Pubmed: 16769123
  • 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
  • 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
  • Kanehisa, M., Goto, S., Sato, Y., Furumichi, M., Tanabe, M. (2012). "KEGG for integration and interpretation of large-scale molecular data sets." Nucleic Acids Res 40:D109-D114. Pubmed: 22080510
  • Keseler, I. M., Collado-Vides, J., Santos-Zavaleta, A., Peralta-Gil, M., Gama-Castro, S., Muniz-Rascado, L., Bonavides-Martinez, C., Paley, S., Krummenacker, M., Altman, T., Kaipa, P., Spaulding, A., Pacheco, J., Latendresse, M., Fulcher, C., Sarker, M., Shearer, A. G., Mackie, A., Paulsen, I., Gunsalus, R. P., Karp, P. D. (2011). "EcoCyc: a comprehensive database of Escherichia coli biology." Nucleic Acids Res 39:D583-D590. Pubmed: 21097882
  • 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
  • Min IM, Selsing E: Antibody class switch recombination: roles for switch sequences and mismatch repair proteins. Adv Immunol. 2005;87:297-328. Pubmed: 16102577
  • Navaratnam N, Sarwar R: An overview of cytidine deaminases. Int J Hematol. 2006 Apr;83(3):195-200. Pubmed: 16720547
  • 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
  • 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
  • van der Werf, M. J., Overkamp, K. M., Muilwijk, B., Coulier, L., Hankemeier, T. (2007). "Microbial metabolomics: toward a platform with full metabolome coverage." Anal Biochem 370:17-25. Pubmed: 17765195
  • Winder, C. L., Dunn, W. B., Schuler, S., Broadhurst, D., Jarvis, R., Stephens, G. M., Goodacre, R. (2008). "Global metabolic profiling of Escherichia coli cultures: an evaluation of methods for quenching and extraction of intracellular metabolites." Anal Chem 80:2939-2948. Pubmed: 18331064
  • 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
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)
External Links:
ResourceLink
CHEBI ID17562
HMDB IDHMDB00089
Pubchem Compound ID6175
Kegg IDC00475
ChemSpider ID5940
WikipediaCytidine
BioCyc IDCYTIDINE
EcoCyc IDCYTIDINE
Ligand ExpoCTN

Enzymes

Protein Details
• Multifunctional protein surE
General function:
Involved in hydrolase activity
Specific function:
Nucleotidase with a broad substrate specificity as it can dephosphorylate various ribo- and deoxyribonucleoside 5'- monophosphates and ribonucleoside 3'-monophosphates with highest affinity to 3'-AMP. Also hydrolyzes polyphosphate (exopolyphosphatase activity) with the preference for short-chain- length substrates (P20-25). Might be involved in the regulation of dNTP and NTP pools, and in the turnover of 3'-mononucleotides produced by numerous intracellular RNases (T1, T2, and F) during the degradation of various RNAs. Also plays a significant physiological role in stress-response and is required for the survival of Pseudomonas aeruginosa in stationary growth phase
Gene Name:
surE
Locus Tag:
PA3625
Molecular weight:
26.4 kDa
Reactions
A 5'-ribonucleotide + H(2)O = a ribonucleoside + phosphate.
A 3'-ribonucleotide + H(2)O = a ribonucleoside + phosphate.
(Polyphosphate)(n) + H(2)O = (polyphosphate)(n-1) + phosphate.
Protein Details
• Class B acid phosphatase
General function:
Involved in acid phosphatase activity
Specific function:
Dephosphorylates several organic phosphomonoesters and catalyzes the transfer of low-energy phosphate groups from phosphomonoesters to hydroxyl groups of various organic compounds. Preferentially acts on aryl phosphoesters. Might function as a broad-spectrum dephosphorylating enzyme able to scavenge both 3'- and 5'-nucleotides and also additional organic phosphomonoesters
Gene Name:
aphA
Locus Tag:
PA1409
Molecular weight:
38 kDa
Reactions
A phosphate monoester + H(2)O = an alcohol + phosphate.

Transporters