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Record Information
Version5.0
StatusDetected and Quantified
Creation Date2005-11-16 15:48:42 UTC
Update Date2021-09-14 15:46:09 UTC
HMDB IDHMDB0000982
Secondary Accession Numbers
  • HMDB00982
Metabolite Identification
Common Name5-Methylcytidine
Description5-Methylcytidine belongs to the class of organic compounds known as pyrimidine nucleosides. Pyrimidine nucleosides are compounds comprising a pyrimidine base attached to a ribosyl or deoxyribosyl moiety. 5-Methylcytidine is a modified nucleoside derived from 5-methylcytosine. 5-Methylcytidine is an extremely weak basic (essentially neutral) compound (based on its pKa).
Structure
Data?1582752169
Synonyms
ValueSource
5-Methyl-cytidineHMDB
5-MethylcytidineHMDB
Chemical FormulaC10H15N3O5
Average Molecular Weight257.2432
Monoisotopic Molecular Weight257.101170605
IUPAC Name4-amino-1-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-5-methyl-1,2-dihydropyrimidin-2-one
Traditional Name5-methylcytidine
CAS Registry Number2140-61-6
SMILES
CC1=CN([C@@H]2O[C@H](CO)[C@@H](O)[C@H]2O)C(=O)N=C1N
InChI Identifier
InChI=1S/C10H15N3O5/c1-4-2-13(10(17)12-8(4)11)9-7(16)6(15)5(3-14)18-9/h2,5-7,9,14-16H,3H2,1H3,(H2,11,12,17)/t5-,6-,7-,9-/m1/s1
InChI KeyZAYHVCMSTBRABG-JXOAFFINSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as pyrimidine nucleosides. Pyrimidine nucleosides are compounds comprising a pyrimidine base attached to a ribosyl or deoxyribosyl moiety.
KingdomOrganic compounds
Super ClassNucleosides, nucleotides, and analogues
ClassPyrimidine nucleosides
Sub ClassNot Available
Direct ParentPyrimidine nucleosides
Alternative Parents
Substituents
  • Pyrimidine nucleoside
  • Glycosyl compound
  • N-glycosyl compound
  • Pentose monosaccharide
  • Hydroxypyrimidine
  • Hydropyrimidine
  • Monosaccharide
  • Pyrimidine
  • Tetrahydrofuran
  • Heteroaromatic compound
  • Secondary alcohol
  • Organoheterocyclic compound
  • Azacycle
  • Oxacycle
  • Organic nitrogen compound
  • Hydrocarbon derivative
  • Primary alcohol
  • Organopnictogen compound
  • Organooxygen compound
  • Organonitrogen compound
  • Alcohol
  • Organic oxygen compound
  • Aromatic heteromonocyclic compound
Molecular FrameworkAromatic heteromonocyclic compounds
External Descriptors
Ontology
Disposition

Source:

Biological location:

Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting Point213 °CNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogP-2.01HANSCH,C ET AL. (1995)
Predicted Molecular Properties
PropertyValueSource
Water Solubility20.8 g/LALOGPS
logP-2.2ALOGPS
logP-2.4ChemAxon
logS-1.1ALOGPS
pKa (Strongest Acidic)12.55ChemAxon
pKa (Strongest Basic)0.14ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count7ChemAxon
Hydrogen Donor Count4ChemAxon
Polar Surface Area128.61 ŲChemAxon
Rotatable Bond Count2ChemAxon
Refractivity58.9 m³·mol⁻¹ChemAxon
Polarizability24.54 ųChemAxon
Number of Rings2ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Predicted Spectral Properties

Collision Cross Sections

NameAdductTypeData SourceValueReference
DeepCCS[M-H]-ExperimentalBaker160.45830932474
DeepCCS[M-H]-ExperimentalMetCCS_train_neg152.62830932474
DeepCCS[M+H]+ExperimentalBaker157.50930932474
DeepCCS[M+H]+ExperimentalMetCCS_train_pos157.39130932474
AllCCS[M-H]-ExperimentalNot Available156.5http://allccs.zhulab.cn/database/detail?ID=AllCCS00000111
AllCCS[M+H]+ExperimentalNot Available157.8http://allccs.zhulab.cn/database/detail?ID=AllCCS00000111
DarkChem[M+H]+PredictedNot Available157.87731661259
DarkChem[M-H]-PredictedNot Available153.52431661259
AllCCS[M+H]+PredictedNot Available158.23432859911
AllCCS[M-H]-PredictedNot Available156.96432859911

Retention Indices

Underivatized

Not Available

Derivatized

DerivativeValueReference
5-Methylcytidine,1TMS,#12477.6729https://arxiv.org/abs/1905.12712
5-Methylcytidine,1TMS,#22481.83https://arxiv.org/abs/1905.12712
5-Methylcytidine,1TMS,#32468.757https://arxiv.org/abs/1905.12712
5-Methylcytidine,1TMS,#42535.8196https://arxiv.org/abs/1905.12712
5-Methylcytidine,2TMS,#12467.8916https://arxiv.org/abs/1905.12712
5-Methylcytidine,2TMS,#22464.8506https://arxiv.org/abs/1905.12712
5-Methylcytidine,2TMS,#32492.8293https://arxiv.org/abs/1905.12712
5-Methylcytidine,2TMS,#42467.739https://arxiv.org/abs/1905.12712
5-Methylcytidine,2TMS,#52507.131https://arxiv.org/abs/1905.12712
5-Methylcytidine,2TMS,#62504.178https://arxiv.org/abs/1905.12712
5-Methylcytidine,2TMS,#72489.4905https://arxiv.org/abs/1905.12712
5-Methylcytidine,3TMS,#12454.336https://arxiv.org/abs/1905.12712
5-Methylcytidine,3TMS,#22489.0034https://arxiv.org/abs/1905.12712
5-Methylcytidine,3TMS,#32492.917https://arxiv.org/abs/1905.12712
5-Methylcytidine,3TMS,#42464.7969https://arxiv.org/abs/1905.12712
5-Methylcytidine,3TMS,#52482.2666https://arxiv.org/abs/1905.12712
5-Methylcytidine,3TMS,#62461.152https://arxiv.org/abs/1905.12712
5-Methylcytidine,3TMS,#72461.0698https://arxiv.org/abs/1905.12712
5-Methylcytidine,1TBDMS,#12749.695https://arxiv.org/abs/1905.12712
5-Methylcytidine,1TBDMS,#22737.498https://arxiv.org/abs/1905.12712
5-Methylcytidine,1TBDMS,#32733.5095https://arxiv.org/abs/1905.12712
5-Methylcytidine,1TBDMS,#42787.1855https://arxiv.org/abs/1905.12712
5-Methylcytidine,2TBDMS,#12940.5518https://arxiv.org/abs/1905.12712
5-Methylcytidine,2TBDMS,#22940.4365https://arxiv.org/abs/1905.12712
5-Methylcytidine,2TBDMS,#32973.0063https://arxiv.org/abs/1905.12712
5-Methylcytidine,2TBDMS,#42926.6553https://arxiv.org/abs/1905.12712
5-Methylcytidine,2TBDMS,#52968.844https://arxiv.org/abs/1905.12712
5-Methylcytidine,2TBDMS,#62952.748https://arxiv.org/abs/1905.12712
5-Methylcytidine,2TBDMS,#72944.6475https://arxiv.org/abs/1905.12712
5-Methylcytidine,3TBDMS,#13151.0986https://arxiv.org/abs/1905.12712
5-Methylcytidine,3TBDMS,#23171.0151https://arxiv.org/abs/1905.12712
5-Methylcytidine,3TBDMS,#33176.6663https://arxiv.org/abs/1905.12712
5-Methylcytidine,3TBDMS,#43144.584https://arxiv.org/abs/1905.12712
5-Methylcytidine,3TBDMS,#53161.27https://arxiv.org/abs/1905.12712
5-Methylcytidine,3TBDMS,#63158.0054https://arxiv.org/abs/1905.12712
5-Methylcytidine,3TBDMS,#73144.0095https://arxiv.org/abs/1905.12712
Spectra

GC-MS

Spectrum TypeDescriptionSplash KeyDeposition DateView
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-0adl-9420000000-0b05b3fff49a937e78cb2017-09-01View Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (3 TMS) - 70eV, Positivesplash10-001i-6921100000-895058c6ba83f084d86e2017-10-06View Spectrum

LC-MS/MS

Spectrum TypeDescriptionSplash KeyDeposition DateView
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 10V, Positive (Annotated)splash10-004i-0900000000-01346f227c58c4e64dd32012-07-24View Spectrum
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 25V, Positive (Annotated)splash10-004i-0900000000-25d8b3fb44e47bc7f5442012-07-24View Spectrum
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 40V, Positive (Annotated)splash10-004i-1900000000-0ad90898ddb462fa200b2012-07-24View Spectrum
LC-MS/MSLC-MS/MS Spectrum - 40V, Positivesplash10-004i-4900000000-ff34d9c361d96f5aa2de2021-09-20View Spectrum
LC-MS/MSLC-MS/MS Spectrum - 20V, Positivesplash10-004i-0900000000-0366c638ef303f3731b32021-09-20View Spectrum
LC-MS/MSLC-MS/MS Spectrum - 35V, Positivesplash10-004i-0900000000-f936466105072c9b573c2021-09-20View Spectrum
LC-MS/MSLC-MS/MS Spectrum - 10V, Positivesplash10-056r-0950000000-10971ba54196bbfdfc8d2021-09-20View Spectrum
LC-MS/MSLC-MS/MS Spectrum - 10V, Negativesplash10-0a4i-0090000000-d8be738cdc4e544772272021-09-20View Spectrum
LC-MS/MSLC-MS/MS Spectrum - 35V, Negativesplash10-0gi0-1490000000-f34a1cb7ce97d538cb7a2021-09-20View Spectrum
LC-MS/MSLC-MS/MS Spectrum - 20V, Negativesplash10-0avi-1960000000-da3e8a4eb805781bcbc62021-09-20View Spectrum
LC-MS/MSLC-MS/MS Spectrum - 40V, Negativesplash10-0002-9000000000-0a9ca0be7ac354db94782021-09-20View Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-004i-0910000000-960e39cedc554f0148632017-09-01View Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-004i-2900000000-2ecbb224dc501d6488862017-09-01View Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-056r-5900000000-55a400dd7cd5fcd9ea3d2017-09-01View Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-00di-0950000000-0275ab78e34a521999fb2017-09-01View Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-00di-3920000000-50690663d91d4d14a39c2017-09-01View Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-007p-9200000000-978b587a0b7b227748392017-09-01View Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0ab9-0890000000-24f0c238f60d3c00adbb2021-09-08View Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-006y-9700000000-c0edbd46e86d76296c582021-09-08View Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-0005-9200000000-9358476776cf6eec42c12021-09-08View Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-004i-0900000000-a1c51dd1d9ae2dee6e382021-09-08View Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-004i-1910000000-f366741e71fc5efb780d2021-09-08View Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-0a7i-8900000000-f063ff1fc5cb2b980e9e2021-09-08View Spectrum

NMR

Spectrum TypeDescriptionDeposition DateView
1D NMR1H NMR Spectrum (1D, 600 MHz, H2O, experimental)2012-12-04View Spectrum
2D NMR[1H, 13C] NMR Spectrum (2D, 600 MHz, H2O, predicted)2012-12-05View Spectrum
Biological Properties
Cellular Locations
  • Cytoplasm (predicted from logP)
Biospecimen Locations
  • Blood
  • Feces
  • Urine
Tissue LocationsNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodExpected but not QuantifiedNot QuantifiedNot AvailableNot Available
Normal
      Not Available
details
UrineDetected and Quantified2.2 (0.00-5.3) umol/mmol creatinineAdult (>18 years old)BothNormal details
Abnormal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)BothCrohns disease details
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)BothIron deficiency details
Associated Disorders and Diseases
Disease References
Crohn's disease
  1. Lee T, Clavel T, Smirnov K, Schmidt A, Lagkouvardos I, Walker A, Lucio M, Michalke B, Schmitt-Kopplin P, Fedorak R, Haller D: Oral versus intravenous iron replacement therapy distinctly alters the gut microbiota and metabolome in patients with IBD. Gut. 2017 May;66(5):863-871. doi: 10.1136/gutjnl-2015-309940. Epub 2016 Feb 4. [PubMed:26848182 ]
Iron deficiency
  1. Lee T, Clavel T, Smirnov K, Schmidt A, Lagkouvardos I, Walker A, Lucio M, Michalke B, Schmitt-Kopplin P, Fedorak R, Haller D: Oral versus intravenous iron replacement therapy distinctly alters the gut microbiota and metabolome in patients with IBD. Gut. 2017 May;66(5):863-871. doi: 10.1136/gutjnl-2015-309940. Epub 2016 Feb 4. [PubMed:26848182 ]
Associated OMIM IDs
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB022351
KNApSAcK IDNot Available
Chemspider ID83877
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia Link5-Methylcytidine
METLIN ID5919
PubChem Compound92918
PDB IDNot Available
ChEBI ID20607
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
References
Synthesis ReferenceMastronicolis S K; Kapoulas V M; Kroger H The isolation of antibodies specific for 5-methyl-cytidine-bovine serum albumin. Zeitschrift fur Naturforschung. Section C: Biosciences (1981), 36(5-6), 459-63.
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 ]
  2. Reynaud C, Bruno C, Boullanger P, Grange J, Barbesti S, Niveleau A: Monitoring of urinary excretion of modified nucleosides in cancer patients using a set of six monoclonal antibodies. Cancer Lett. 1992 Jan 31;61(3):255-62. [PubMed:1739950 ]
  3. Itoh K, Aida S, Ishiwata S, Yamaguchi T, Ishida N, Mizugaki M: Immunochemical detection of urinary 5-methyl-2'-deoxycytidine as a potential biologic marker for leukemia. Clin Chim Acta. 1995 Jan 31;234(1-2):37-45. [PubMed:7758221 ]
  4. Strong LC: The nature of cancer and the mechanisms of its control: a review. Cytobios. 1980;28(111-112):187-208. [PubMed:6260434 ]