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Bovine Metabolome Database



Showing metabocard for Deoxycytidine (BMDB00014)

Legend: metabolite field enzyme field

Version 1.0
Creation Date 2005-11-16 15:48:42
Update Date 2009-05-05 20:57:37
Accession Number BMDB00014
Common Name Deoxycytidine
Description One 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).
Synonyms
  1. 1-(2-Deoxy-b-D-ribofuranosyl)cytosine
  2. 1-(2-deoxy-beta-D-erythro-pentofuranosyl)-Cytosine
  3. 2'-Deoxycytidine
  4. 2-deoxy-Cytidine
  5. 4-Amino-1-(2-deoxy-b-D-erythro-pentofuranosyl)-2(1H)-pyrimidinone
  6. Cytosine deoxyribonucleoside
  7. Cytosine deoxyriboside
  8. Deoxyribose cytidine
  9. Desoxycytidine
  10. deoxy-Cytidine
  11. 1-(2-Deoxy-beta-delta-ribofuranosyl)cytosine
  12. 1-(2-deoxy-beta-delta-erythro-pentofuranosyl)-Cytosine
  13. 4-Amino-1-(2-deoxy-beta-delta-erythro-pentofuranosyl)-2(1H)-pyrimidinone
  14. 1-(2-Deoxy-beta-D-ribofuranosyl)cytosine
  15. 4-Amino-1-(2-deoxy-beta-D-erythro-pentofuranosyl)-2(1H)-pyrimidinone
Chemical IUPAC Name 4-amino-1-[4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]-pyrimidin-2-one
Chemical Formula C9H13N3O4
Chemical Structure Structure
Chemical Taxonomy
Kingdom
  • Organic
Super Class
  • Nucleosides and Nucleoside conjugates
Class
  • Nucleoside Analogues
Sub Class
  • Deoxy nucleosides
Family
  • Mammalian_Metabolite
Species
  • primary alcohol; secondary alcohol; primary amine; primary aromatic amine; oxo(het)arene; aromatic compound; heterocyclic compound
Biofunction
  • Component of Purine metabolism; Component of Pyrimidine metabolism
Application
Source
  • Endogenous
Average Molecular Weight 227.217
Monoisotopic Molecular Weight 227.090607
Isomeric SMILES NC1=NC(=O)N(C=C1)[C@H]1C[C@H](O)[C@@H](CO)O1
Canonical SMILES NC1=NC(=O)N(C=C1)C1CC(O)C(CO)O1
KEGG Compound ID C00881 Link Image
BioCyc ID DEOXYCYTIDINE Link Image
BiGG ID 36280 Link Image
Wikipedia Link Deoxycytidine Link Image
METLIN ID 3367 Link Image
PubChem Compound 13711 Link Image
PubChem Substance 829250 Link Image
ChEBI ID Not Available
CAS Registry Number 951-77-9
InChI Identifier InChI=1/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
Synthesis Reference Fox, Jack F.; Yung, Naishun; Wempen, Iris; Hoffer, Max. Pyrimidine nucleosides. XII. Direct synthesis of 2'-deoxycytidine and its a-anomer. Journal of the American Chemical Society (1961), 83 4066-50.
Melting Point (Experimental) 207-210 oC
Experimental Water Solubility 870 mg/mL [free base, HMP experimental] Source: PhysProp
Predicted Water Solubility 63.4 mg/mL [MEYLAN,WM et al. (1996)]; 15.900001 mg/mL [Predicted by ALOGPS] Calculated using ALOGPS
Physiological Charge 0
State Solid
Experimental LogP/Hydrophobicity -1.77 [HANSCH,C ET AL. (1995)] Source: PhysProp
Predicted LogP/Hydrophobicity -1.93 [Predicted by ALOGPS]; -1.9 [Predicted by PubChem via XLOGP] Calculated using ALOGPS
Material Safety Data Sheet (MSDS) Not Available
MOL File Show
SDF File Show
PDB File Show
2D Structure
3D Structure
Experimental PDB ID 1J90 Link Image
Experimental PDB File Show
Experimental PDB Structure
Experimental 1H NMR Spectrum Download Spectrum
Download FID (Varian)
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Experimental 13C NMR Spectrum Download Spectrum
Download FID (Bruker)
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Experimental 13C HSQC Spectrum Download Spectrum
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Predicted 1H NMR Spectrum Show Image
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Predicted 13C NMR Spectrum Show Image
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Mass Spectrum
Low Energy
Download File
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Medium Energy
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High Energy
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Simplified TOCSY Spectrum Not Available
BMRB Spectrum Not Available
Cellular Location
  • Cytoplasm (Predicted from LogP)
  • Extracellular
  • lysosome
  • mitochondria
  • nucleus
Biofluid Location Not Available
Tissue Location
Tissue References
All Tissues
Concentrations (Normal) Not Available
Concentrations (Abnormal) Not Available
Pathway Names
  • Pyrimidine Metabolism
HMDB Pathways
Name Pyrimidine Metabolism
Image Show Link Image
KEGG Pathways
Name Pyrimidine Metabolism
Image Show Link Image
SimCell Pathways
Name Pyrimidine Metabolism
Image Show Link Image
Graph
SBML
General References
  1. Wikipedia Link Image
Metabolic Enzymes
  1. Deoxycytidine kinase
Enzyme 1 [top]
Enzyme 1 ID 863
Enzyme 1 Name Deoxycytidine kinase
Enzyme 1 Synonyms
  1. dCK
Enzyme 1 Gene Name DCK
Enzyme 1 Protein Sequence >Deoxycytidine kinase
MATPPKRSCPSPAASSEGTRIKKISIEGNIAAGKSTFVNILKQVCEDWEVVPEPVARWCN
VQSTQDEFEELTTSQKSGGNVLQMMYEKPERWSFTFQSYACLSRIRAQLAALNGKLKDAE
KPVLFFERSVYSDRYIFASNLYESDCMNETEWTIYQDWHDWMNNQFGQSLELDGIIYLRA
TPEKCLNRIYLRGRNEEQGIPLEYLEKLHYKHESWLLHRTLKTNFDYLQEVPILTLDVNE
DFKDKHDSLIEKVKDFLSTL
Enzyme 1 Number of Residues 260
Enzyme 1 Molecular Weight 30329.1
Enzyme 1 Theoretical pI 5.09
Enzyme 1 GO Classification
Function
Process
Component
Enzyme 1 General Function Nucleotide transport and metabolism
Enzyme 1 Specific Function Required for the phosphorylation of the deoxyribonucleosides deoxycytidine (dC), deoxyguanosine (dG) and deoxyadenosine (dA)
Enzyme 1 Pathways Not Available
Enzyme 1 Reactions Not Available
Enzyme 1 Pfam Domain Function
Enzyme 1 Signals
  • None
Enzyme 1 Transmembrane Regions
  • None
Enzyme 1 Essentiality Not Available
Enzyme 1 GenBank ID Protein 75773424 Link Image
Enzyme 1 UniProtKB/Swiss-Prot ID Q3MHR2 Link Image
Enzyme 1 UniProtKB/Swiss-Prot Entry Name DCK_BOVIN Link Image
Enzyme 1 PDB ID 1P62 Link Image
Enzyme 1 PDB File Show
Enzyme 1 3D Structure
Enzyme 1 Cellular Location Not Available
Enzyme 1 Gene Sequence >783 bp
ATGGCCACCCCACCCAAGAGGAGCTGCCCGTCTCCCGCAGCCAGCTCTGAGGGGACCCGC
ATCAAGAAAATTTCCATCGAAGGGAACATCGCTGCTGGGAAGTCAACATTTGTGAATATC
CTTAAACAAGTCTGTGAGGACTGGGAAGTGGTGCCTGAACCTGTTGCCAGGTGGTGCAAT
GTTCAGAGTACTCAGGATGAATTTGAGGAACTGACAACATCTCAGAAAAGTGGCGGGAAT
GTTCTTCAGATGATGTATGAGAAACCTGAACGATGGTCTTTTACCTTCCAGTCATATGCC
TGCCTCAGTCGAATACGAGCTCAGCTTGCCGCTCTCAATGGAAAACTCAAAGATGCAGAG
AAACCAGTATTATTTTTTGAACGATCTGTGTATAGTGACAGGTATATTTTTGCATCTAAT
TTGTATGAATCTGACTGCATGAATGAAACAGAGTGGACCATTTATCAAGACTGGCATGAC
TGGATGAATAACCAGTTTGGCCAAAGCCTTGAACTGGATGGAATCATTTATCTTAGAGCC
ACTCCAGAGAAATGCTTGAATAGAATATATTTACGGGGAAGAAATGAAGAACAAGGCATT
CCTCTTGAATATTTGGAGAAACTTCACTATAAGCATGAAAGCTGGCTCCTGCATAGAACA
CTAAAAACCAACTTTGATTATCTACAAGAAGTGCCTATCTTAACACTGGATGTTAATGAA
GACTTTAAAGACAAACATGACAGTCTAATTGAAAAGGTAAAAGACTTTTTGAGCACTTTG
TGA
Enzyme 1 GenBank Gene ID BC105141 Link Image
Enzyme 1 GeneCard ID DCK Link Image
Enzyme 1 GenAtlas ID Not Available
Enzyme 1 HGNC ID Not Available
Enzyme 1 Chromosome Location Chromosome:4
Enzyme 1 Locus 4q13.3-q21.1
Enzyme 1 SNPs SNPJam Report Link Image
Enzyme 1 General References Not Available
Enzyme 1 Metabolite References Not Available