Livestock Metabolome Database: Showing metabocard for Thymine (LMDB00121)

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

Record Information

Version

1.0

Creation Date

2016-07-13 19:42:49 UTC

Update Date

2016-07-20 20:50:53 UTC

Lmdb

LMDB00121

Secondary Accession Numbers

None

Metabolite Identification

Common Name

Thymine

Description

Thymine, also known as 5-methyluracil, belongs to the class of organic compounds known as hydroxypyrimidines. These are organic compounds containing a hydroxyl group attached to a pyrimidine ring. Pyrimidine is a 6-membered ring consisting of four carbon atoms and two nitrogen centers at the 1- and 3- ring positions. Thymine is an extremely weak basic (essentially neutral) compound (based on its pKa). Thymine exists in all living species, ranging from bacteria to humans. Within humans, thymine participates in a number of enzymatic reactions. In particular, thymine and deoxyribose 1-phosphate can be biosynthesized from thymidine through its interaction with the enzyme thymidine phosphorylase. In addition, thymine can be converted into dihydrothymine; which is mediated by the enzyme dihydropyrimidine dehydrogenase [nadp(+)]. A pyrimidine nucleobase that is uracil in which the hydrogen at position 5 is replaced by a methyl group. In humans, thymine is involved in the metabolic disorder called ump synthase deficiency (orotic aciduria). Outside of the human body, Thymine has been detected, but not quantified in, several different foods, such as peanuts, breakfast cereals, common beets, black mulberries, and winged beans. This could make thymine a potential biomarker for the consumption of these foods. Thymine is a potentially toxic compound. Thymine, with regard to humans, has been found to be associated with several diseases such as thymidine treatment, periodontal probing depth, colorectal cancer, and temporomandibular joint disorder; thymine has also been linked to the inborn metabolic disorder beta-ureidopropionase deficiency.

Structure

MOL SDF PDB SMILES InChI

Synonyms

Value	Source
2,4-Dihydroxy-5-methylpyrimidine	ChEBI
5-Methyl-2,4(1H,3H)-pyrimidinedione	ChEBI
5-Methylpyrimidine-2,4(1H,3H)-dione	ChEBI
5-Methyluracil	ChEBI
T	ChEBI
Thy	ChEBI
Thymin	ChEBI
4-Hydroxy-5-methylpyrimidin-2(1H)-one	HMDB
5-Methyl-1,2,3,4-tetrahydropyrimidine-2,4-dione	HMDB
5-Methyl-2,4-dihydroxypyrimidine	HMDB
5-Methylpyrimidine-2,4-dione	HMDB
5 Methyluracil	HMDB

Chemical Formula

C₅H₆N₂O₂

Average Molecular Weight

126.1133

Monoisotopic Molecular Weight

126.042927446

IUPAC Name

5-methyl-1,2,3,4-tetrahydropyrimidine-2,4-dione

Traditional Name

thymine

CAS Registry Number

65-71-4

SMILES

CC1=CNC(=O)NC1=O

InChI Identifier

InChI=1S/C5H6N2O2/c1-3-2-6-5(9)7-4(3)8/h2H,1H3,(H2,6,7,8,9)

InChI Key

RWQNBRDOKXIBIV-UHFFFAOYSA-N

Chemical Taxonomy

Description

belongs to the class of organic compounds known as hydroxypyrimidines. These are organic compounds containing a hydroxyl group attached to a pyrimidine ring. Pyrimidine is a 6-membered ring consisting of four carbon atoms and two nitrogen centers at the 1- and 3- ring positions.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Diazines

Sub Class

Pyrimidines and pyrimidine derivatives

Direct Parent

Hydroxypyrimidines

Alternative Parents

Substituents

Hydroxypyrimidine
Heteroaromatic compound
Azacycle
Organic nitrogen compound
Organic oxygen compound
Organopnictogen compound
Hydrocarbon derivative
Organooxygen compound
Organonitrogen compound
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

pyrimidone (CHEBI:17821 )
pyrimidine nucleobase (CHEBI:17821 )
pyrimidines (C00178 )
a pyrimidine-related compound (THYMINE )
a pyrimidine base (THYMINE )

Ontology

Status

Detected and 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	-0.99	ALOGPS
logP	-0.46	ChemAxon
logS	-1.1	ALOGPS
pKa (Strongest Acidic)	9.06	ChemAxon
pKa (Strongest Basic)	-5	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	2	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	58.2 Å²	ChemAxon
Rotatable Bond Count	0	ChemAxon
Refractivity	30.33 m³·mol⁻¹	ChemAxon
Polarizability	11.42 Å³	ChemAxon
Number of Rings	1	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) (2 TMS)	splash10-0bt9-0960000000-50722d1f64f22b69e207	Spectrum
GC-MS	GC-MS Spectrum - GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies) (Non-derivatized)	splash10-0bta-0940000000-ff59d40c1a93e04954ab	Spectrum
GC-MS	GC-MS Spectrum - GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies) (2 TMS)	splash10-05fr-7940000000-a0ebb190eba32aceac56	Spectrum
GC-MS	GC-MS Spectrum - GC-MS (2 TMS)	splash10-0ab9-1980000000-5b95ad97f31d8176a0c6	Spectrum
GC-MS	GC-MS Spectrum - EI-B (Non-derivatized)	splash10-004i-9500000000-74b6d7909610070d30d0	Spectrum
GC-MS	GC-MS Spectrum - GC-EI-TOF (Non-derivatized)	splash10-0bt9-0960000000-50722d1f64f22b69e207	Spectrum
GC-MS	GC-MS Spectrum - GC-EI-TOF (Non-derivatized)	splash10-0bta-0940000000-ff59d40c1a93e04954ab	Spectrum
GC-MS	GC-MS Spectrum - GC-EI-TOF (Non-derivatized)	splash10-05fr-7940000000-a0ebb190eba32aceac56	Spectrum
GC-MS	GC-MS Spectrum - GC-MS (Non-derivatized)	splash10-0ab9-1980000000-5b95ad97f31d8176a0c6	Spectrum
GC-MS	GC-MS Spectrum - GC-EI-TOF (Non-derivatized)	splash10-0bta-0930000000-a2d3bc738d3f9e60aeb7	Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	splash10-004i-9500000000-33bb743c9a1a77fe4e47	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 (Non-derivatized) - 70eV, Positive	Not Available	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 10V, Negative	splash10-004i-9100000000-1e96fdb2525aace8b29d	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 20V, Negative	splash10-0a6r-9000000000-34edf89b8a99493ed897	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 30V, Negative	splash10-0a4i-9000000000-7d381bc0d559ed8150e9	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 40V, Negative	splash10-0a4i-9000000000-90f8edce6ae2b6f83347	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 50V, Negative	splash10-0a4l-9000000000-445d07aed275008cfe2d	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QTOF (UPLC Q-Tof Premier, Waters) , Negative	splash10-004i-0900000000-deb5e6830bc01a0c870e	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ , negative	splash10-004i-9100000000-1e96fdb2525aace8b29d	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ , negative	splash10-0a6r-9000000000-34edf89b8a99493ed897	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ , negative	splash10-0a4i-9000000000-fbf8dadffeee1dead341	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ , negative	splash10-0a4i-9000000000-0ee2bab9c37212ccf44e	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ , negative	splash10-0a4l-9000000000-599b8dcd618a9b96df4b	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QTOF , negative	splash10-004i-0900000000-deb5e6830bc01a0c870e	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - 40V, Negative	splash10-0006-9000000000-97236a7217f3f91298c3	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - 10V, Negative	splash10-0006-9200000000-5e679d49ba14eea7448e	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - 20V, Negative	splash10-0006-9000000000-90b5a25f7c3ef33245ba	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 10V, Positive (Annotated)	splash10-004i-0900000000-a3779faac812139c6333	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 25V, Positive (Annotated)	splash10-004i-0900000000-a3779faac812139c6333	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 40V, Positive (Annotated)	splash10-0udi-9200000000-0e7d9466530de47896d9	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - EI-B (HITACHI M-80) , Positive	splash10-004i-9400000000-7ff00d5a94e12e6e1701	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 10V, Positive	splash10-056r-8900000000-96370e30b48d3270abaa	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 20V, Positive	splash10-0bwc-9600000000-b988fb9252c409b19c33	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 30V, Positive	splash10-01q9-9100000000-8c82d68e9ec8594b1fff	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 40V, Positive	splash10-001i-9000000000-f69c5d963b845f8b3cfb	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 50V, Positive	splash10-0a4i-0900000000-3a9af2cf67d3f113fa7f	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QTOF (UPLC Q-Tof Premier, Waters) , Positive	splash10-004i-0900000000-97549ff58b84351d860c	Spectrum
MS	Mass Spectrum (Electron Ionization)	splash10-056r-9400000000-5dd0bc0194a302d8ee95	Spectrum
1D NMR	13C NMR Spectrum	Not Available	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	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
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

Biological Properties

Cellular Locations

Not Available

Biofluid Locations and Tissue Locations

Milk
Ruminal Fluid

Concentrations

Biofluid	Status	Value	Condition	Species	Reference	Details
Milk	Detected but not Quantified	Not Applicable	Not Available	Bovine	23438684	details
Ruminal Fluid	Detected but not Quantified	Not Applicable	Not Available	Bovine	Fozia Saleem, Sou...	details
Ruminal Fluid	Detected and Quantified	27 +/- 12 uM	Not Available	Bovine	Saleem F, Bouatra...	details
Ruminal Fluid	Detected and Quantified	30 +/- 14 uM	Not Available	Bovine	Saleem F, Bouatra...	details
Ruminal Fluid	Detected and Quantified	35 +/- 30 uM	Not Available	Bovine	Saleem F, Bouatra...	details
Ruminal Fluid	Detected and Quantified	40 +/- 23 uM	Not Available	Bovine	Saleem F, Bouatra...	details
Ruminal Fluid	Detected and Quantified	40 +/- 23 uM	Not Available	Bovine	Saleem F, Bouatra...	details
Ruminal Fluid	Detected but not Quantified	Not Applicable	Not Available	Bovine	25599412	details
Ruminal Fluid	Detected and Quantified	26.3 uM	Not Available	Bovine	22959937	details
Ruminal Fluid	Detected and Quantified	30.1 uM	Not Available	Bovine	22959937	details
Ruminal Fluid	Detected and Quantified	30.2 uM	Not Available	Bovine	22959937	details
Ruminal Fluid	Detected and Quantified	39.7 uM	Not Available	Bovine	22959937	details