Livestock Metabolome Database: Showing metabocard for Deoxyuridine (LMDB00004)

Identification Taxonomy Ontology Physical properties Spectra Biological properties Concentrations Links References XML

Record Information

Version

1.0

Creation Date

2016-07-13 19:22:10 UTC

Update Date

2016-07-20 20:54:12 UTC

Lmdb

LMDB00004

Secondary Accession Numbers

None

Metabolite Identification

Common Name

Deoxyuridine

Description

Deoxyuridine, 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.

Structure

MOL SDF PDB SMILES InChI

Synonyms

Value	Source
2-Deoxyuridine	ChEBI
dU	ChEBI
2'-Deoxyuridine	Kegg
1-(2-Deoxy-beta-D-erythro-pentofuranosyl)-2,4(1H,3H)-pyrimidinedione	HMDB
1-(2-Deoxy-beta-D-ribofuranosyl)-2,4(1H,3H)-pyrimidinedione	HMDB
1-(2-Deoxy-beta-delta-erythro-pentofuranosyl)-2,4(1H,3H)-pyrimidinedione	HMDB
1-(2-Deoxy-beta-delta-ribofuranosyl)-2,4(1H,3H)-pyrimidinedione	HMDB
1-(2-Deoxy-D-erythro-pentofuranosyl)uracil	HMDB
1-(2-Deoxy-delta-erythro-pentofuranosyl)uracil	HMDB
2'-Desoxyuridine	HMDB
Deoxyribose uracil	HMDB
Desoxyuridine	HMDB
Uracil deoxyriboside	HMDB
Uracil desoxyuridine	HMDB
(beta 1-(2-Deoxyribopyranosyl))thymidine	HMDB
Deoxyuridine	ChEBI

Chemical Formula

C₉H₁₂N₂O₅

Average Molecular Weight

228.202

Monoisotopic Molecular Weight

228.074621504

IUPAC Name

1-[(2R,4S,5R)-4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]-1,2,3,4-tetrahydropyrimidine-2,4-dione

Traditional Name

2'-deoxyuridine

CAS Registry Number

951-78-0

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 Key

MXHRCPNRJAMMIM-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.

Kingdom

Organic compounds

Super Class

Nucleosides, nucleotides, and analogues

Class

Pyrimidine nucleosides

Sub Class

Pyrimidine 2'-deoxyribonucleosides

Direct Parent

Pyrimidine 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 Framework

Aromatic heteromonocyclic compounds

External Descriptors

pyrimidine 2'-deoxyribonucleoside (CHEBI:16450 )
Deoxyribonucleosides (C00526 )

Ontology

Status

Detected but not Quantified

Origin

Not Available

Biofunction

Not Available

Application

Not Available

Cellular locations

Not Available

Physical Properties

State

Not Available

Experimental Properties

Property	Value	Reference
Melting Point	Not Available	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	Not Available	Not Available
LogP	Not Available	Not Available

Predicted Properties

Property	Value	Source
logP	-1.5	ALOGPS
logP	-1.5	ChemAxon
logS	-0.4	ALOGPS
pKa (Strongest Acidic)	9.71	ChemAxon
pKa (Strongest Basic)	-3	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	99.1 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	51.05 m³·mol⁻¹	ChemAxon
Polarizability	21.06 Å³	ChemAxon
Number of Rings	2	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	Yes	ChemAxon
MDDR-like Rule	Yes	ChemAxon

Spectra

Spectrum Type	Description	Splash Key	View
GC-MS	GC-MS Spectrum - GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies) (Non-derivatized)	splash10-0udi-0900000000-c680f47a48626bc1de41	Spectrum
GC-MS	GC-MS Spectrum - GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies) (Non-derivatized)	splash10-0udi-0900000000-13135426d5efdf47090c	Spectrum
GC-MS	GC-MS Spectrum - GC-MS (3 TMS)	splash10-0v4i-2910000000-b0c82cef369c86d585bc	Spectrum
GC-MS	GC-MS Spectrum - GC-MS (3 TMS)	splash10-0udi-2900000000-c2cdba9e46defe05a225	Spectrum
GC-MS	GC-MS Spectrum - GC-EI-TOF (Non-derivatized)	splash10-0udi-0900000000-c680f47a48626bc1de41	Spectrum
GC-MS	GC-MS Spectrum - GC-EI-TOF (Non-derivatized)	splash10-0udi-0900000000-13135426d5efdf47090c	Spectrum
GC-MS	GC-MS Spectrum - GC-MS (Non-derivatized)	splash10-0v4i-2910000000-b0c82cef369c86d585bc	Spectrum
GC-MS	GC-MS Spectrum - GC-MS (Non-derivatized)	splash10-0udi-2900000000-c2cdba9e46defe05a225	Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	splash10-01r7-9610000000-dfaab249ec8e9361b4bf	Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (2 TMS) - 70eV, Positive	splash10-0g06-9621000000-32e72b8293f4e226223b	Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_1) - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_2) - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_3) - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_2) - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_3) - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_1_1) - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_1_2) - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_1_3) - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_2_1) - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_2_2) - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_2_3) - 70eV, Positive	Not Available	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 10V, Positive (Annotated)	splash10-03di-1900000000-6610506190427bbb3b6c	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 25V, Positive (Annotated)	splash10-03di-9800000000-af237f79161aa13a5893	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 40V, Positive (Annotated)	splash10-022d-9100000000-a06cdd7ea870d049c8a9	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - Linear Ion Trap , negative	splash10-001r-0900000000-87d0da98372c9c5a167a	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - Linear Ion Trap , negative	splash10-001r-0900000000-795c89de7cd09998501c	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - Linear Ion Trap , negative	splash10-03di-0910000000-0f40c1aaec53591fe03d	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - Linear Ion Trap , negative	splash10-03di-0900000000-35312c7170aff90afa68	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - Linear Ion Trap , negative	splash10-004i-0090000000-dd791cff5aab8928952f	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - Linear Ion Trap , negative	splash10-004i-0090000000-e5c282f6027560386d07	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - , negative	splash10-001l-5900000000-4660ec5181499087824f	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - Linear Ion Trap , positive	splash10-001i-0910000000-8cef8299b80deeefe1ae	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - Linear Ion Trap , positive	splash10-001i-0900000000-043d88b7ac473889f319	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - 20V, Negative	splash10-0006-9100000000-5731c423bed1902e4aa1	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - 10V, Negative	splash10-000x-9820000000-29ea64a90c8736117d03	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - 40V, Positive	splash10-006t-9400000000-edbb071fcbfdfc740d5c	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - 10V, Positive	splash10-03di-2910000000-76f9f11531932d11318e	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - 20V, Positive	splash10-03di-4900000000-996ec7312bb565deb6f8	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - 35V, Negative	splash10-001i-0900000000-45855a2f2673a9e095e8	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - 40V, Positive	splash10-006w-9100000000-75bb83f5ee43bb79add3	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-03di-1900000000-4e3e387ebbab12abe1fd	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-03di-5900000000-e483c01cc3a2bd6439c1	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-03di-9800000000-e0e5bb84af10a0c46b95	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-0036-8960000000-f6a195e38452cd824d19	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-000f-7910000000-8de672c701d38c2dd5d3	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-00kf-9100000000-6e86ecc024dbcde80d90	Spectrum
1D NMR	1H NMR Spectrum	Not Available	Spectrum
1D NMR	1H NMR Spectrum	Not Available	Spectrum
1D NMR	13C NMR Spectrum	Not Available	Spectrum
1D NMR	1H NMR Spectrum	Not Available	Spectrum
1D NMR	13C NMR Spectrum	Not Available	Spectrum
1D NMR	1H NMR Spectrum	Not Available	Spectrum
1D NMR	13C NMR Spectrum	Not Available	Spectrum
1D NMR	1H NMR Spectrum	Not Available	Spectrum
1D NMR	13C NMR Spectrum	Not Available	Spectrum
1D NMR	1H NMR Spectrum	Not Available	Spectrum
1D NMR	13C NMR Spectrum	Not Available	Spectrum
1D NMR	1H NMR Spectrum	Not Available	Spectrum
1D NMR	13C NMR Spectrum	Not Available	Spectrum
1D NMR	1H NMR Spectrum	Not Available	Spectrum
1D NMR	13C NMR Spectrum	Not Available	Spectrum
1D NMR	1H NMR Spectrum	Not Available	Spectrum
1D NMR	13C NMR Spectrum	Not Available	Spectrum
1D NMR	1H NMR Spectrum	Not Available	Spectrum
1D NMR	13C NMR Spectrum	Not Available	Spectrum
1D NMR	1H NMR Spectrum	Not Available	Spectrum
1D NMR	13C NMR Spectrum	Not Available	Spectrum
2D NMR	[1H,13C] 2D NMR Spectrum	Not Available	Spectrum