Bovine Metabolome Database: Showing metabocard for Uracil (BMDB0000300)

Identification Taxonomy Physical properties Pathways Spectra Concentrations Links References enzymes (3) Show 3 proteins XML

Record Information

Version

1.0

Creation Date

2016-09-30 22:28:03 UTC

Update Date

2020-06-04 20:52:17 UTC

BMDB ID

BMDB0000300

Secondary Accession Numbers

BMDB00300

Metabolite Identification

Common Name

Uracil

Description

Uracil, also known as U or hybar X, 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. Uracil exists as a solid, possibly soluble (in water), and an extremely weak basic (essentially neutral) compound (based on its pKa) molecule. Uracil exists in all living species, ranging from bacteria to humans. Uracil is a potentially toxic compound.

Structure

MOL SDF 3D-SDF PDB SMILES InChI View 3D Structure

Synonyms

Value	Source
2,4(1H,3H)-Pyrimidinedione	ChEBI
2,4-Dioxopyrimidine	ChEBI
2,4-Pyrimidinedione	ChEBI
U	ChEBI
Ura	ChEBI
Urazil	ChEBI
2,4-Dihydroxypyrimidine	HMDB
2,4-Pyrimidinediol	HMDB
Hybar X	HMDB
Pirod	HMDB
Pyrod	HMDB

Chemical Formula

C₄H₄N₂O₂

Average Molecular Weight

112.0868

Monoisotopic Molecular Weight

112.027277382

IUPAC Name

1,2,3,4-tetrahydropyrimidine-2,4-dione

Traditional Name

uracil

CAS Registry Number

66-22-8

SMILES

O=C1NC=CC(=O)N1

InChI Identifier

InChI=1S/C4H4N2O2/c7-3-1-2-5-4(8)6-3/h1-2H,(H2,5,6,7,8)

InChI Key

ISAKRJDGNUQOIC-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

Pyrimidone
Hydropyrimidine
Heteroaromatic compound
Vinylogous amide
Urea
Lactam
Azacycle
Organic nitrogen compound
Organic oxygen compound
Organopnictogen compound
Organic oxide
Hydrocarbon derivative
Organooxygen compound
Organonitrogen compound
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

pyrimidone (CHEBI:17568 )
pyrimidine nucleobase (CHEBI:17568 )
pyrimidines (C00106 )
a pyrimidine-related compound (URACIL )
a pyrimidine base (URACIL )

Ontology

Status

Detected and Quantified

Origin

Endogenous

Biofunction

Not Available

Application

Not Available

Cellular locations

Extracellular

Physical Properties

State

Solid

Experimental Properties

Property	Value	Reference
Melting Point	330 °C	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	3.6 mg/mL	Not Available
LogP	-1.07	HANSCH,C ET AL. (1995)

Predicted Properties

Property	Value	Source
logP	-1.2	ALOGPS
logP	-0.86	ChemAxon
logS	-0.63	ALOGPS
pKa (Strongest Acidic)	8.8	ChemAxon
pKa (Strongest Basic)	-5.5	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	25.97 m³·mol⁻¹	ChemAxon
Polarizability	9.37 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) (Non-derivatized)	splash10-0002-5950000000-18425875415ad150c4fc	View in MoNA
GC-MS	GC-MS Spectrum - GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies) (2 TMS)	splash10-006t-9740000000-e884a4b98e7e9dc75e5f	View in MoNA
GC-MS	GC-MS Spectrum - GC-MS (2 TMS)	splash10-052e-7790000000-026cb6beb5cde6a61b80	View in MoNA
GC-MS	GC-MS Spectrum - EI-B (Non-derivatized)	splash10-02tc-9200000000-4a57c4e06fd552d6a9bf	View in MoNA
GC-MS	GC-MS Spectrum - EI-B (Non-derivatized)	splash10-03xu-9400000000-1c29f070a8135b06f88b	View in MoNA
GC-MS	GC-MS Spectrum - GC-EI-TOF (Non-derivatized)	splash10-0002-5950000000-18425875415ad150c4fc	View in MoNA
GC-MS	GC-MS Spectrum - GC-EI-TOF (Non-derivatized)	splash10-006t-9740000000-e884a4b98e7e9dc75e5f	View in MoNA
GC-MS	GC-MS Spectrum - GC-MS (Non-derivatized)	splash10-052e-7790000000-026cb6beb5cde6a61b80	View in MoNA
GC-MS	GC-MS Spectrum - GC-EI-TOF (Non-derivatized)	splash10-0002-6940000000-a726178341f6443e60cc	View in MoNA
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	splash10-03xu-9300000000-6a96f6ce1ef731689107	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)	splash10-03di-3900000000-e422eda255a4b6414f86	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 25V, Positive (Annotated)	splash10-006y-9000000000-130eb5f4414426e03667	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 40V, Positive (Annotated)	splash10-0006-9100000000-c096d08ca715d97cd732	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - EI-B (HITACHI M-60) , Positive	splash10-02tc-9200000000-83a0a6ad4fc1b407e570	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - EI-B (HITACHI M-80) , Positive	splash10-03xu-9400000000-acd0cfd54af7d6a55283	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 10V, Negative	splash10-03di-0900000000-309fe212c929f3c6a930	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 20V, Negative	splash10-03di-6900000000-55a7de75a40eab61da8b	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 30V, Negative	splash10-0006-9000000000-1c3caab26eb7e359db92	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 40V, Negative	splash10-0006-9000000000-7494d4e611a73ecb79ea	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 50V, Negative	splash10-0006-9000000000-ed4046b040337db620d8	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QTOF (UPLC Q-Tof Premier, Waters) , Positive	splash10-03di-0900000000-ff54f3083ce4ccccfd95	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QTOF (UPLC Q-Tof Premier, Waters) , Negative	splash10-03di-0900000000-6728c1eb6f68b40c09f8	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ , negative	splash10-03di-0900000000-309fe212c929f3c6a930	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ , negative	splash10-03di-6900000000-55a7de75a40eab61da8b	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ , negative	splash10-0006-9000000000-1c3caab26eb7e359db92	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ , negative	splash10-0006-9000000000-7494d4e611a73ecb79ea	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ , negative	splash10-0006-9000000000-ed4046b040337db620d8	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QTOF , negative	splash10-03di-0900000000-6728c1eb6f68b40c09f8	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - , negative	splash10-03di-0900000000-a21102c708f8d5eaf262	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-03di-1900000000-0029cbdcaa1377a4d03e	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0229-9400000000-c227e1deb392170cb323	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0006-9000000000-3cf6f9fc3ab6890266ac	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-03di-4900000000-67a3d94ab649e28bda13	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-0006-9100000000-bbf50de54fc413b6588e	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0006-9000000000-98042b91f1087b0c2563	View in MoNA
MS	Mass Spectrum (Electron Ionization)	splash10-03xu-9400000000-d7ffe72f606f1af3349b	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, 100.72 MHz, DMSO-d6, experimental)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, D₂O, 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, 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, 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
2D NMR	[¹H, ¹H]-TOCSY. Unexported temporarily by An Chi on Oct 15, 2021 until json or nmrML file is generated. 2D NMR Spectrum (experimental)	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

Extracellular

Biospecimen Locations

All Tissues
Liver
Mammary Gland
Milk
Placenta
Prostate Tissue
Ruminal Fluid

Pathways

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

Normal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
All Tissues	Expected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	Not Applicable	details
Liver	Detected and Quantified	76 +/- 30 nmol/g of tissue	Not Specified	Not Specified	Normal	Aidin Foroutan, C...	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
Liver	Detected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	PMID: 31867104	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: 28306241	details
Milk	Detected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	PMID: 23438684	details
Milk	Detected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	Kurt J. Boudonck,...	details
Milk	Detected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	Kurt J. Boudonck,...	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	113.18 +/- 24.69 uM	Not Specified	Not Specified	Normal	Fozia Saleem, Sou...	details
Ruminal Fluid	Detected and Quantified	142.5 uM	Not Specified	Not Specified	Normal	PMID: 22959937	details
Ruminal Fluid	Detected and Quantified	234.6 uM	Not Specified	Not Specified	Normal	PMID: 22959937	details
Ruminal Fluid	Detected and Quantified	270.2 uM	Not Specified	Not Specified	Normal	PMID: 22959937	details
Ruminal Fluid	Detected and Quantified	113.2 uM	Not Specified	Not Specified	Normal	PMID: 22959937	details
Ruminal Fluid	Detected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	PMID: 25599412	details
Ruminal Fluid	Detected and Quantified	1007 +/- 230 uM	Not Specified	Not Specified	Normal	Aidin Foroutan, C...	details
Ruminal Fluid	Detected and Quantified	109-405 uM	Not Specified	Not Specified	Normal	PMID: 29642378	details
Ruminal Fluid	Detected and Quantified	122 +/- 127 uM	Not Specified	Not Specified	Normal	Fozia Saleem, Sou...	details
Ruminal Fluid	Detected and Quantified	199 +/- 91 uM	Not Specified	Not Specified	Normal	Fozia Saleem, Sou...	details
Ruminal Fluid	Detected and Quantified	246 +/- 48 uM	Not Specified	Not Specified	Normal	Fozia Saleem, Sou...	details
Ruminal Fluid	Detected and Quantified	104 +/- 25 uM	Not Specified	Not Specified	Normal	Fozia Saleem, Sou...	details
Ruminal Fluid	Detected and Quantified	104 +/- 25 uM	Not Specified	Not Specified	Normal	Fozia Saleem, Sou...	details
Ruminal Fluid	Detected and Quantified	149 uM	Not Specified	Not Specified	Normal	Burim NA, Qendrim...	details
Ruminal Fluid	Detected and Quantified	193 uM	Not Specified	Not Specified	Normal	Burim NA, Qendrim...	details
Ruminal Fluid	Detected and Quantified	224 uM	Not Specified	Not Specified	Normal	Burim NA, Qendrim...	details
Ruminal Fluid	Detected and Quantified	92.6 uM	Not Specified	Not Specified	Normal	Burim NA, Qendrim...	details

Abnormal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Ruminal Fluid	Detected and Quantified	270.19 +/- 43.37 uM	Not Specified	Not Specified	Rumen acidosis	Fozia Saleem, Sou...	details

External Links

HMDB ID

HMDB0000300

DrugBank ID

DB03419

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

17568

References

Synthesis Reference

Burckhalter, J. H.; Scarborough, Homer C. The synthesis of uracils as anticonvulsants. Journal of the American Pharmaceutical Association (1912-1977) (1955), 44 545-50.

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 ]
Mung D, Li L: Development of Chemical Isotope Labeling LC-MS for Milk Metabolomics: Comprehensive and Quantitative Profiling of the Amine/Phenol Submetabolome. Anal Chem. 2017 Apr 18;89(8):4435-4443. doi: 10.1021/acs.analchem.6b03737. Epub 2017 Mar 28. [PubMed:28306241 ]
Kurt J. Boudonck, Matthew W. Mitchell, Jacob Wulff and John A. Ryals (2009). Kurt J. Boudonck, Matthew W. Mitchell, Jacob Wulff and John A. Ryals. Characterization of the biochemical variability of bovine milk using metabolomics. Metabolomics (2009) 5:375?386. Metabolomics.

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. Uracil phosphoribosyltransferase homolog

General function:: Nucleotide transport and metabolism
Specific function:: Not Available
Gene Name:: UPRT
Uniprot ID:: Q32LA4
Molecular weight:: 33355.0

Enzyme Details

3. Uridine phosphorylase

General function:: Not Available
Specific function:: Catalyzes the reversible phosphorylytic cleavage of uridine and deoxyuridine to uracil and ribose- or deoxyribose-1-phosphate. The produced molecules are then utilized as carbon and energy sources or in the rescue of pyrimidine bases for nucleotide synthesis.
Gene Name:: UPP2
Uniprot ID:: Q0VCM7
Molecular weight:: 35805.0

Reactions

Uridine + Hydrogen phosphate → Uracil + Ribose 1-phosphate	details

Showing metabocard for Uracil (BMDB0000300)

Structure for BMDB0000300 (Uracil)

Enzymes

Reactions

Reactions