Milk Composition Database: Showing metabocard for Dihydrothymine (BMDB0000079)

Identification Taxonomy Physical properties Spectra Concentrations Links References XML

Record Information

Version

1.0

Creation Date

2016-09-30 22:19:24 UTC

Update Date

2020-05-21 16:29:01 UTC

MCDB ID

BMDB0000079

Secondary Accession Numbers

BMDB00079

Metabolite Identification

Common Name

Dihydrothymine

Description

Dihydrothymine belongs to the class of organic compounds known as hydropyrimidines. Hydropyrimidines are compounds containing a hydrogenated pyrimidine ring (i.e. containing less than the maximum number of double bonds.). Dihydrothymine is possibly soluble (in water) and an extremely weak basic (essentially neutral) compound (based on its pKa). Dihydrothymine exists in all living organisms, ranging from bacteria to humans. Dihydrothymine is a potentially toxic compound.

Structure

MOL SDF PDB SMILES InChI

Synonyms

Value	Source
5,6-Dihydro-5-methyluracil	ChEBI
5-Methyl-5,6-dihydrouracil	ChEBI
5,6-Dihydrothymine	HMDB, MeSH
5-Methyl-hydrouracil	HMDB
5-Methyldihydropyrimidine-2,4(1H,3H)-dione	HMDB
dihydro-5-Methyl-2,4(1H,3H)-pyrimidinedione	HMDB
5-Methyldihydrouracil	MeSH, HMDB
5,6-Dihydrothymine, (S)-isomer	MeSH, HMDB

Chemical Formula

C₅H₈N₂O₂

Average Molecular Weight

128.1292

Monoisotopic Molecular Weight

128.05857751

IUPAC Name

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

Traditional Name

dihydrothymine

CAS Registry Number

696-04-8

SMILES

CC1CNC(=O)NC1=O

InChI Identifier

InChI=1S/C5H8N2O2/c1-3-2-6-5(9)7-4(3)8/h3H,2H2,1H3,(H2,6,7,8,9)

InChI Key

NBAKTGXDIBVZOO-UHFFFAOYSA-N

Chemical Taxonomy

Description

belongs to the class of organic compounds known as hydropyrimidines. Hydropyrimidines are compounds containing a hydrogenated pyrimidine ring (i.e. containing less than the maximum number of double bonds.).

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Diazines

Sub Class

Pyrimidines and pyrimidine derivatives

Direct Parent

Hydropyrimidines

Alternative Parents

Substituents

5,6-dihydropyrimidine
Hydropyrimidine
Azacycle
Organic 1,3-dipolar compound
Propargyl-type 1,3-dipolar organic compound
Organic nitrogen compound
Organic oxygen compound
Organopnictogen compound
Hydrocarbon derivative
Organooxygen compound
Organonitrogen compound
Aliphatic heteromonocyclic compound

Molecular Framework

Aliphatic heteromonocyclic compounds

External Descriptors

pyrimidone (CHEBI:27468 )
a base derivative (DIHYDRO-THYMINE )
a pyrimidine-related compound (DIHYDRO-THYMINE )

Physical Properties

State

Solid

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	-0.8	ALOGPS
logP	-0.67	ChemAxon
logS	-0.84	ALOGPS
pKa (Strongest Acidic)	11.7	ChemAxon
pKa (Strongest Basic)	-7.4	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	30.32 m³·mol⁻¹	ChemAxon
Polarizability	12.03 Å³	ChemAxon
Number of Rings	1	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	Deposition Date	View
GC-MS	GC-MS Spectrum - GC-MS (1 TMS)	splash10-000i-5900000000-0b84b9786838d29e07ab	2014-06-16	View Spectrum
GC-MS	GC-MS Spectrum - GC-MS (2 TMS)	splash10-0zmi-8980000000-d75d30c6e5fdb4643aa5	2014-06-16	View Spectrum
GC-MS	GC-MS Spectrum - GC-MS (Non-derivatized)	splash10-000i-5900000000-0b84b9786838d29e07ab	2017-09-12	View Spectrum
GC-MS	GC-MS Spectrum - GC-MS (Non-derivatized)	splash10-0zmi-8980000000-d75d30c6e5fdb4643aa5	2017-09-12	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	splash10-004i-9300000000-05ab95b9effabc03847d	2017-09-01	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 10V, Positive (Annotated)	splash10-004i-8900000000-db662635cbae4d48204b	2012-07-24	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 25V, Positive (Annotated)	splash10-0006-9000000000-c3960ffe99d74c617000	2012-07-24	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 40V, Positive (Annotated)	splash10-0006-9000000000-9a6c2715f931ff084157	2012-07-24	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-004i-0900000000-b0b2721bf2e4a74bbba2	2017-09-01	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0a4l-9100000000-b89dfebf5db699f3651c	2017-09-01	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-052f-9000000000-97f152f0bbe6fb600c5c	2017-09-01	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-004i-3900000000-98c26fdc1559c4c1afc2	2017-09-01	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-0006-9000000000-320f4c88705757a63b75	2017-09-01	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0006-9000000000-76fbb95e0354defdb94e	2017-09-01	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-004i-0900000000-7c6c3743140aa087d39c	2021-10-21	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-004i-4900000000-70eb9f3b90f3b230f593	2021-10-21	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0a4l-9000000000-e84dd91c5dd8c38010f7	2021-10-21	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-004i-3900000000-b1b06bf61dca14c34015	2021-10-21	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-0006-9200000000-a8831b6e3dbc59c56963	2021-10-21	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0006-9000000000-90726b17dc36e29c5299	2021-10-21	View Spectrum
MS	Mass Spectrum (Electron Ionization)	splash10-004l-9200000000-873ae62dcdf602237ec1	2014-09-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, experimental)	Not Available	2012-12-04	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, DMSO-d6, experimental)	Not Available	2014-09-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 15.09 MHz, DMSO-d6, experimental)	Not Available	2014-09-23	View Spectrum
2D NMR	[¹H, ¹³C]-HSQC NMR Spectrum (2D, 600 MHz, H₂O, experimental)	Not Available	2012-12-04	View Spectrum

Concentrations

Status	Value		Reference	Details
Detected but not Quantified	Not Applicable		PMID: 23438684	details

External Links

HMDB ID

HMDB0304210

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

KNApSAcK ID

Chemspider ID

KEGG Compound ID

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

Not Available

PDB ID

Not Available

ChEBI ID

27468

References

Synthesis Reference

Yamane, Tetsuo; Wyluda, Benjamin J.; Shulman, Robert G. Dihydrothymine from ultraviolet-irradiated DNA. Proceedings of the National Academy of Sciences of the United States of America (1967), 58(2), 439-42.

Material Safety Data Sheet (MSDS)

Download (PDF)

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 ]

Showing metabocard for Dihydrothymine (BMDB0000079)

Structure for BMDB0000079 (Dihydrothymine)