Bovine Metabolome Database: Showing metabocard for Thymine (BMDB0000262)

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 22:27:34 UTC

Update Date

2020-06-04 20:48:21 UTC

BMDB ID

BMDB0000262

Secondary Accession Numbers

BMDB00262

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 exists as a solid, possibly soluble (in water), and an extremely weak basic (essentially neutral) compound (based on its pKa) molecule. Thymine exists in all living species, ranging from bacteria to humans. Thymine is a potentially toxic compound. Thymine has been found to be associated with several diseases known as colorectal cancer, thymidine treatment, and temporomandibular joint disorder; also thymine has been linked to the inborn metabolic disorders including dihydropyrimidine dehydrogenase 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

Endogenous

Biofunction

Not Available

Application

Not Available

Cellular locations

Not Available

Physical Properties

State

Solid

Experimental Properties

Property	Value	Reference
Melting Point	320 °C	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	3.82 mg/mL	YALKOWSKY,SH & DANNENFELSER,RM (1992)
LogP	-0.62	HANSCH,C ET AL. (1995)

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
GC-MS	GC-MS Spectrum - GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies) (2 TMS)	splash10-0bt9-0960000000-50722d1f64f22b69e207	View in MoNA
GC-MS	GC-MS Spectrum - GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies) (Non-derivatized)	splash10-0bta-0940000000-ff59d40c1a93e04954ab	View in MoNA
GC-MS	GC-MS Spectrum - GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies) (2 TMS)	splash10-05fr-7940000000-a0ebb190eba32aceac56	View in MoNA
GC-MS	GC-MS Spectrum - GC-MS (2 TMS)	splash10-0ab9-1980000000-5b95ad97f31d8176a0c6	View in MoNA
GC-MS	GC-MS Spectrum - EI-B (Non-derivatized)	splash10-004i-9500000000-74b6d7909610070d30d0	View in MoNA
GC-MS	GC-MS Spectrum - GC-EI-TOF (Non-derivatized)	splash10-0bt9-0960000000-50722d1f64f22b69e207	View in MoNA
GC-MS	GC-MS Spectrum - GC-EI-TOF (Non-derivatized)	splash10-0bta-0940000000-ff59d40c1a93e04954ab	View in MoNA
GC-MS	GC-MS Spectrum - GC-EI-TOF (Non-derivatized)	splash10-05fr-7940000000-a0ebb190eba32aceac56	View in MoNA
GC-MS	GC-MS Spectrum - GC-MS (Non-derivatized)	splash10-0ab9-1980000000-5b95ad97f31d8176a0c6	View in MoNA
GC-MS	GC-MS Spectrum - GC-EI-TOF (Non-derivatized)	splash10-0bta-0930000000-a2d3bc738d3f9e60aeb7	View in MoNA
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	splash10-004i-9500000000-33bb743c9a1a77fe4e47	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 (Non-derivatized) - 70eV, Positive	Not Available	View in JSpectraViewer
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 10V, Negative	splash10-004i-9100000000-1e96fdb2525aace8b29d	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 20V, Negative	splash10-0a6r-9000000000-34edf89b8a99493ed897	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 30V, Negative	splash10-0a4i-9000000000-7d381bc0d559ed8150e9	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 40V, Negative	splash10-0a4i-9000000000-90f8edce6ae2b6f83347	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 50V, Negative	splash10-0a4l-9000000000-445d07aed275008cfe2d	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QTOF (UPLC Q-Tof Premier, Waters) , Negative	splash10-004i-0900000000-deb5e6830bc01a0c870e	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ , negative	splash10-004i-9100000000-1e96fdb2525aace8b29d	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ , negative	splash10-0a6r-9000000000-34edf89b8a99493ed897	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ , negative	splash10-0a4i-9000000000-fbf8dadffeee1dead341	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ , negative	splash10-0a4i-9000000000-0ee2bab9c37212ccf44e	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ , negative	splash10-0a4l-9000000000-599b8dcd618a9b96df4b	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QTOF , negative	splash10-004i-0900000000-deb5e6830bc01a0c870e	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - 40V, Negative	splash10-0006-9000000000-97236a7217f3f91298c3	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - 10V, Negative	splash10-0006-9200000000-5e679d49ba14eea7448e	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - 20V, Negative	splash10-0006-9000000000-90b5a25f7c3ef33245ba	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 10V, Positive (Annotated)	splash10-004i-0900000000-a3779faac812139c6333	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 25V, Positive (Annotated)	splash10-004i-0900000000-a3779faac812139c6333	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 40V, Positive (Annotated)	splash10-0udi-9200000000-0e7d9466530de47896d9	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - EI-B (HITACHI M-80) , Positive	splash10-004i-9400000000-7ff00d5a94e12e6e1701	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 10V, Positive	splash10-056r-8900000000-96370e30b48d3270abaa	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 20V, Positive	splash10-0bwc-9600000000-b988fb9252c409b19c33	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 30V, Positive	splash10-01q9-9100000000-8c82d68e9ec8594b1fff	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 40V, Positive	splash10-001i-9000000000-f69c5d963b845f8b3cfb	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 50V, Positive	splash10-0a4i-0900000000-3a9af2cf67d3f113fa7f	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QTOF (UPLC Q-Tof Premier, Waters) , Positive	splash10-004i-0900000000-97549ff58b84351d860c	View in MoNA
MS	Mass Spectrum (Electron Ionization)	splash10-056r-9400000000-5dd0bc0194a302d8ee95	View in MoNA
1D NMR	¹³C NMR Spectrum (1D, 125 MHz, H₂O, experimental)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, experimental)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 400 MHz, DMSO-d6, experimental)	Not Available	View in JSpectraViewer
1D NMR	¹³C NMR Spectrum (1D, 22.53 MHz, DMSO-d6, experimental)	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, 100 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, 200 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, 300 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, 400 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, 500 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, 600 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, 700 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, 800 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹³C NMR Spectrum (1D, 900 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, 1000 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, 400 MHz, H₂O, experimental)	Not Available	View in JSpectraViewer
2D NMR	[¹H, ¹³C]-HSQC NMR Spectrum (2D, 400 MHz, H₂O, experimental)	Not Available	View in JSpectraViewer

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Epidermis
Fibroblasts
Liver
Mammary Gland
Milk
Placenta
Prostate Tissue
Ruminal Fluid

Pathways

Name	SMPDB/Pathwhiz	KEGG
Pyrimidine Metabolism		Not Available

Normal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Epidermis	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
Liver	Detected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	PMID: 31873721	details
Liver	Detected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	PMID: 31873721	details
Mammary Gland	Detected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	PMID: 31873721	details
Mammary Gland	Detected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	PMID: 31873721	details
Milk	Detected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	PMID: 23438684	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 and Quantified	188 +/- 45 uM	Not Specified	Not Specified	Normal	Aidin Foroutan, C...	details
Ruminal Fluid	Detected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	PMID: 25599412	details
Ruminal Fluid	Detected and Quantified	26.3 uM	Not Specified	Not Specified	Normal	PMID: 22959937	details
Ruminal Fluid	Detected and Quantified	30.1 uM	Not Specified	Not Specified	Normal	PMID: 22959937	details
Ruminal Fluid	Detected and Quantified	30.2 uM	Not Specified	Not Specified	Normal	PMID: 22959937	details
Ruminal Fluid	Detected and Quantified	39.7 uM	Not Specified	Not Specified	Normal	PMID: 22959937	details
Ruminal Fluid	Detected and Quantified	27 +/- 12 uM	Not Specified	Not Specified	Normal	Fozia Saleem, Sou...	details
Ruminal Fluid	Detected and Quantified	30 +/- 14 uM	Not Specified	Not Specified	Normal	Fozia Saleem, Sou...	details
Ruminal Fluid	Detected and Quantified	35 +/- 30 uM	Not Specified	Not Specified	Normal	Fozia Saleem, Sou...	details
Ruminal Fluid	Detected and Quantified	40 +/- 23 uM	Not Specified	Not Specified	Normal	Fozia Saleem, Sou...	details
Ruminal Fluid	Detected and Quantified	40 +/- 23 uM	Not Specified	Not Specified	Normal	Fozia Saleem, Sou...	details
Ruminal Fluid	Detected and Quantified	39.78 +/- 46.65 uM	Not Specified	Not Specified	Normal	Fozia Saleem, Sou...	details

Abnormal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Ruminal Fluid	Detected and Quantified	30.27 +/- 29.58 uM	Not Specified	Not Specified	Rumen acidosis	Fozia Saleem, Sou...	details

External Links

HMDB ID

HMDB0000262

DrugBank ID

DB03462

Phenol Explorer Compound ID

Not Available

FooDB ID

KNApSAcK ID

Chemspider ID

KEGG Compound ID

BioCyc ID

BiGG ID

Wikipedia Link

METLIN ID

PubChem Compound

PDB ID

Not Available

ChEBI ID

17821

References

Synthesis Reference

Zhang, Shi-Ying; Wu, Da-Jun; Zhang, Yan-Ping. Synthesis of thymine. Zhongguo Yiyao Gongye Zazhi (1999), 30(7), 325.

Material Safety Data Sheet (MSDS)

Not Available

General References

Melzer N, Wittenburg D, Hartwig S, Jakubowski S, Kesting U, Willmitzer L, Lisec J, Reinsch N, Repsilber D: Investigating associations between milk metabolite profiles and milk traits of Holstein cows. J Dairy Sci. 2013 Mar;96(3):1521-34. doi: 10.3168/jds.2012-5743. [PubMed:23438684 ]
Pan L, Yu J, Mi Z, Mo L, Jin H, Yao C, Ren D, Menghe B: A Metabolomics Approach Uncovers Differences between Traditional and Commercial Dairy Products in Buryatia (Russian Federation). Molecules. 2018 Mar 22;23(4). pii: molecules23040735. doi: 10.3390/molecules23040735. [PubMed:29565828 ]

Enzymes

Enzyme Details

1. Dihydropyrimidine dehydrogenase [NADP(+)]

General function:: Amino acid transport and metabolism
Specific function:: Involved in pyrimidine base degradation. Catalyzes the reduction of uracil and thymine.
Gene Name:: DPYD
Uniprot ID:: Q28007
Molecular weight:: 111697.0

Reactions

Thymine + NADP → Dihydrothymine + NADPH	details

Showing metabocard for Thymine (BMDB0000262)

Structure for BMDB0000262 (Thymine)

Enzymes

Reactions