Bovine Metabolome Database: Showing metabocard for Dihydrouracil (BMDB0000076)

Identification Taxonomy Physical properties Pathways Spectra Concentrations Links References enzymes (2) Show 2 proteins XML

Record Information

Version

1.0

Creation Date

2016-09-30 22:19:20 UTC

Update Date

2020-05-21 16:28:29 UTC

BMDB ID

BMDB0000076

Secondary Accession Numbers

BMDB00076

Metabolite Identification

Common Name

Dihydrouracil

Description

Dihydrouracil belongs to the class of organic compounds known as pyrimidones. Pyrimidones are compounds that contain a pyrimidine ring, which bears a ketone. Pyrimidine is a 6-membered ring consisting of four carbon atoms and two nitrogen centers at the 1- and 3- ring positions. Dihydrouracil exists as a solid, possibly soluble (in water), and an extremely weak basic (essentially neutral) compound (based on its pKa) molecule. Dihydrouracil exists in all living organisms, ranging from bacteria to humans. Dihydrouracil is a potentially toxic compound. Dihydrouracil has been found to be associated with several diseases known as liver disease, colorectal cancer, hypertension, and cerebral infarction; also dihydrouracil has been linked to the inborn metabolic disorders including dihydropyrimidine dehydrogenase deficiency.

Structure

MOL SDF PDB SMILES InChI

Synonyms

Value	Source
2,4-Dioxotetrahydropyrimidine	ChEBI
5,6-Dihydro-2,4-dihydroxypyrimidine	ChEBI
Dihydro-2,4(1H,3H)-pyrimidinedione	ChEBI
DIHYDROPYRIMIDINE-2,4(1H,3H)-dione	ChEBI
Dihydrouracile	ChEBI
Hydrouracil	ChEBI
5,6-Dihydro-2,4(1H,3H)-pyrimidinedione	HMDB
5,6-Dihydrouracil	HMDB
Dihydro-pyrimidine-2,4-dione	HMDB

Chemical Formula

C₄H₆N₂O₂

Average Molecular Weight

114.1026

Monoisotopic Molecular Weight

114.042927446

IUPAC Name

1,3-diazinane-2,4-dione

Traditional Name

dihydrouracil

CAS Registry Number

504-07-4

SMILES

O=C1CCNC(=O)N1

InChI Identifier

InChI=1S/C4H6N2O2/c7-3-1-2-5-4(8)6-3/h1-2H2,(H2,5,6,7,8)

InChI Key

OIVLITBTBDPEFK-UHFFFAOYSA-N

Chemical Taxonomy

Description

belongs to the class of organic compounds known as pyrimidones. Pyrimidones are compounds that contain a pyrimidine ring, which bears a ketone. 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

Pyrimidones

Alternative Parents

Substituents

N-acyl urea
Pyrimidone
Ureide
1,3-diazinane
Dicarboximide
Urea
Carbonic acid derivative
Azacycle
Carboxylic acid derivative
Organic oxide
Organopnictogen compound
Organooxygen compound
Organonitrogen compound
Organic oxygen compound
Organic nitrogen compound
Carbonyl group
Hydrocarbon derivative
Aliphatic heteromonocyclic compound

Molecular Framework

Aliphatic heteromonocyclic compounds

External Descriptors

pyrimidone (CHEBI:15901 )
a base derivative (DI-H-URACIL )
a pyrimidine-related compound (DI-H-URACIL )

Ontology

Status

Detected but not Quantified

Origin

Endogenous

Biofunction

Not Available

Application

Not Available

Cellular locations

Cytoplasm
Nucleus

Physical Properties

State

Solid

Experimental Properties

Property	Value	Reference
Melting Point	279 - 281 °C	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	-1.3	ALOGPS
logP	-1.2	ChemAxon
logS	-0.64	ALOGPS
pKa (Strongest Acidic)	11.73	ChemAxon
pKa (Strongest Basic)	-7.6	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	25.75 m³·mol⁻¹	ChemAxon
Polarizability	10.13 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)	splash10-00di-9700000000-4adeeb2f4f5a1111afb7	View in MoNA
GC-MS	GC-MS Spectrum - GC-MS (1 TMS)	splash10-00di-5900000000-8af1b81502646fa5b417	View in MoNA
GC-MS	GC-MS Spectrum - GC-MS (2 TMS)	splash10-0fdo-9750000000-d2aaeeba1cf962175f84	View in MoNA
GC-MS	GC-MS Spectrum - GC-EI-TOF (Non-derivatized)	splash10-00di-9700000000-4adeeb2f4f5a1111afb7	View in MoNA
GC-MS	GC-MS Spectrum - GC-MS (Non-derivatized)	splash10-00di-5900000000-8af1b81502646fa5b417	View in MoNA
GC-MS	GC-MS Spectrum - GC-MS (Non-derivatized)	splash10-0fdo-9750000000-d2aaeeba1cf962175f84	View in MoNA
GC-MS	GC-MS Spectrum - GC-EI-TOF (Non-derivatized)	splash10-0f6w-2940000000-3430a0e2d1819021af1d	View in MoNA
GC-MS	GC-MS Spectrum - GC-EI-TOF (Non-derivatized)	splash10-00di-3900000000-79f2d90a419b7469cb61	View in MoNA
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	splash10-004l-9100000000-55536f0571922b6c69fe	View in MoNA
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 - Quattro_QQQ 10V, Positive (Annotated)	splash10-03k9-9800000000-da772cea603c785c1df4	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 25V, Positive (Annotated)	splash10-0a4i-9100000000-94a5f543e8c6be7b3204	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 40V, Positive (Annotated)	splash10-0btc-9200000000-e9bf2ae82714a2a3a737	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QTOF (UPLC Q-Tof Premier, Waters) , Positive	splash10-014i-5900000000-0fe83e63f6e5d1347894	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - , negative	splash10-03xr-6900000000-08aca1bc7f27b0e7cb08	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QTOF , positive	splash10-014i-5900000000-53ea361c86b4f9fa284b	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - , positive	splash10-00di-9300000000-a8599c09cd21e2f84329	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - 10V, Positive	splash10-01b9-9500000000-03c8b6a5b2dc3625d5d3	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - 20V, Positive	splash10-0ab9-9000000000-331f648f78f506788b99	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - 40V, Positive	splash10-052f-9000000000-824aa91d3f2de539f0bd	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-014i-2900000000-ad7f91d5265e53403dd6	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0603-9200000000-4b30a83fb454e5bbffb8	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0006-9000000000-ce54e3c860a95b0af401	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-03di-9800000000-d705e188f6700a76ef72	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-0006-9000000000-a26409d69a4259731004	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0006-9000000000-f00c4df547660023bee4	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-014i-0900000000-b8f2cf36966bbbbb3285	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-014i-9500000000-44775319047d2eddad49	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-052f-9000000000-3cb7005ca8389854848e	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-03dl-7900000000-9d78d5698ad7865d1789	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-0006-9000000000-997cffdd9ad85c899225	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0006-9000000000-a88e812ae86e53f6c2d6	View in MoNA
MS	Mass Spectrum (Electron Ionization)	splash10-03fu-9400000000-5b9edda3479e7d0a0d28	View in MoNA
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, 15.08 MHz, DMSO-d6, experimental)	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, 100 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, 200 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, 300 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, 400 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, 500 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, 600 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, 700 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, 800 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, 900 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, 1000 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
2D NMR	[¹H, ¹³C]-HSQC NMR Spectrum (2D, 600 MHz, H₂O, experimental)	Not Available	View in JSpectraViewer

Biological Properties

Cellular Locations

Cytoplasm
Nucleus

Biospecimen Locations

Fibroblasts
Kidney
Liver
Mammary Gland
Milk
Prostate Tissue

Pathways

Name	SMPDB/Pathwhiz	KEGG
beta-Alanine Metabolism		Not Available
Pyrimidine Metabolism		Not Available

Normal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Fibroblasts	Expected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	Not Applicable	details
Kidney	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
Prostate Tissue	Expected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	Not Applicable	details

Abnormal Concentrations

Not Available

External Links

HMDB ID

HMDB0000076

DrugBank ID

DB01849

Phenol Explorer Compound ID

Not Available

FooDB ID

FDB030556

KNApSAcK ID

Not Available

Chemspider ID

KEGG Compound ID

BioCyc ID

BiGG ID

Wikipedia Link

METLIN ID

PubChem Compound

PDB ID

Not Available

ChEBI ID

15901

References

Synthesis Reference

Bhat, K. S.; Rao, A. S. Synthesis of uracil, 6-methyluracil and some dihydrouracils. Organic Preparations and Procedures International (1983), 15(5), 303-13.

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 ]

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

Dihydrouracil + NADP → Uracil + NADPH	details
Uracil + NADP → Dihydrouracil + NADPH	details

Enzyme Details

2. Dihydropyrimidinase-related protein 2

General function:: Not Available
Specific function:: Plays a role in neuronal development and polarity, as well as in axon growth and guidance, neuronal growth cone collapse and cell migration. Necessary for signaling by class 3 semaphorins and subsequent remodeling of the cytoskeleton. May play a role in endocytosis (By similarity).
Gene Name:: DPYSL2
Uniprot ID:: O02675
Molecular weight:: 62278.0

Reactions

Dihydrouracil + Water → Ureidopropionic acid	details

Showing metabocard for Dihydrouracil (BMDB0000076)

Structure for BMDB0000076 (Dihydrouracil)

Enzymes

Reactions

Reactions