Showing metabocard for 5-Methyldeoxycytidine (BMDB0002224)

IdentificationTaxonomyPhysical propertiesPathwaysSpectraConcentrationsLinksReferencesXML
Record Information
Version1.0
Creation Date2016-09-30 22:52:54 UTC
Update Date2020-04-22 15:10:16 UTC
BMDB IDBMDB0002224
Secondary Accession Numbers
  • BMDB02224
Metabolite Identification
Common Name5-Methyldeoxycytidine
Description5-Methyldeoxycytidine belongs to the class of organic compounds known as pyrimidine 2'-deoxyribonucleosides. Pyrimidine 2'-deoxyribonucleosides are compounds consisting of a pyrimidine linked to a ribose which lacks a hydroxyl group at position 2. Based on a literature review a significant number of articles have been published on 5-Methyldeoxycytidine.
Structure
Thumb
MOLSDFPDBSMILESInChI
Synonyms
ValueSource
2'-Deoxy-5-methylcytidineHMDB
5-Methyl-2'-deoxycytidineHMDB
5-MethyldeoxycytidineMeSH
Chemical FormulaC10H15N3O4
Average Molecular Weight241.2438
Monoisotopic Molecular Weight241.106255983
IUPAC Name4-amino-1-[(2R,5R)-4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]-5-methyl-1,2-dihydropyrimidin-2-one
Traditional Name4-amino-1-[(2R,5R)-4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]-5-methylpyrimidin-2-one
CAS Registry Number838-07-3
SMILES
CC1=CN([C@H]2CC(O)[C@@H](CO)O2)C(=O)N=C1N
InChI Identifier
InChI=1S/C10H15N3O4/c1-5-3-13(10(16)12-9(5)11)8-2-6(15)7(4-14)17-8/h3,6-8,14-15H,2,4H2,1H3,(H2,11,12,16)/t6?,7-,8-/m1/s1
InChI KeyLUCHPKXVUGJYGU-SPDVFEMOSA-N
Chemical Taxonomy
Description belongs to the class of organic compounds known as pyrimidine 2'-deoxyribonucleosides. Pyrimidine 2'-deoxyribonucleosides are compounds consisting of a pyrimidine linked to a ribose which lacks a hydroxyl group at position 2.
KingdomOrganic compounds
Super ClassNucleosides, nucleotides, and analogues
ClassPyrimidine nucleosides
Sub ClassPyrimidine 2'-deoxyribonucleosides
Direct ParentPyrimidine 2'-deoxyribonucleosides
Alternative Parents
Substituents
  • Pyrimidine 2'-deoxyribonucleoside
  • Aminopyrimidine
  • Pyrimidone
  • Hydropyrimidine
  • Pyrimidine
  • Imidolactam
  • Heteroaromatic compound
  • Tetrahydrofuran
  • Secondary alcohol
  • Azacycle
  • Oxacycle
  • Organoheterocyclic compound
  • Alcohol
  • Hydrocarbon derivative
  • Organic oxide
  • Organopnictogen compound
  • Primary amine
  • Primary alcohol
  • Organooxygen compound
  • Organonitrogen compound
  • Organic oxygen compound
  • Organic nitrogen compound
  • Amine
  • Aromatic heteromonocyclic compound
Molecular FrameworkAromatic heteromonocyclic compounds
External DescriptorsNot Available
Ontology
StatusExpected but not Quantified
Origin
  • Endogenous
BiofunctionNot Available
ApplicationNot Available
Cellular locationsNot Available
Physical Properties
StateSolid
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
logP-1.7ALOGPS
logP-1.5ChemAxon
logS-1.4ALOGPS
pKa (Strongest Acidic)13.89ChemAxon
pKa (Strongest Basic)0.41ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count6ChemAxon
Hydrogen Donor Count3ChemAxon
Polar Surface Area108.38 ŲChemAxon
Rotatable Bond Count2ChemAxon
Refractivity57.39 m³·mol⁻¹ChemAxon
Polarizability23.34 ųChemAxon
Number of Rings2ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Spectra
Spectra
Spectrum TypeDescriptionSplash Key
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-0006-9420000000-4af773e99af76af961eaView in MoNA
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (2 TMS) - 70eV, Positivesplash10-0006-9014000000-1fd11a88c9a0762a6b1dView in MoNA
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, PositiveNot AvailableView in JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-004i-0900000000-d1d23649ec4fa9201ebaView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-004i-2900000000-d21a1bb287e1d523b6c2View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-004i-3900000000-b4f3cca0a164fdbc5031View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0a4j-0920000000-6aa55dc948aac874e1a0View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-0uk9-2920000000-6d51e08eb5820a748902View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-007p-9400000000-77fb64e0199129096777View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-00dl-0970000000-a011cf5a5c3613811717View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-00dl-9600000000-ee60e868c938ff348f09View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-006y-9500000000-81204e67016c197ad16fView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-004i-0900000000-a1c51dd1d9ae2dee6e38View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-00b9-2900000000-7c9c6f54bbfba0acc135View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-0059-6900000000-9559671d86d852719546View in MoNA
1D NMR13C NMR Spectrum (1D, 100 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 200 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 200 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 300 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 300 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 400 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 500 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 600 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 600 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 700 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 700 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 800 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 800 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 900 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 1000 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 1000 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
Biological Properties
Cellular LocationsNot Available
Biospecimen LocationsNot Available
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
Not Available
HMDB IDHMDB0002224
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB022917
KNApSAcK IDNot Available
Chemspider ID12719
KEGG Compound IDC03592
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound13279
PDB IDNot Available
ChEBI ID27964
References
Synthesis ReferenceVorbrueggen, Helmut; Krolikiewicz, Konrad. 2'-Deoxy-5-methylcytidine: Amination of thymidine. Nucleic Acid Chem. (1978), 1 227-9.
Material Safety Data Sheet (MSDS)Not Available
General ReferencesNot Available