Record Information
Version1.0
Creation date2011-09-21 00:21:41 UTC
Update date2015-07-21 06:57:25 UTC
Primary IDFDB022917
Secondary Accession NumbersNot Available
Chemical Information
FooDB Name5-Methyldeoxycytidine
Description5-Methyldeoxycytidine is a dinucleotide. Methylation of cytosine-guanine dinucleotide sequences (CpG dinucleotides) catalyzed by DNA methyltransferase, particularly in the 5′-promoter regions of mammalian genes, forms 5-methyldeoxycytidine (5-mdc) whose levels may regulate gene expression. Levels of 5-mdc and the expression of nm23-H1 (an anti-metastatic gene identified in and human cancer lines) are highly correlated with human hepatoma cells with different invasion activities. DNA hypermethylation is a common finding in malignant cells and has been explored as a therapeutic target for hypomethylating agents. The levels of 5-mdc in the urine of patients with breast cancer is not significantly different than controls. (PMID: 17044778, 17264127, 16799933) [HMDB]
CAS Number838-07-3
Structure
Thumb
Synonyms
Predicted Properties
PropertyValueSource
Water Solubility10.8 g/LALOGPS
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 FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Chemical FormulaC10H15N3O4
IUPAC name4-amino-1-[(2R,5R)-4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]-5-methyl-1,2-dihydropyrimidin-2-one
InChI IdentifierInChI=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
Isomeric SMILESCC1=CN([C@H]2CC(O)[C@@H](CO)O2)C(=O)N=C1N
Average Molecular Weight241.2438
Monoisotopic Molecular Weight241.106255983
Classification
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
Disposition

Source:

Physico-Chemical Properties
Physico-Chemical Properties - Experimental
Spectra
Spectra
EI-MS/GC-MS
TypeDescriptionSplash KeyView
Predicted GC-MS5-Methyldeoxycytidine, non-derivatized, Predicted GC-MS Spectrum - 70eV, Positivesplash10-0006-9420000000-4af773e99af76af961eaSpectrum
Predicted GC-MS5-Methyldeoxycytidine, 2 TMS, Predicted GC-MS Spectrum - 70eV, Positivesplash10-0006-9014000000-1fd11a88c9a0762a6b1dSpectrum
Predicted GC-MS5-Methyldeoxycytidine, non-derivatized, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
MS/MS
TypeDescriptionSplash KeyView
Predicted MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-004i-0900000000-d1d23649ec4fa9201eba2017-09-01View Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-004i-2900000000-d21a1bb287e1d523b6c22017-09-01View Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-004i-3900000000-b4f3cca0a164fdbc50312017-09-01View Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0a4j-0920000000-6aa55dc948aac874e1a02017-09-01View Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-0uk9-2920000000-6d51e08eb5820a7489022017-09-01View Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-007p-9400000000-77fb64e01991290967772017-09-01View Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-00dl-0970000000-a011cf5a5c36138117172021-09-24View Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-00dl-9600000000-ee60e868c938ff348f092021-09-24View Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-006y-9500000000-81204e67016c197ad16f2021-09-24View Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-004i-0900000000-a1c51dd1d9ae2dee6e382021-09-24View Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-00b9-2900000000-7c9c6f54bbfba0acc1352021-09-24View Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-0059-6900000000-9559671d86d8527195462021-09-24View Spectrum
NMRNot Available
ChemSpider ID12719
ChEMBL IDNot Available
KEGG Compound IDC03592
Pubchem Compound ID13279
Pubchem Substance IDNot Available
ChEBI ID27964
Phenol-Explorer IDNot Available
DrugBank IDNot Available
HMDB IDHMDB02224
CRC / DFC (Dictionary of Food Compounds) IDNot Available
EAFUS IDNot Available
Dr. Duke IDNot Available
BIGG IDNot Available
KNApSAcK IDNot Available
HET IDNot Available
Food Biomarker OntologyNot Available
VMH IDNot Available
Flavornet IDNot Available
GoodScent IDNot Available
SuperScent IDNot Available
Wikipedia IDNot Available
Phenol-Explorer Metabolite IDNot Available
Duplicate IDSNot Available
Old DFC IDSNot Available
Associated Foods
FoodContent Range AverageReference
AnatidaeExpected but not quantifiedNot AvailableHMDB
BeefaloExpected but not quantifiedNot AvailableHMDB
BisonExpected but not quantifiedNot AvailableHMDB
BuffaloExpected but not quantifiedNot AvailableHMDB
Cattle (Beef, Veal)Expected but not quantifiedNot AvailableHMDB
ChickenExpected but not quantifiedNot AvailableHMDB
Columbidae (Dove, Pigeon)Expected but not quantifiedNot AvailableHMDB
DeerExpected but not quantifiedNot AvailableHMDB
Domestic goatExpected but not quantifiedNot AvailableHMDB
Domestic pigExpected but not quantifiedNot AvailableHMDB
Showing 1 to 10 of 29 entries
Biological Effects and Interactions
Health Effects / BioactivitiesNot Available
EnzymesNot Available
PathwaysNot Available
MetabolismNot Available
BiosynthesisNot Available
Organoleptic Properties
FlavoursNot Available
Files
MSDSNot Available
References
Synthesis ReferenceNot Available
General ReferenceNot Available
Content Reference