Bovine Metabolome Database: Showing metabocard for Deoxyuridine (BMDB0000012)

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Identification Taxonomy Physical properties Pathways Spectra Concentrations Links References enzymes (1) Show 1 protein XML

Record Information

Version

1.0

Creation Date

2016-09-30 22:18:25 UTC

Update Date

2020-05-21 16:29:01 UTC

BMDB ID

BMDB0000012

Secondary Accession Numbers

BMDB00012

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. Deoxyuridine is a potentially toxic compound.

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

Endogenous

Biofunction

Not Available

Application

Not Available

Cellular locations

Mitochondria
Nucleus

Physical Properties

State

Solid

Experimental Properties

Property	Value	Reference
Melting Point	167 °C	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	Not Available	Not Available
LogP	-1.51	BALZARINI,JM ET AL. (1989)

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
GC-MS	GC-MS Spectrum - GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies) (Non-derivatized)	splash10-0udi-0900000000-c680f47a48626bc1de41	View in MoNA
GC-MS	GC-MS Spectrum - GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies) (Non-derivatized)	splash10-0udi-0900000000-13135426d5efdf47090c	View in MoNA
GC-MS	GC-MS Spectrum - GC-MS (3 TMS)	splash10-0v4i-2910000000-b0c82cef369c86d585bc	View in MoNA
GC-MS	GC-MS Spectrum - GC-MS (3 TMS)	splash10-0udi-2900000000-c2cdba9e46defe05a225	View in MoNA
GC-MS	GC-MS Spectrum - GC-EI-TOF (Non-derivatized)	splash10-0udi-0900000000-c680f47a48626bc1de41	View in MoNA
GC-MS	GC-MS Spectrum - GC-EI-TOF (Non-derivatized)	splash10-0udi-0900000000-13135426d5efdf47090c	View in MoNA
GC-MS	GC-MS Spectrum - GC-MS (Non-derivatized)	splash10-0v4i-2910000000-b0c82cef369c86d585bc	View in MoNA
GC-MS	GC-MS Spectrum - GC-MS (Non-derivatized)	splash10-0udi-2900000000-c2cdba9e46defe05a225	View in MoNA
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	splash10-01r7-9610000000-dfaab249ec8e9361b4bf	View in MoNA
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (2 TMS) - 70eV, Positive	splash10-0g06-9621000000-32e72b8293f4e226223b	View in MoNA
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_1) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_2) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_3) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_2) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_3) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_1_1) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_1_2) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_1_3) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_2_1) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_2_2) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_2_3) - 70eV, Positive	Not Available	View in JSpectraViewer
LC-MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 10V, Positive (Annotated)	splash10-03di-1900000000-6610506190427bbb3b6c	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 25V, Positive (Annotated)	splash10-03di-9800000000-af237f79161aa13a5893	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 40V, Positive (Annotated)	splash10-022d-9100000000-a06cdd7ea870d049c8a9	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - Linear Ion Trap , negative	splash10-001r-0900000000-87d0da98372c9c5a167a	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - Linear Ion Trap , negative	splash10-001r-0900000000-795c89de7cd09998501c	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - Linear Ion Trap , negative	splash10-03di-0910000000-0f40c1aaec53591fe03d	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - Linear Ion Trap , negative	splash10-03di-0900000000-35312c7170aff90afa68	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - Linear Ion Trap , negative	splash10-004i-0090000000-dd791cff5aab8928952f	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - Linear Ion Trap , negative	splash10-004i-0090000000-e5c282f6027560386d07	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - , negative	splash10-001l-5900000000-4660ec5181499087824f	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - Linear Ion Trap , positive	splash10-001i-0910000000-8cef8299b80deeefe1ae	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - Linear Ion Trap , positive	splash10-001i-0900000000-043d88b7ac473889f319	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - 20V, Negative	splash10-0006-9100000000-5731c423bed1902e4aa1	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - 10V, Negative	splash10-000x-9820000000-29ea64a90c8736117d03	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - 40V, Positive	splash10-006t-9400000000-edbb071fcbfdfc740d5c	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - 10V, Positive	splash10-03di-2910000000-76f9f11531932d11318e	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - 20V, Positive	splash10-03di-4900000000-996ec7312bb565deb6f8	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - 35V, Negative	splash10-001i-0900000000-45855a2f2673a9e095e8	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - 40V, Positive	splash10-006w-9100000000-75bb83f5ee43bb79add3	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-03di-1900000000-4e3e387ebbab12abe1fd	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-03di-5900000000-e483c01cc3a2bd6439c1	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-03di-9800000000-e0e5bb84af10a0c46b95	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-0036-8960000000-f6a195e38452cd824d19	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-000f-7910000000-8de672c701d38c2dd5d3	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-00kf-9100000000-6e86ecc024dbcde80d90	View in MoNA
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, experimental)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
2D NMR	[¹H, ¹³C]-HSQC NMR Spectrum (2D, 600 MHz, H₂O, experimental)	Not Available	View in JSpectraViewer

Biological Properties

Cellular Locations

Mitochondria
Nucleus

Biospecimen Locations

Bladder
Bone Marrow
Fibroblasts
Intestine
Leukocyte
Neuron
Pancreas
Placenta
Prostate Tissue
Ruminal Fluid
Skeletal Muscle
Testis

Pathways

Name	SMPDB/Pathwhiz	KEGG
Pyrimidine Metabolism		Not Available

Normal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Bladder	Expected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	Not Applicable	details
Bone Marrow	Expected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	Not Applicable	details
Fibroblasts	Expected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	Not Applicable	details
Intestine	Expected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	Not Applicable	details
Leukocyte	Expected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	Not Applicable	details
Neuron	Expected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	Not Applicable	details
Pancreas	Expected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	Not Applicable	details
Placenta	Expected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	Not Applicable	details
Prostate Tissue	Expected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	Not Applicable	details
Ruminal Fluid	Detected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	PMID: 25599412	details
Skeletal Muscle	Expected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	Not Applicable	details
Testis	Expected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	Not Applicable	details