Showing Compound Deoxyuridine (FDB021870)

Record Information

Version

1.0

Creation date

2011-09-21 00:04:16 UTC

Update date

2020-09-17 15:38:09 UTC

Primary ID

FDB021870

Secondary Accession Numbers

Not Available

Chemical Information

FooDB 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.

CAS Number

951-78-0

Structure

MOL SDF PDB SMILES InChI

Synonyms

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Synonym	Source
(beta 1-(2-Deoxyribopyranosyl))thymidine	HMDB
1-(2-Deoxy-beta-D-erythro-pentofuranosyl)-2,4(1H,3H)-pyrimidinedione	HMDB
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-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-erythro-pentofuranosyl)-2,4(1H,3H)-Pyrimidinedione	hmdb
1-(2-Deoxy-beta-delta-ribofuranosyl)-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

Showing 1 to 10 of 20 entries

Predicted Properties

Property	Value	Source
Water Solubility	90.6 g/L	ALOGPS
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	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Chemical Formula

C9H12N2O5

IUPAC name

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

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

Isomeric SMILES

OC[C@H]1O[C@H](C[C@@H]1O)N1C=CC(=O)NC1=O

Average Molecular Weight

228.202

Monoisotopic Molecular Weight

228.074621504

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.

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

Disposition

Route of exposure:

Enteral:

Ingestion

Source:

Biological:

Plant:

Animal

Biological location:

Role

Industrial application:

Pharmaceutical industry:

Pharmaceutical

Physico-Chemical Properties

Physico-Chemical Properties - Experimental

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Property	Value	Reference
Boiling Point	Not Available
Charge	Not Available
Density	Not Available
Experimental logP	Not Available
Experimental pKa	Not Available
Experimental Water Solubility	Not Available
Isoelectric point	Not Available
Mass Composition	Not Available
Melting Point	Not Available
Optical Rotation	Not Available

Showing 1 to 10 of 14 entries

Spectra

EI-MS/GC-MS

Type	Description	Splash Key	View
GC-MS	Deoxyuridine, non-derivatized, GC-MS Spectrum	splash10-0udi-0900000000-c680f47a48626bc1de41	Spectrum
GC-MS	Deoxyuridine, non-derivatized, GC-MS Spectrum	splash10-0udi-0900000000-13135426d5efdf47090c	Spectrum
GC-MS	Deoxyuridine, 3 TMS, GC-MS Spectrum	splash10-0v4i-2910000000-b0c82cef369c86d585bc	Spectrum
GC-MS	Deoxyuridine, 3 TMS, GC-MS Spectrum	splash10-0udi-2900000000-c2cdba9e46defe05a225	Spectrum
GC-MS	Deoxyuridine, non-derivatized, GC-MS Spectrum	splash10-0udi-0900000000-c680f47a48626bc1de41	Spectrum
GC-MS	Deoxyuridine, non-derivatized, GC-MS Spectrum	splash10-0udi-0900000000-13135426d5efdf47090c	Spectrum
GC-MS	Deoxyuridine, non-derivatized, GC-MS Spectrum	splash10-0v4i-2910000000-b0c82cef369c86d585bc	Spectrum
GC-MS	Deoxyuridine, non-derivatized, GC-MS Spectrum	splash10-0udi-2900000000-c2cdba9e46defe05a225	Spectrum
Predicted GC-MS	Deoxyuridine, non-derivatized, Predicted GC-MS Spectrum - 70eV, Positive	splash10-01r7-9610000000-dfaab249ec8e9361b4bf	Spectrum
Predicted GC-MS	Deoxyuridine, 2 TMS, Predicted GC-MS Spectrum - 70eV, Positive	splash10-0g06-9621000000-32e72b8293f4e226223b	Spectrum
Predicted GC-MS	Deoxyuridine, non-derivatized, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Deoxyuridine, TMS_1_1, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Deoxyuridine, TMS_1_2, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Deoxyuridine, TMS_1_3, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Deoxyuridine, TMS_2_2, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Deoxyuridine, TMS_2_3, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Deoxyuridine, TBDMS_1_1, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Deoxyuridine, TBDMS_1_2, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Deoxyuridine, TBDMS_1_3, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Deoxyuridine, TBDMS_2_1, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Deoxyuridine, TBDMS_2_2, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Deoxyuridine, TBDMS_2_3, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum

MS/MS

Type	Description	Splash Key	View
MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 10V, Positive (Annotated)	splash10-03di-1900000000-6610506190427bbb3b6c	2012-07-24	View Spectrum
MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 25V, Positive (Annotated)	splash10-03di-9800000000-af237f79161aa13a5893	2012-07-24	View Spectrum
MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 40V, Positive (Annotated)	splash10-022d-9100000000-a06cdd7ea870d049c8a9	2012-07-24	View Spectrum
MS/MS	LC-MS/MS Spectrum - Linear Ion Trap , negative	splash10-001r-0900000000-87d0da98372c9c5a167a	2017-09-14	View Spectrum
MS/MS	LC-MS/MS Spectrum - Linear Ion Trap , negative	splash10-001r-0900000000-795c89de7cd09998501c	2017-09-14	View Spectrum
MS/MS	LC-MS/MS Spectrum - Linear Ion Trap , negative	splash10-03di-0910000000-0f40c1aaec53591fe03d	2017-09-14	View Spectrum
MS/MS	LC-MS/MS Spectrum - Linear Ion Trap , negative	splash10-03di-0900000000-35312c7170aff90afa68	2017-09-14	View Spectrum
MS/MS	LC-MS/MS Spectrum - Linear Ion Trap , negative	splash10-004i-0090000000-dd791cff5aab8928952f	2017-09-14	View Spectrum
MS/MS	LC-MS/MS Spectrum - Linear Ion Trap , negative	splash10-004i-0090000000-e5c282f6027560386d07	2017-09-14	View Spectrum
MS/MS	LC-MS/MS Spectrum - , negative	splash10-001l-5900000000-4660ec5181499087824f	2017-09-14	View Spectrum
MS/MS	LC-MS/MS Spectrum - Linear Ion Trap , positive	splash10-001i-0910000000-8cef8299b80deeefe1ae	2017-09-14	View Spectrum
MS/MS	LC-MS/MS Spectrum - Linear Ion Trap , positive	splash10-001i-0900000000-043d88b7ac473889f319	2017-09-14	View Spectrum
MS/MS	LC-MS/MS Spectrum - 20V, Negative	splash10-0006-9100000000-5731c423bed1902e4aa1	2021-09-20	View Spectrum
MS/MS	LC-MS/MS Spectrum - 10V, Negative	splash10-000x-9820000000-29ea64a90c8736117d03	2021-09-20	View Spectrum
MS/MS	LC-MS/MS Spectrum - 40V, Positive	splash10-006t-9400000000-edbb071fcbfdfc740d5c	2021-09-20	View Spectrum
MS/MS	LC-MS/MS Spectrum - 10V, Positive	splash10-03di-2910000000-76f9f11531932d11318e	2021-09-20	View Spectrum
MS/MS	LC-MS/MS Spectrum - 20V, Positive	splash10-03di-4900000000-996ec7312bb565deb6f8	2021-09-20	View Spectrum
MS/MS	LC-MS/MS Spectrum - 35V, Negative	splash10-001i-0900000000-45855a2f2673a9e095e8	2021-09-20	View Spectrum
MS/MS	LC-MS/MS Spectrum - 40V, Positive	splash10-006w-9100000000-75bb83f5ee43bb79add3	2021-09-20	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-03di-1900000000-4e3e387ebbab12abe1fd	2017-07-25	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-03di-5900000000-e483c01cc3a2bd6439c1	2017-07-25	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-03di-9800000000-e0e5bb84af10a0c46b95	2017-07-25	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-0036-8960000000-f6a195e38452cd824d19	2017-07-26	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-000f-7910000000-8de672c701d38c2dd5d3	2017-07-26	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-00kf-9100000000-6e86ecc024dbcde80d90	2017-07-26	View Spectrum

NMR

Type	Description	View
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, experimental)	Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	Spectrum
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, D₂O, predicted)	Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	Spectrum
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, D₂O, predicted)	Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	Spectrum
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, D₂O, predicted)	Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, D₂O, predicted)	Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	Spectrum
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, predicted)	Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	Spectrum
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, D₂O, predicted)	Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	Spectrum
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, D₂O, predicted)	Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	Spectrum
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, D₂O, predicted)	Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, predicted)	Spectrum
2D NMR	[¹H, ¹³C]-HSQC NMR Spectrum (2D, 600 MHz, H₂O, experimental)	Spectrum

External Links

ChemSpider ID

ChEMBL ID

KEGG Compound ID

Pubchem Compound ID

Pubchem Substance ID

Not Available

ChEBI ID

16450

Phenol-Explorer ID

Not Available

DrugBank ID

Not Available

HMDB ID

HMDB00012

CRC / DFC (Dictionary of Food Compounds) ID

Not Available

EAFUS ID

Not Available

Dr. Duke ID

Not Available

BIGG ID

35251

KNApSAcK ID

Not Available

HET ID

DUR

Food Biomarker Ontology

Not Available

VMH ID

Not Available

Flavornet ID

Not Available

GoodScent ID

Not Available

SuperScent ID

Not Available

Wikipedia ID

Deoxyuridine

Phenol-Explorer Metabolite ID

Not Available

Duplicate IDS

Not Available

Old DFC IDS

Not Available

Associated Foods

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Food	Content Range	Average	Reference

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Biological Effects and Interactions

Health Effects / Bioactivities

Not Available

Enzymes

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Name	Gene Name	UniProt ID
AID	AID	Q546Y9
Purine nucleoside phosphorylase	PNP	P00491
Thymidine kinase 2, mitochondrial	TK2	O00142
Thymidine kinase, cytosolic	TK1	P04183
Thymidine phosphorylase	TYMP	P19971
Uridine-cytidine kinase-like 1	UCKL1	Q9NWZ5