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2'-Deoxyuridine (YMDB00508)

Identification
YMDB IDYMDB00508
Name2'-Deoxyuridine
SpeciesSaccharomyces cerevisiae
StrainBaker's yeast
Description2'-Deoxyuridine 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. 2'-Deoxyuridine is an extremely weak basic (essentially neutral) compound (based on its pKa). 2'-Deoxyuridine may be a unique S. cerevisiae (yeast) metabolite.
Structure
Thumb
MOLSDFPDBSMILESInChI
Synonyms
  • 1-(2-deoxy-beta-D-ribofuranosyl)-2,4(1H,3H)-Pyrimidinedione
  • 1-(2-Deoxy-D-erythro-pentofuranosyl)uracil
  • 1-(2-Deoxy-delta-erythro-pentofuranosyl)uracil
  • 2-deoxyuridine
  • 2'-Deoxyuridine
  • 2'-Desoxyuridine
  • Deoxyribose uracil
  • Deoxyuridine
  • Desoxyuridine
  • dU
  • dUrd
  • Uracil deoxyriboside
  • Uracil desoxyuridine
  • Uridine, 2-deoxy-
  • Uridine, 2'-deoxy-
CAS number951-78-0
WeightAverage: 228.202
Monoisotopic: 228.074621504
InChI KeyMXHRCPNRJAMMIM-FWHJPCMOSA-N
InChIInChI=1S/C9H12N2O5/c12-4-6-5(13)3-8(16-6)11-2-1-7(14)10-9(11)15/h1-2,5-6,8,12-13H,3-4H2,(H,10,14,15)/t5-,6+,8?/m0/s1
IUPAC Name1-[(4S,5R)-4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]-1,2,3,4-tetrahydropyrimidine-2,4-dione
Traditional IUPAC Nameuracil deoxyriboside
Chemical FormulaC9H12N2O5
SMILESOC[C@H]1OC(C[C@@H]1O)N1C=CC(=O)NC1=O
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
  • Pyrimidone
  • Hydropyrimidine
  • Pyrimidine
  • Heteroaromatic compound
  • Tetrahydrofuran
  • Vinylogous amide
  • Lactam
  • Secondary alcohol
  • Urea
  • Oxacycle
  • Azacycle
  • Organoheterocyclic compound
  • Hydrocarbon derivative
  • Organic oxide
  • Organopnictogen compound
  • Primary alcohol
  • Organooxygen compound
  • Organonitrogen compound
  • Organic oxygen compound
  • Alcohol
  • Organic nitrogen compound
  • Aromatic heteromonocyclic compound
Molecular FrameworkAromatic heteromonocyclic compounds
External DescriptorsNot Available
Physical Properties
StateSolid
Charge0
Melting point167 °C
Experimental Properties
PropertyValueReference
Water SolubilityNot AvailablePhysProp
LogP-1.51 [BALZARINI,JM ET AL. (1989)]PhysProp
Predicted Properties
PropertyValueSource
Water Solubility90.6 g/LALOGPS
logP-1.5ALOGPS
logP-1.5ChemAxon
logS-0.4ALOGPS
pKa (Strongest Acidic)9.71ChemAxon
pKa (Strongest Basic)-3ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count5ChemAxon
Hydrogen Donor Count3ChemAxon
Polar Surface Area99.1 ŲChemAxon
Rotatable Bond Count2ChemAxon
Refractivity51.05 m³·mol⁻¹ChemAxon
Polarizability21 ųChemAxon
Number of Rings2ChemAxon
Bioavailability1ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations
  • extracellular
  • cytoplasm
Organoleptic PropertiesNot Available
SMPDB Pathways
Pyrimidine metabolismPW002469 ThumbThumb?image type=greyscaleThumb?image type=simple
KEGG Pathways
Pyrimidine metabolismec00240 Map00240
SMPDB ReactionsNot Available
KEGG Reactions
dUMP + water → phosphate + 2'-Deoxyuridine
water + hydron + 2'-Deoxycytidine → 2'-Deoxyuridine + Ammonium
Adenosine triphosphate + 2'-Deoxyuridine → dUMP + hydron + ADP
phosphate + 2'-Deoxyuridine ↔ Uracil + 2-deoxy-D-ribofuranose 1-phosphate
Concentrations
Intracellular ConcentrationsNot Available
Extracellular ConcentrationsNot Available
Spectra
Spectra
Spectrum TypeDescriptionSplash KeyView
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-01r7-9610000000-dfaab249ec8e9361b4bfJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-03di-1900000000-4e3e387ebbab12abe1fdJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-03di-5900000000-e483c01cc3a2bd6439c1JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-03di-9800000000-e0e5bb84af10a0c46b95JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0036-8960000000-f6a195e38452cd824d19JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-000f-7910000000-8de672c701d38c2dd5d3JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-00kf-9100000000-6e86ecc024dbcde80d90JSpectraViewer
References
References:
  • Herrgard, M. J., Swainston, N., Dobson, P., Dunn, W. B., Arga, K. Y., Arvas, M., Bluthgen, N., Borger, S., Costenoble, R., Heinemann, M., Hucka, M., Le Novere, N., Li, P., Liebermeister, W., Mo, M. L., Oliveira, A. P., Petranovic, D., Pettifer, S., Simeonidis, E., Smallbone, K., Spasic, I., Weichart, D., Brent, R., Broomhead, D. S., Westerhoff, H. V., Kirdar, B., Penttila, M., Klipp, E., Palsson, B. O., Sauer, U., Oliver, S. G., Mendes, P., Nielsen, J., Kell, D. B. (2008). "A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology." Nat Biotechnol 26:1155-1160.18846089
Synthesis Reference:Huang, Haoqiang; Chu, Chung K. A practical synthesis of 2'-deoxyuridine from uridine. Synthetic Communications (1990), 20(7), 1039-46.
External Links:
ResourceLink
CHEBI ID16450
HMDB IDHMDB00012
Pubchem Compound ID13712
Kegg IDC00526
ChemSpider ID23630211
FOODB IDNot Available
WikipediaDeoxyuridine
BioCyc IDDEOXYURIDINE

Enzymes

Protein Details
1. Purine nucleoside phosphorylase
General function:
Involved in purine-nucleoside phosphorylase activity
Specific function:
Cleavage of guanosine or inosine to respective bases and sugar-1-phosphate molecules
Gene Name:
PNP1
Uniprot ID:
Q05788
Molecular weight:
33754.60156
Reactions
Purine nucleoside + phosphate → purine + alpha-D-ribose 1-phosphate.
Protein Details
2. Cytidine deaminase
General function:
Involved in zinc ion binding
Specific function:
This enzyme scavenge exogenous and endogenous cytidine and 2'-deoxycytidine for UMP synthesis
Gene Name:
CDD1
Uniprot ID:
Q06549
Molecular weight:
15535.90039
Reactions
Cytidine + H(2)O → uridine + NH(3).