ContaminantDB: Deoxyuridine

Identification Taxonomy Biological Properties Physical Properties Toxicity Profile Spectra Concentrations Links References Targets (4)XML

Record Information

Version

1.0

Creation Date

2014-08-29 06:51:15 UTC

Update Date

2026-05-14 17:32:33 UTC

Accession Number

CHEM003391

Identification

Common Name

Deoxyuridine

Class

Small Molecule

Description

2'-Deoxyuridine is a naturally occurring nucleoside. It is similar in chemical structure to uridine, but without the 2'-hydroxyl group. It is considered to be an antimetabolite that is converted to deoxyuridine triphosphate during DNA synthesis. Laboratory suppression of deoxyuridine is used to diagnose megaloblastic anemia due to vitamin B12 and folate deficiencies.

Contaminant Sources

FooDB Chemicals
HMDB Contaminants - Urine
T3DB toxins

Contaminant Type

Amine
Animal Toxin
Ether
Food Toxin
Metabolite
Natural Compound
Organic Compound

Chemical 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 Mass

228.202 g/mol

Monoisotopic Mass

228.075 g/mol

CAS Registry Number

951-78-0

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

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 )

Biological Properties

Status

Detected and Not Quantified

Origin

Endogenous

Cellular Locations

Cytoplasm
Extracellular
Mitochondria
Nucleus

Biofluid Locations

Not Available

Tissue Locations

Bladder
Bone Marrow
Fibroblasts
Intestine
Lymphocyte
Most Tissues
Muscle
Neuron
Pancreas
Placenta
Prostate
Testes

Pathways

Name	SMPDB Link	KEGG Link
Pyrimidine Metabolism	SMP00046	map00240
MNGIE (Mitochondrial Neurogastrointestinal Encephalopathy)	SMP00202	Not Available

Applications

Not Available

Biological Roles

Chemical Roles

Not Available

Physical Properties

State

Solid

Appearance

White powder.

Experimental Properties

Property	Value
Melting Point	167°C
Boiling Point	Not Available
Solubility	Not Available

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	1	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	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

Toxicity Profile

Route of Exposure

Not Available

Mechanism of Toxicity

Not Available

Metabolism

Not Available

Toxicity Values

Not Available

Lethal Dose

Not Available

Carcinogenicity (IARC Classification)

No indication of carcinogenicity to humans (not listed by IARC).

Uses/Sources

This is an endogenously produced metabolite found in the human body. It is used in metabolic reactions, catabolic reactions or waste generation.

Minimum Risk Level

Not Available

Health Effects

Not Available

Symptoms

Not Available

Treatment

Not Available

Concentrations

Not Available

External Links

DrugBank ID

DB02256

HMDB ID

HMDB0000012

FooDB ID

FDB021870

Phenol Explorer ID

Not Available

KNApSAcK ID

BiGG ID

BioCyc ID

METLIN ID

PDB ID

Not Available

Wikipedia Link

Chemspider ID

ChEBI ID

PubChem Compound ID

Kegg Compound ID

YMDB ID

Not Available

ECMDB ID

ECMDB00012

References

Synthesis Reference

Kenzo Watanabe, Yoshinori Kato, Masahiko Saito, Takeo Oba, Hisashi Fukushima, Takeshi Hara, “5-fluoro-2’-deoxyuridine derivatives and a process for the preparation thereof.” U.S. Patent US4605645, issued May, 1984.

MSDS

Link

General References

1. Huang, Haoqiang; Chu, Chung K. A practical synthesis of 2'-deoxyuridine from uridine. Synthetic Communications (1990), 20(7), 1039-46.

2. Huang, Haoqiang; Chu, Chung K. A practical synthesis of 2'-deoxyuridine from uridine. Synthetic Communications (1990), 20(7), 1039-46.

3. Li KM, Rivory LP, Clarke SJ: Rapid quantitation of plasma 2'-deoxyuridine by high-performance liquid chromatography/atmospheric pressure chemical ionization mass spectrometry and its application to pharmacodynamic studies in cancer patients. J Chromatogr B Analyt Technol Biomed Life Sci. 2005 Jun 5;820(1):121-30. Epub 2005 Apr 19.

4. Di Stefano G, Busi C, Derenzini M, Trere D, Fiume L: Conjugation of 5-fluoro-2'-deoxyuridine with lactosaminated poly-l-lysine to reduce extrahepatic toxicity in the treatment of hepatocarcinomas. Ital J Gastroenterol Hepatol. 1998 Apr;30(2):173-7.

5. Reidy JA: Deoxyuridine increases folate-sensitive fragile site expression in human lymphocytes. Am J Med Genet. 1987 Jan;26(1):1-5.

6. Eells JT, Spector R: Purine and pyrimidine base and nucleoside concentrations in human cerebrospinal fluid and plasma. Neurochem Res. 1983 Nov;8(11):1451-7.

7. Huong PL, Kolk AH, Eggelte TA, Verstijnen CP, Gilis H, Hendriks JT: Measurement of antigen specific lymphocyte proliferation using 5-bromo-deoxyuridine incorporation. An easy and low cost alternative to radioactive thymidine incorporation. J Immunol Methods. 1991 Jul 5;140(2):243-8.

8. Kanazawa S, Herbert V: Detection of folate deficiency in alcoholism using the peripheral blood lymphocyte deoxyuridine suppression test. J Nutr Sci Vitaminol (Tokyo). 1986 Jun;32(3):251-7.

9. Zittoun J, Zittoun R: Modern clinical testing strategies in cobalamin and folate deficiency. Semin Hematol. 1999 Jan;36(1):35-46.