ContaminantDB: Dihydrothymine

Identification Taxonomy Biological Properties Physical Properties Toxicity Profile Spectra Concentrations Links References XML

Record Information

Version

1.0

Creation Date

2014-08-29 06:28:37 UTC

Update Date

2026-04-02 23:54:27 UTC

Accession Number

CHEM003292

Identification

Common Name

Dihydrothymine

Class

Small Molecule

Description

Dihydrothymine is an intermediate breakdown product of thymine. Dihydropyrimidine dehydrogenase catalyzes the reduction of thymine to 5, 6-dihydrothymine then dihydropyrimidinase hydrolyzes 5, 6-dihydrothymine to N-carbamyl-b-alanine. Finally, beta-ureidopropionase catalyzes the conversion of N-carbamyl-b-alanine to beta-alanine. Patients with dihydropyrimidinase deficiency exhibit highly increased concentrations of 5, 6-dihydrouracil and 5, 6-dihydrothymine and moderately increased concentrations of uracil and thymine can be detected in urine.

Contaminant Sources

FooDB Chemicals
HMDB Contaminants - Urine
T3DB toxins

Contaminant Type

Animal Toxin
Food Toxin
Metabolite
Natural Compound
Organic Compound

Chemical 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 Mass

128.129 g/mol

Monoisotopic Mass

128.059 g/mol

CAS Registry Number

696-04-8

IUPAC Name

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

Traditional Name

dihydrothymine

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 )

Biological Properties

Status

Detected and Not Quantified

Origin

Endogenous

Cellular Locations

Cytoplasm
Extracellular

Biofluid Locations

Not Available

Tissue Locations

Prostate

Pathways

Name	SMPDB Link	KEGG Link
Pyrimidine Metabolism	SMP00046	map00240
Dihydropyrimidinase Deficiency	SMP00178	Not Available

Applications

Not Available

Biological Roles

Chemical Roles

Not Available

Physical Properties

State

Solid

Appearance

White powder.

Experimental Properties

Property	Value
Melting Point	Not Available
Boiling Point	Not Available
Solubility	Not Available

Predicted Properties

Property	Value	Source
Water Solubility	18.7 g/L	ALOGPS
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	View
GC-MS	GC-MS Spectrum - GC-MS (1 TMS)	splash10-000i-5900000000-0b84b9786838d29e07ab	Spectrum
GC-MS	GC-MS Spectrum - GC-MS (2 TMS)	splash10-0zmi-8980000000-d75d30c6e5fdb4643aa5	Spectrum
GC-MS	GC-MS Spectrum - GC-MS (Non-derivatized)	splash10-000i-5900000000-0b84b9786838d29e07ab	Spectrum
GC-MS	GC-MS Spectrum - GC-MS (Non-derivatized)	splash10-0zmi-8980000000-d75d30c6e5fdb4643aa5	Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	splash10-004i-9300000000-05ab95b9effabc03847d	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 10V, Positive (Annotated)	splash10-004i-8900000000-db662635cbae4d48204b	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 25V, Positive (Annotated)	splash10-0006-9000000000-c3960ffe99d74c617000	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 40V, Positive (Annotated)	splash10-0006-9000000000-9a6c2715f931ff084157	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-004i-0900000000-b0b2721bf2e4a74bbba2	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0a4l-9100000000-b89dfebf5db699f3651c	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-052f-9000000000-97f152f0bbe6fb600c5c	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-004i-3900000000-98c26fdc1559c4c1afc2	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-0006-9000000000-320f4c88705757a63b75	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0006-9000000000-76fbb95e0354defdb94e	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-004i-0900000000-7c6c3743140aa087d39c	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-004i-4900000000-70eb9f3b90f3b230f593	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0a4l-9000000000-e84dd91c5dd8c38010f7	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-004i-3900000000-b1b06bf61dca14c34015	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-0006-9200000000-a8831b6e3dbc59c56963	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0006-9000000000-90726b17dc36e29c5299	Spectrum
MS	Mass Spectrum (Electron Ionization)	splash10-004l-9200000000-873ae62dcdf602237ec1	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
2D NMR	[1H,13C] 2D NMR Spectrum	Not Available	Spectrum

Toxicity Profile

Route of Exposure

Not Available

Mechanism of Toxicity

Dihydropyrimidine dehydrogenase catalyzes the reduction of thymine to 5, 6-dihydrothymine then dihydropyrimidinase hydrolyzes 5, 6-dihydrothymine to N-carbamyl-b-alanine. Finally, beta-ureidopropionase catalyzes the conversion of N-carbamyl-b-alanine to beta-alanine. Accumulation of dihydrothymine in the body has been shown to be toxic.

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

Not Available

HMDB ID

HMDB0304210

FooDB ID

FDB030555

Phenol Explorer ID

Not Available

KNApSAcK ID

C00052265

BiGG ID

Not Available

BioCyc ID

Not Available

METLIN ID

Not Available

PDB ID

Not Available

Wikipedia Link

Not Available

Chemspider ID

84456

ChEBI ID

27468

PubChem Compound ID

Not Available

Kegg Compound ID

C00906

YMDB ID

Not Available

ECMDB ID

ECMDB00079

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.

MSDS

Link

General References

1. https://www.ncbi.nlm.nih.gov/pubmed/?term=12798197

2. https://www.ncbi.nlm.nih.gov/pubmed/?term=20509700

3. https://www.ncbi.nlm.nih.gov/pubmed/?term=2669952

Dihydrothymine (CHEM003292)

Structure for CHEM003292: Dihydrothymine