Record Information
Version1.0
Creation date2011-09-21 00:04:17 UTC
Update date2019-11-27 17:42:25 UTC
Primary IDFDB021871
Secondary Accession NumbersNot Available
Chemical Information
FooDB NameDeoxycytidine
DescriptionOne of the principal nucleosides of DNA composed of cytosine and deoxyribose. A nucleoside consists of only a pentose sugar linked to a purine or pyrimidine base, without a phosphate group. When N1 is linked to the C1 of deoxyribose, deoxynucleosides and nucleotides are formed from cytosine and deoxyribose; deoxycytidine monophosphate (dCMP), deoxycytidine diphosphate (dCDP), deoxycytidine triphosphate (dCTP). CTP is the source of the cytidine in RNA (ribonucleic acid) and deoxycytidine triphosphate (dCTP) is the source of the deoxycytidine in DNA (deoxyribonucleic acid). [HMDB]. Deoxycytidine is found in many foods, some of which are japanese pumpkin, turmeric, prairie turnip, and kai-lan.
CAS Number951-77-9
Structure
Thumb
Synonyms
SynonymSource
4-Amino-1-[(2R,4S,5R)-4-hydroxy-5-(hydroxymethyl)tetrahydrofuran-2-yl]pyrimidin-2(1H)-oneChEBI
dCChEBI
DCYDChEBI
2'-DeoxycytidineKegg
1-(2-Deoxy-b-D-ribofuranosyl)cytosineHMDB
1-(2-Deoxy-beta-D-erythro-pentofuranosyl)-cytosineHMDB
1-(2-Deoxy-beta-D-ribofuranosyl)cytosineHMDB
1-(2-Deoxy-beta-delta-erythro-pentofuranosyl)-cytosineHMDB
1-(2-Deoxy-beta-delta-ribofuranosyl)cytosineHMDB
2-Deoxy-cytidineHMDB
4-Amino-1-(2-deoxy-b-D-erythro-pentofuranosyl)-2(1H)-pyrimidinoneHMDB
4-Amino-1-(2-deoxy-beta-D-erythro-pentofuranosyl)-2(1H)-pyrimidinoneHMDB
4-Amino-1-(2-deoxy-beta-delta-erythro-pentofuranosyl)-2(1H)-pyrimidinoneHMDB
Cytosine deoxyribonucleosideHMDB
Cytosine deoxyribosideHMDB
Deoxy-cytidineHMDB
Deoxyribose cytidineHMDB
DesoxycytidineHMDB
Deoxyribonucleoside, cytosineHMDB
Deoxyriboside, cytosineHMDB
DeoxycytidineChEBI
1-(2-deoxy-beta-D-erythro-pentofuranosyl)-Cytosinehmdb
1-(2-deoxy-beta-delta-erythro-pentofuranosyl)-Cytosinehmdb
2-deoxy-Cytidinehmdb
4-amino-1-[(2R,4S,5R)-4-Hydroxy-5-(hydroxymethyl)tetrahydrofuran-2-yl]pyrimidin-2(1H)-oneChEBI
deoxy-Cytidinehmdb
Predicted Properties
PropertyValueSource
Water Solubility15.9 g/LALOGPS
logP-1.9ALOGPS
logP-1.9ChemAxon
logS-1.2ALOGPS
pKa (Strongest Acidic)13.89ChemAxon
pKa (Strongest Basic)0.31ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count6ChemAxon
Hydrogen Donor Count3ChemAxon
Polar Surface Area108.38 ŲChemAxon
Rotatable Bond Count2ChemAxon
Refractivity53.03 m³·mol⁻¹ChemAxon
Polarizability21.65 ųChemAxon
Number of Rings2ChemAxon
Bioavailability1ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Chemical FormulaC9H13N3O4
IUPAC name4-amino-1-[(2R,4S,5R)-4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]-1,2-dihydropyrimidin-2-one
InChI IdentifierInChI=1S/C9H13N3O4/c10-7-1-2-12(9(15)11-7)8-3-5(14)6(4-13)16-8/h1-2,5-6,8,13-14H,3-4H2,(H2,10,11,15)/t5-,6+,8+/m0/s1
InChI KeyCKTSBUTUHBMZGZ-SHYZEUOFSA-N
Isomeric SMILESNC1=NC(=O)N(C=C1)[C@H]1C[C@H](O)[C@@H](CO)O1
Average Molecular Weight227.2172
Monoisotopic Molecular Weight227.090605919
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 Descriptors
Ontology
Disposition

Route of exposure:

Source:

Biological location:

Role

Industrial application:

Physico-Chemical Properties - Experimental
Physico-Chemical Properties - Experimental
PropertyValueReference
Physical stateSolid
Physical DescriptionNot Available
Mass CompositionNot Available
Melting PointNot Available
Boiling PointNot Available
Experimental Water SolubilityNot Available
Experimental logPNot Available
Experimental pKaNot Available
Isoelectric pointNot Available
ChargeNot Available
Optical RotationNot Available
Spectroscopic UV DataNot Available
DensityNot Available
Refractive IndexNot Available
Spectra
Spectra
Spectrum TypeDescriptionSplash Key
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-0006-9510000000-43f83823bd8a63669514View in MoNA
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (2 TMS) - 70eV, Positivesplash10-0gb9-4912000000-fef878d78b0000e850bbView in MoNA
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 10V, Positive (Annotated)splash10-03di-0900000000-27431bdd2327f6f2b886View in MoNA
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 25V, Positive (Annotated)splash10-03di-1900000000-0ea85f3f3940843e385bView in MoNA
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 40V, Positive (Annotated)splash10-03dl-9500000000-569e473eba0b700f5b6eView in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 10V, Negativesplash10-004i-0090000000-5c8c0fde4f2163fbc335View in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 20V, Negativesplash10-0006-9420000000-28279714b575d59761ceView in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 30V, Negativesplash10-0006-9200000000-df7c76b755c9fac5267bView in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 40V, Negativesplash10-0006-9100000000-acbd1d7557be6d716a19View in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 50V, Negativesplash10-00kf-9100000000-056ef35d3aa743e0d5cfView in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 10V, Positivesplash10-03di-0910000000-52e9d173bb94576f7d9eView in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 20V, Positivesplash10-03di-0900000000-e06e5a9f19c4162aa24fView in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 30V, Positivesplash10-03di-0900000000-551d8ee9679ef3fb65faView in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 40V, Positivesplash10-03di-3900000000-4c62633283ba566dbee0View in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-IT (LC/MSD Trap XCT, Agilent Technologies) , Positivesplash10-03di-0900000000-bac3656523b118a2c1bcView in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-IT (LC/MSD Trap XCT, Agilent Technologies) , Positivesplash10-03dj-6900000000-dfa8435d3dd8b8981621View in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF (UPLC Q-Tof Premier, Waters) , Positivesplash10-01t9-0690000000-72302b09c51553dde169View in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF (UPLC Q-Tof Premier, Waters) 30V, Positivesplash10-03fr-0930000000-f5c80400a73719f6211fView in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF (UPLC Q-Tof Premier, Waters) , Negativesplash10-0006-9130000000-c7f95a478d22e3cc83f4View in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , negativesplash10-004i-0090000000-af75883dba546c82e7bcView in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , negativesplash10-0006-9420000000-562a675c6278a4ae2bc4View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-03di-0900000000-e9d4ffd1148d792f5132View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-03di-4900000000-b2a5f419f882d45f6ae7View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-03di-8900000000-0bbcfd7be44c4f38c4fcView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-004i-1890000000-395ff33971fbc8368ecaView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-0016-4910000000-2dc8aa3aad2b1c83316fView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-0006-9200000000-cc82bf3d145faf0a6ca3View in MoNA
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
2D NMR[1H,13C] 2D NMR SpectrumNot AvailableView in JSpectraViewer
ChemSpider ID13117
ChEMBL IDCHEMBL66115
KEGG Compound IDC00881
Pubchem Compound ID13711
Pubchem Substance IDNot Available
ChEBI IDNot Available
Phenol-Explorer IDNot Available
DrugBank IDNot Available
HMDB IDHMDB00014
CRC / DFC (Dictionary of Food Compounds) IDNot Available
EAFUS IDNot Available
Dr. Duke IDNot Available
BIGG ID36280
KNApSAcK IDNot Available
HET IDDCZ
Food Biomarker OntologyNot Available
VMH IDNot Available
Flavornet IDNot Available
GoodScent IDNot Available
SuperScent IDNot Available
Wikipedia IDDeoxycytidine
Phenol-Explorer Metabolite IDNot Available
Duplicate IDSNot Available
Old DFC IDSNot Available
Associated Foods
FoodContent Range AverageReference
FoodReference
Biological Effects and Interactions
Health Effects / BioactivitiesNot Available
Enzymes
NameGene NameUniProt ID
Deoxycytidine kinaseDCKP27707
Cytosolic 5'-nucleotidase 3NT5C3Q9H0P0
AIDAIDQ546Y9
Uridine-cytidine kinase-like 1UCKL1Q9NWZ5
Pathways
NameSMPDB LinkKEGG Link
Pyrimidine MetabolismSMP00046 map00240
MetabolismNot Available
BiosynthesisNot Available
Organoleptic Properties
FlavoursNot Available
Files
MSDSshow
References
Synthesis ReferenceNot Available
General ReferenceNot Available
Content Reference