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Record Information

Version

5.0

Status

Detected but not Quantified

Creation Date

2021-09-24 08:02:49 UTC

Update Date

2022-09-22 18:34:37 UTC

HMDB ID

HMDB0304210

Secondary Accession Numbers

None

Metabolite Identification

Common Name

5,6-dihydrothymine

Description

Dihydrothymine, also known as 5,6-dihydro-5-methyluracil or 5,6-dihydrothymine, (S)-isomer, is a member of the class of 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 soluble (in water) and a very weakly acidic compound (based on its pKa). Dihydrothymine can be found in a number of food items such as hyssop, arrowroot, nopal, and red rice, which makes dihydrothymine a potential biomarker for the consumption of these food products. Dihydrothymine can be found primarily in blood, cerebrospinal fluid (CSF), saliva, and urine, as well as in human prostate tissue. Dihydrothymine exists in all living organisms, ranging from bacteria to humans. In humans, dihydrothymine is involved in the pyrimidine metabolism. Dihydrothymine is also involved in few metabolic disorders, which include beta ureidopropionase deficiency, dihydropyrimidinase deficiency, MNGIE (mitochondrial neurogastrointestinal encephalopathy), and UMP synthase deficiency (orotic aciduria). Moreover, dihydrothymine is found to be associated with beta-ureidopropionase deficiency and dihydropyrimidinase deficiency. Dihydrothymine is a non-carcinogenic (not listed by IARC) potentially toxic compound. Dihydrothymine is an intermediate in the metabolism 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. Accumulation of dihydrothymine in the body has been shown to be toxic (T3DB).

Structure

MOL 3D MOL SDF 3D SDF PDB 3D PDB SMILES InChI

View in JSmol View Stereo Labels

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

Not Available

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 )

Ontology

Not Available

Physical Properties

State

Not Available

Experimental Molecular 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

Experimental Chromatographic Properties

Not Available

Predicted Molecular 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	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Predicted Chromatographic Properties

Predicted Collision Cross Sections

Predictor	Adduct Type	CCS Value (Å²)	Reference
AllCCS	[M+H]+	127.106	32859911
AllCCS	[M+H-H2O]+	122.392	32859911
AllCCS	[M+Na]+	132.777	32859911
AllCCS	[M+NH4]+	131.507	32859911
AllCCS	[M-H]-	124.412	32859911
AllCCS	[M+Na-2H]-	126.606	32859911
AllCCS	[M+HCOO]-	129.057	32859911
DeepCCS	[M+H]+	130.156	30932474
DeepCCS	[M-H]-	127.207	30932474
DeepCCS	[M-2H]-	163.508	30932474
DeepCCS	[M+Na]+	138.744	30932474

Predicted Retention Times

Underivatized

Chromatographic Method	Retention Time	Reference
Predicted by Siyang on May 30, 2022	9.2631 minutes	33406817
Predicted by Siyang using ReTip algorithm on June 8, 2022	1.98 minutes	32390414
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid	983.4 seconds	40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid	321.9 seconds	40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid	82.0 seconds	40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid	195.1 seconds	40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	59.7 seconds	40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid	246.2 seconds	40023050
BfG_NTS_RP1 =Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) with Water:ACN and 0.1% Formic Acid	331.8 seconds	40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)	292.5 seconds	40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid	635.2 seconds	40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid	178.3 seconds	40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid	921.0 seconds	40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	199.5 seconds	40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	208.3 seconds	40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate	515.5 seconds	40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA	263.8 seconds	40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water	155.7 seconds	40023050

Predicted Kovats Retention Indices

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
5,6-dihydrothymine,1TMS,isomer #1	CC1CN([Si](C)(C)C)C(=O)NC1=O	1409.1	Semi standard non polar	33892256
5,6-dihydrothymine,1TMS,isomer #1	CC1CN([Si](C)(C)C)C(=O)NC1=O	1398.2	Standard non polar	33892256
5,6-dihydrothymine,1TMS,isomer #1	CC1CN([Si](C)(C)C)C(=O)NC1=O	2363.5	Standard polar	33892256
5,6-dihydrothymine,1TMS,isomer #2	CC1CNC(=O)N([Si](C)(C)C)C1=O	1361.4	Semi standard non polar	33892256
5,6-dihydrothymine,1TMS,isomer #2	CC1CNC(=O)N([Si](C)(C)C)C1=O	1344.6	Standard non polar	33892256
5,6-dihydrothymine,1TMS,isomer #2	CC1CNC(=O)N([Si](C)(C)C)C1=O	2297.0	Standard polar	33892256
5,6-dihydrothymine,2TMS,isomer #1	CC1CN([Si](C)(C)C)C(=O)N([Si](C)(C)C)C1=O	1405.0	Semi standard non polar	33892256
5,6-dihydrothymine,2TMS,isomer #1	CC1CN([Si](C)(C)C)C(=O)N([Si](C)(C)C)C1=O	1470.8	Standard non polar	33892256
5,6-dihydrothymine,2TMS,isomer #1	CC1CN([Si](C)(C)C)C(=O)N([Si](C)(C)C)C1=O	1886.6	Standard polar	33892256
5,6-dihydrothymine,1TBDMS,isomer #1	CC1CN([Si](C)(C)C(C)(C)C)C(=O)NC1=O	1679.0	Semi standard non polar	33892256
5,6-dihydrothymine,1TBDMS,isomer #1	CC1CN([Si](C)(C)C(C)(C)C)C(=O)NC1=O	1653.3	Standard non polar	33892256
5,6-dihydrothymine,1TBDMS,isomer #1	CC1CN([Si](C)(C)C(C)(C)C)C(=O)NC1=O	2567.4	Standard polar	33892256
5,6-dihydrothymine,1TBDMS,isomer #2	CC1CNC(=O)N([Si](C)(C)C(C)(C)C)C1=O	1628.5	Semi standard non polar	33892256
5,6-dihydrothymine,1TBDMS,isomer #2	CC1CNC(=O)N([Si](C)(C)C(C)(C)C)C1=O	1594.2	Standard non polar	33892256
5,6-dihydrothymine,1TBDMS,isomer #2	CC1CNC(=O)N([Si](C)(C)C(C)(C)C)C1=O	2365.6	Standard polar	33892256
5,6-dihydrothymine,2TBDMS,isomer #1	CC1CN([Si](C)(C)C(C)(C)C)C(=O)N([Si](C)(C)C(C)(C)C)C1=O	1850.7	Semi standard non polar	33892256
5,6-dihydrothymine,2TBDMS,isomer #1	CC1CN([Si](C)(C)C(C)(C)C)C(=O)N([Si](C)(C)C(C)(C)C)C1=O	1943.9	Standard non polar	33892256
5,6-dihydrothymine,2TBDMS,isomer #1	CC1CN([Si](C)(C)C(C)(C)C)C(=O)N([Si](C)(C)C(C)(C)C)C1=O	2077.0	Standard polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Experimental GC-MS	GC-MS Spectrum - 5,6-dihydrothymine GC-MS (1 TMS)	splash10-000i-5900000000-0b84b9786838d29e07ab	2014-06-16	HMDB team, MONA, MassBank	View Spectrum
Experimental GC-MS	GC-MS Spectrum - 5,6-dihydrothymine GC-MS (2 TMS)	splash10-0zmi-8980000000-d75d30c6e5fdb4643aa5	2014-06-16	HMDB team, MONA, MassBank	View Spectrum
Experimental GC-MS	GC-MS Spectrum - 5,6-dihydrothymine GC-MS (Non-derivatized)	splash10-000i-5900000000-0b84b9786838d29e07ab	2017-09-12	HMDB team, MONA, MassBank	View Spectrum
Experimental GC-MS	GC-MS Spectrum - 5,6-dihydrothymine GC-MS (Non-derivatized)	splash10-0zmi-8980000000-d75d30c6e5fdb4643aa5	2017-09-12	HMDB team, MONA, MassBank	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 5,6-dihydrothymine GC-MS (Non-derivatized) - 70eV, Positive	splash10-004i-9300000000-05ab95b9effabc03847d	2017-09-01	Wishart Lab	View Spectrum
MS	Mass Spectrum (Electron Ionization)	splash10-004l-9200000000-873ae62dcdf602237ec1	2014-09-20	Not Available	View Spectrum

MS/MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Experimental LC-MS/MS	LC-MS/MS Spectrum - 5,6-dihydrothymine Quattro_QQQ 10V, Positive-QTOF (Annotated)	splash10-004i-8900000000-db662635cbae4d48204b	2012-07-24	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - 5,6-dihydrothymine Quattro_QQQ 25V, Positive-QTOF (Annotated)	splash10-0006-9000000000-c3960ffe99d74c617000	2012-07-24	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - 5,6-dihydrothymine Quattro_QQQ 40V, Positive-QTOF (Annotated)	splash10-0006-9000000000-9a6c2715f931ff084157	2012-07-24	HMDB team, MONA	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5,6-dihydrothymine 10V, Positive-QTOF	splash10-004i-0900000000-b0b2721bf2e4a74bbba2	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5,6-dihydrothymine 20V, Positive-QTOF	splash10-0a4l-9100000000-b89dfebf5db699f3651c	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5,6-dihydrothymine 40V, Positive-QTOF	splash10-052f-9000000000-97f152f0bbe6fb600c5c	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5,6-dihydrothymine 10V, Negative-QTOF	splash10-004i-3900000000-98c26fdc1559c4c1afc2	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5,6-dihydrothymine 20V, Negative-QTOF	splash10-0006-9000000000-320f4c88705757a63b75	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5,6-dihydrothymine 40V, Negative-QTOF	splash10-0006-9000000000-76fbb95e0354defdb94e	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5,6-dihydrothymine 10V, Positive-QTOF	splash10-004i-0900000000-7c6c3743140aa087d39c	2021-10-21	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5,6-dihydrothymine 20V, Positive-QTOF	splash10-004i-4900000000-70eb9f3b90f3b230f593	2021-10-21	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5,6-dihydrothymine 40V, Positive-QTOF	splash10-0a4l-9000000000-e84dd91c5dd8c38010f7	2021-10-21	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5,6-dihydrothymine 10V, Negative-QTOF	splash10-004i-3900000000-b1b06bf61dca14c34015	2021-10-21	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5,6-dihydrothymine 20V, Negative-QTOF	splash10-0006-9200000000-a8831b6e3dbc59c56963	2021-10-21	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5,6-dihydrothymine 40V, Negative-QTOF	splash10-0006-9000000000-90726b17dc36e29c5299	2021-10-21	Wishart Lab	View Spectrum

NMR Spectra

Spectrum Type	Description	Deposition Date	Source	View
Experimental 1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, experimental)	2012-12-04	Wishart Lab	View Spectrum
Experimental 2D NMR	[¹H, ¹³C]-HSQC NMR Spectrum (2D, 600 MHz, H₂O, experimental)	2012-12-04	Wishart Lab	View Spectrum

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Blood
Urine

Tissue Locations

Not Available

Pathways

Not Available

Name	SMPDB/PathBank	KEGG

Normal Concentrations

Not Available

Abnormal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Blood	Expected but not Quantified	Not Quantified	Not Specified	Not Specified	Cancer patients undergoing total body irradiation	31424920	details
Urine	Detected but not Quantified	Not Quantified	Not Specified	Not Specified	Cancer patients undergoing total body irradiation	31424920	details

Associated Disorders and Diseases

Disease References

None

Associated OMIM IDs

None

External Links

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB 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

Food Biomarker Ontology

Not Available

VMH ID

Not Available

MarkerDB ID

Not Available

Good Scents ID

Not Available

References

Synthesis Reference

Not Available

Material Safety Data Sheet (MSDS)

Not Available

General References

Not Available

Showing metabocard for 5,6-dihydrothymine (HMDB0304210)

MOL for HMDB0304210 (5,6-dihydrothymine)

3D MOL for HMDB0304210 (5,6-dihydrothymine)

3D SDF for HMDB0304210 (5,6-dihydrothymine)

3D-SDF for HMDB0304210 (5,6-dihydrothymine)

PDB for HMDB0304210 (5,6-dihydrothymine)

3D PDB for HMDB0304210 (5,6-dihydrothymine)

SMILES for HMDB0304210 (5,6-dihydrothymine)

INCHI for HMDB0304210 (5,6-dihydrothymine)

Structure for HMDB0304210 (5,6-dihydrothymine)

3D Structure for HMDB0304210 (5,6-dihydrothymine)

Predicted Collision Cross Sections

Predicted Retention Times

Underivatized

Predicted Kovats Retention Indices

Derivatized

GC-MS Spectra

MS/MS Spectra

NMR Spectra