Showing Compound Card for Deoxyuridine (CDB004781)

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Record Information
Version1.0
Created at2020-04-17 18:36:06 UTC
Updated at2020-11-18 16:38:40 UTC
CannabisDB IDCDB004781
Secondary Accession NumbersNot Available
Cannabis Compound Identification
Common NameDeoxyuridine
DescriptionDeoxyuridine, also known as dU, 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. Deoxyuridine is an extremely weak basic (essentially neutral) compound (based on its pKa). Deoxyuridine exists in all living organisms, ranging from bacteria to humans. Within humans, deoxyuridine participates in a number of enzymatic reactions. In particular, deoxyuridine can be biosynthesized from deoxycytidine through its interaction with the enzyme cytidine deaminase. In addition, deoxyuridine can be converted into uracil and deoxyribose 1-phosphate through its interaction with the enzyme thymidine phosphorylase. In humans, deoxyuridine is involved in the metabolic disorder called ump synthase deficiency (orotic aciduria). Outside of the human body, Deoxyuridine is found, on average, in the highest concentration within beers. Deoxyuridine has also been detected, but not quantified in, several different foods, such as cornmints, globe artichokes, lotus, conchs, and lambsquarters. This could make deoxyuridine a potential biomarker for the consumption of these foods. Deoxyuridine is a potentially toxic compound. A pyrimidine 2'-deoxyribonucleoside having uracil as the nucleobase. Deoxyuridine is expected to be in Cannabis as all living plants are known to produce and metabolize it.
Structure
Thumb
MOLSDFPDBSMILESInChI
Synonyms
ValueSource
2-DeoxyuridineChEBI
dUChEBI
2'-DeoxyuridineKegg
1-(2-Deoxy-beta-D-erythro-pentofuranosyl)-2,4(1H,3H)-pyrimidinedioneHMDB
1-(2-Deoxy-beta-D-ribofuranosyl)-2,4(1H,3H)-pyrimidinedioneHMDB
1-(2-Deoxy-beta-delta-erythro-pentofuranosyl)-2,4(1H,3H)-pyrimidinedioneHMDB
1-(2-Deoxy-beta-delta-ribofuranosyl)-2,4(1H,3H)-pyrimidinedioneHMDB
1-(2-Deoxy-D-erythro-pentofuranosyl)uracilHMDB
1-(2-Deoxy-delta-erythro-pentofuranosyl)uracilHMDB
2'-DesoxyuridineHMDB
Deoxyribose uracilHMDB
DesoxyuridineHMDB
Uracil deoxyribosideHMDB
Uracil desoxyuridineHMDB
(beta 1-(2-Deoxyribopyranosyl))thymidineHMDB
DeoxyuridineChEBI
Chemical FormulaC9H12N2O5
Average Molecular Weight228.2
Monoisotopic Molecular Weight228.0746
IUPAC Name1-[(2R,4S,5R)-4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]-1,2,3,4-tetrahydropyrimidine-2,4-dione
Traditional Name2'-deoxyuridine
CAS Registry Number951-78-0
SMILES
OC[C@H]1O[C@H](C[C@@H]1O)N1C=CC(=O)NC1=O
InChI Identifier
InChI=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
InChI KeyMXHRCPNRJAMMIM-SHYZEUOFSA-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
  • 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 Descriptors
Ontology
Disposition

Route of exposure:

Source:

Biological location:

Role

Industrial application:

Physical Properties
StateSolid
Experimental Properties
PropertyValueReference
Melting Point167 °CNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
logP-1.51BALZARINI,JM ET AL. (1989)
Predicted Properties
PropertyValueSource
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
Polarizability21.06 ųChemAxon
Number of Rings2ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Spectra
EI-MS/GC-MS
TypeDescriptionSplash KeyView
GC-MSDeoxyuridine, non-derivatized, GC-MS Spectrumsplash10-0udi-0900000000-c680f47a48626bc1de41Spectrum
GC-MSDeoxyuridine, non-derivatized, GC-MS Spectrumsplash10-0udi-0900000000-13135426d5efdf47090cSpectrum
GC-MSDeoxyuridine, 3 TMS, GC-MS Spectrumsplash10-0v4i-2910000000-b0c82cef369c86d585bcSpectrum
GC-MSDeoxyuridine, 3 TMS, GC-MS Spectrumsplash10-0udi-2900000000-c2cdba9e46defe05a225Spectrum
GC-MSDeoxyuridine, non-derivatized, GC-MS Spectrumsplash10-0udi-0900000000-c680f47a48626bc1de41Spectrum
GC-MSDeoxyuridine, non-derivatized, GC-MS Spectrumsplash10-0udi-0900000000-13135426d5efdf47090cSpectrum
GC-MSDeoxyuridine, non-derivatized, GC-MS Spectrumsplash10-0v4i-2910000000-b0c82cef369c86d585bcSpectrum
GC-MSDeoxyuridine, non-derivatized, GC-MS Spectrumsplash10-0udi-2900000000-c2cdba9e46defe05a225Spectrum
Predicted GC-MSDeoxyuridine, non-derivatized, Predicted GC-MS Spectrum - 70eV, Positivesplash10-01r7-9610000000-dfaab249ec8e9361b4bfSpectrum
Predicted GC-MSDeoxyuridine, 2 TMS, Predicted GC-MS Spectrum - 70eV, Positivesplash10-0g06-9621000000-32e72b8293f4e226223bSpectrum
Predicted GC-MSDeoxyuridine, non-derivatized, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSDeoxyuridine, TMS_1_1, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSDeoxyuridine, TMS_1_2, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSDeoxyuridine, TMS_1_3, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSDeoxyuridine, TMS_2_2, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSDeoxyuridine, TMS_2_3, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSDeoxyuridine, TBDMS_1_1, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSDeoxyuridine, TBDMS_1_2, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSDeoxyuridine, TBDMS_1_3, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSDeoxyuridine, TBDMS_2_1, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSDeoxyuridine, TBDMS_2_2, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSDeoxyuridine, TBDMS_2_3, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
MS/MS
TypeDescriptionSplash KeyView
MS/MSLC-MS/MS Spectrum - Quattro_QQQ 10V, Positive (Annotated)splash10-03di-1900000000-6610506190427bbb3b6c2012-07-24View Spectrum
MS/MSLC-MS/MS Spectrum - Quattro_QQQ 25V, Positive (Annotated)splash10-03di-9800000000-af237f79161aa13a58932012-07-24View Spectrum
MS/MSLC-MS/MS Spectrum - Quattro_QQQ 40V, Positive (Annotated)splash10-022d-9100000000-a06cdd7ea870d049c8a92012-07-24View Spectrum
MS/MSLC-MS/MS Spectrum - Linear Ion Trap , negativesplash10-001r-0900000000-87d0da98372c9c5a167a2017-09-14View Spectrum
MS/MSLC-MS/MS Spectrum - Linear Ion Trap , negativesplash10-001r-0900000000-795c89de7cd09998501c2017-09-14View Spectrum
MS/MSLC-MS/MS Spectrum - Linear Ion Trap , negativesplash10-03di-0910000000-0f40c1aaec53591fe03d2017-09-14View Spectrum
MS/MSLC-MS/MS Spectrum - Linear Ion Trap , negativesplash10-03di-0900000000-35312c7170aff90afa682017-09-14View Spectrum
MS/MSLC-MS/MS Spectrum - Linear Ion Trap , negativesplash10-004i-0090000000-dd791cff5aab8928952f2017-09-14View Spectrum
MS/MSLC-MS/MS Spectrum - Linear Ion Trap , negativesplash10-004i-0090000000-e5c282f6027560386d072017-09-14View Spectrum
MS/MSLC-MS/MS Spectrum - , negativesplash10-001l-5900000000-4660ec5181499087824f2017-09-14View Spectrum
MS/MSLC-MS/MS Spectrum - Linear Ion Trap , positivesplash10-001i-0910000000-8cef8299b80deeefe1ae2017-09-14View Spectrum
MS/MSLC-MS/MS Spectrum - Linear Ion Trap , positivesplash10-001i-0900000000-043d88b7ac473889f3192017-09-14View Spectrum
MS/MSLC-MS/MS Spectrum - 20V, Negativesplash10-0006-9100000000-5731c423bed1902e4aa12021-09-20View Spectrum
MS/MSLC-MS/MS Spectrum - 10V, Negativesplash10-000x-9820000000-29ea64a90c8736117d032021-09-20View Spectrum
MS/MSLC-MS/MS Spectrum - 40V, Positivesplash10-006t-9400000000-edbb071fcbfdfc740d5c2021-09-20View Spectrum
MS/MSLC-MS/MS Spectrum - 10V, Positivesplash10-03di-2910000000-76f9f11531932d11318e2021-09-20View Spectrum
MS/MSLC-MS/MS Spectrum - 20V, Positivesplash10-03di-4900000000-996ec7312bb565deb6f82021-09-20View Spectrum
MS/MSLC-MS/MS Spectrum - 35V, Negativesplash10-001i-0900000000-45855a2f2673a9e095e82021-09-20View Spectrum
MS/MSLC-MS/MS Spectrum - 40V, Positivesplash10-006w-9100000000-75bb83f5ee43bb79add32021-09-20View Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-03di-1900000000-4e3e387ebbab12abe1fd2017-07-25View Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-03di-5900000000-e483c01cc3a2bd6439c12017-07-25View Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-03di-9800000000-e0e5bb84af10a0c46b952017-07-25View Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0036-8960000000-f6a195e38452cd824d192017-07-26View Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-000f-7910000000-8de672c701d38c2dd5d32017-07-26View Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-00kf-9100000000-6e86ecc024dbcde80d902017-07-26View Spectrum
NMR
TypeDescriptionView
1D NMR1H NMR Spectrum (1D, 500 MHz, H2O, experimental)Spectrum
1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)Spectrum
1D NMR13C NMR Spectrum (1D, 100 MHz, D2O, predicted)Spectrum
1D NMR1H NMR Spectrum (1D, 1000 MHz, D2O, predicted)Spectrum
1D NMR13C NMR Spectrum (1D, 1000 MHz, D2O, predicted)Spectrum
1D NMR1H NMR Spectrum (1D, 200 MHz, D2O, predicted)Spectrum
1D NMR13C NMR Spectrum (1D, 200 MHz, D2O, predicted)Spectrum
1D NMR1H NMR Spectrum (1D, 300 MHz, D2O, predicted)Spectrum
1D NMR13C NMR Spectrum (1D, 300 MHz, D2O, predicted)Spectrum
1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, predicted)Spectrum
1D NMR13C NMR Spectrum (1D, 400 MHz, D2O, predicted)Spectrum
1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, predicted)Spectrum
1D NMR13C NMR Spectrum (1D, 500 MHz, D2O, predicted)Spectrum
1D NMR1H NMR Spectrum (1D, 600 MHz, D2O, predicted)Spectrum
1D NMR13C NMR Spectrum (1D, 600 MHz, D2O, predicted)Spectrum
1D NMR1H NMR Spectrum (1D, 700 MHz, D2O, predicted)Spectrum
1D NMR13C NMR Spectrum (1D, 700 MHz, D2O, predicted)Spectrum
1D NMR1H NMR Spectrum (1D, 800 MHz, D2O, predicted)Spectrum
1D NMR13C NMR Spectrum (1D, 800 MHz, D2O, predicted)Spectrum
1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)Spectrum
1D NMR13C NMR Spectrum (1D, 900 MHz, D2O, predicted)Spectrum
2D NMR[1H, 13C]-HSQC NMR Spectrum (2D, 600 MHz, H2O, experimental)Spectrum
Pathways
Pathways
Protein Targets
Enzymes
Protein NameGene NameLocusUniprot IDDetails
AIDAIDQ546Y9 details
Purine nucleoside phosphorylasePNP14q13.1P00491 details
Thymidine kinase, cytosolicTK117q23.2-q25.3P04183 details
Thymidine kinase 2, mitochondrialTK216q22-q23.1O00142 details
Thymidine phosphorylaseTYMP22q13.33P19971 details
Cytidine deaminaseCDA1p36.2-p35P32320 details
Uridine-cytidine kinase-like 1UCKL120q13.33Q9NWZ5 details
Thymidine kinaseQ8IZR3 details
TransportersNot Available
Metal Bindings
Protein NameGene NameLocusUniprot IDDetails
AIDAIDQ546Y9 details
Thymidine kinase, cytosolicTK117q23.2-q25.3P04183 details
Cytidine deaminaseCDA1p36.2-p35P32320 details
DNA dC->dU-editing enzyme APOBEC-3GAPOBEC3G22q13.1-q13.2Q9HC16 details
Receptors
Protein NameGene NameLocusUniprot IDDetails
Thymidine phosphorylaseTYMP22q13.33P19971 details
Cytidine deaminaseCDA1p36.2-p35P32320 details
Transcriptional FactorsNot Available
Concentrations Data
Not Available
HMDB IDHMDB0000012
DrugBank IDDB02256
Phenol Explorer Compound IDNot Available
FoodDB IDFDB021870
KNApSAcK IDC00019697
Chemspider ID13118
KEGG Compound IDC00526
BioCyc IDDEOXYURIDINE
BiGG ID35251
Wikipedia LinkDeoxyuridine
METLIN ID5086
PubChem Compound13712
PDB IDNot Available
ChEBI ID16450
References
General ReferencesNot Available

Only showing the first 10 proteins. There are 14 proteins in total.

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Enzymes

Enzyme Details
1. AID
General function:
Involved in zinc ion binding
Specific function:
Not Available
Gene Name:
AID
Uniprot ID:
Q546Y9
Molecular weight:
23953.3
Enzyme Details
2. Purine nucleoside phosphorylase
General function:
Involved in purine-nucleoside phosphorylase activity
Specific function:
The purine nucleoside phosphorylases catalyze the phosphorolytic breakdown of the N-glycosidic bond in the beta-(deoxy)ribonucleoside molecules, with the formation of the corresponding free purine bases and pentose-1-phosphate.
Gene Name:
PNP
Uniprot ID:
P00491
Molecular weight:
32117.69
Enzyme Details
3. Thymidine kinase, cytosolic
General function:
Nucleotide transport and metabolism
Specific function:
Not Available
Gene Name:
TK1
Uniprot ID:
P04183
Molecular weight:
25468.455
Enzyme Details
4. Thymidine kinase 2, mitochondrial
General function:
Involved in ATP binding
Specific function:
Deoxyribonucleoside kinase that phosphorylates thymidine, deoxycytidine, and deoxyuridine. Also phosphorylates anti-viral and anti-cancer nucleoside analogs.
Gene Name:
TK2
Uniprot ID:
O00142
Molecular weight:
27561.495
Enzyme Details
5. Thymidine phosphorylase
General function:
Involved in transferase activity, transferring glycosyl groups
Specific function:
May have a role in maintaining the integrity of the blood vessels. Has growth promoting activity on endothelial cells, angiogenic activity in vivo and chemotactic activity on endothelial cells in vitro. Catalyzes the reversible phosphorolysis of thymidine. The produced molecules are then utilized as carbon and energy sources or in the rescue of pyrimidine bases for nucleotide synthesis.
Gene Name:
TYMP
Uniprot ID:
P19971
Molecular weight:
49954.965
Enzyme Details
6. 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:
CDA
Uniprot ID:
P32320
Molecular weight:
16184.545
Enzyme Details
7. Uridine-cytidine kinase-like 1
General function:
Involved in ATP binding
Specific function:
May contribute to UTP accumulation needed for blast transformation and proliferation.
Gene Name:
UCKL1
Uniprot ID:
Q9NWZ5
Molecular weight:
59465.77
Enzyme Details
8. Thymidine kinase
General function:
Involved in ATP binding
Specific function:
Not Available
Gene Name:
Not Available
Uniprot ID:
Q8IZR3
Molecular weight:
35439.6

Only showing the first 10 proteins. There are 14 proteins in total.

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