Livestock Metabolome Database: Showing metabocard for Uracil (LMDB00133)

Identification Taxonomy Ontology Physical properties Spectra Biological properties Concentrations Links References XML

Record Information

Version

1.0

Creation Date

2016-07-13 19:43:05 UTC

Update Date

2016-08-01 19:10:41 UTC

Lmdb

LMDB00133

Secondary Accession Numbers

None

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 is an extremely weak basic (essentially neutral) compound (based on its pKa). Uracil exists in all living species, ranging from bacteria to humans. Within humans, uracil participates in a number of enzymatic reactions. In particular, uracil and ribose 1-phosphate can be biosynthesized from uridine; which is catalyzed by the enzyme uridine phosphorylase 2. In addition, uracil can be converted into dihydrouracil through its interaction with the enzyme dihydropyrimidine dehydrogenase [nadp(+)]. In humans, uracil is involved in pyrimidine metabolism. Outside of the human body, Uracil is found, on average, in the highest concentration within beers. Uracil has also been detected, but not quantified in, several different foods, such as radish (var.), green beans, cauliflowers, prickly pears, and citrus. This could make uracil a potential biomarker for the consumption of these foods. Uracil is a potentially toxic compound. Uracil, with regard to humans, has been found to be associated with several diseases such as canavan disease, hypertension, and cerebral infarction; uracil has also been linked to several inborn metabolic disorders including carbamoyl phosphate synthetase deficiency and dihydropyrimidine dehydrogenase deficiency.

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

Not Available

Biofunction

Not Available

Application

Not Available

Cellular locations

Not Available

Physical Properties

State

Not Available

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	-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	View
GC-MS	GC-MS Spectrum - GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies) (Non-derivatized)	splash10-0002-5950000000-18425875415ad150c4fc	Spectrum
GC-MS	GC-MS Spectrum - GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies) (2 TMS)	splash10-006t-9740000000-e884a4b98e7e9dc75e5f	Spectrum
GC-MS	GC-MS Spectrum - GC-MS (2 TMS)	splash10-052e-7790000000-026cb6beb5cde6a61b80	Spectrum
GC-MS	GC-MS Spectrum - EI-B (Non-derivatized)	splash10-02tc-9200000000-4a57c4e06fd552d6a9bf	Spectrum
GC-MS	GC-MS Spectrum - EI-B (Non-derivatized)	splash10-03xu-9400000000-1c29f070a8135b06f88b	Spectrum
GC-MS	GC-MS Spectrum - GC-EI-TOF (Non-derivatized)	splash10-0002-5950000000-18425875415ad150c4fc	Spectrum
GC-MS	GC-MS Spectrum - GC-EI-TOF (Non-derivatized)	splash10-006t-9740000000-e884a4b98e7e9dc75e5f	Spectrum
GC-MS	GC-MS Spectrum - GC-MS (Non-derivatized)	splash10-052e-7790000000-026cb6beb5cde6a61b80	Spectrum
GC-MS	GC-MS Spectrum - GC-EI-TOF (Non-derivatized)	splash10-0002-6940000000-a726178341f6443e60cc	Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	splash10-03xu-9300000000-6a96f6ce1ef731689107	Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	Not Available	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 10V, Positive (Annotated)	splash10-03di-3900000000-e422eda255a4b6414f86	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 25V, Positive (Annotated)	splash10-006y-9000000000-130eb5f4414426e03667	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 40V, Positive (Annotated)	splash10-0006-9100000000-c096d08ca715d97cd732	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - EI-B (HITACHI M-60) , Positive	splash10-02tc-9200000000-83a0a6ad4fc1b407e570	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - EI-B (HITACHI M-80) , Positive	splash10-03xu-9400000000-acd0cfd54af7d6a55283	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 10V, Negative	splash10-03di-0900000000-309fe212c929f3c6a930	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 20V, Negative	splash10-03di-6900000000-55a7de75a40eab61da8b	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 30V, Negative	splash10-0006-9000000000-1c3caab26eb7e359db92	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 40V, Negative	splash10-0006-9000000000-7494d4e611a73ecb79ea	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 50V, Negative	splash10-0006-9000000000-ed4046b040337db620d8	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QTOF (UPLC Q-Tof Premier, Waters) , Positive	splash10-03di-0900000000-ff54f3083ce4ccccfd95	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QTOF (UPLC Q-Tof Premier, Waters) , Negative	splash10-03di-0900000000-6728c1eb6f68b40c09f8	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ , negative	splash10-03di-0900000000-309fe212c929f3c6a930	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ , negative	splash10-03di-6900000000-55a7de75a40eab61da8b	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ , negative	splash10-0006-9000000000-1c3caab26eb7e359db92	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ , negative	splash10-0006-9000000000-7494d4e611a73ecb79ea	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ , negative	splash10-0006-9000000000-ed4046b040337db620d8	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QTOF , negative	splash10-03di-0900000000-6728c1eb6f68b40c09f8	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - , negative	splash10-03di-0900000000-a21102c708f8d5eaf262	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-03di-1900000000-0029cbdcaa1377a4d03e	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0229-9400000000-c227e1deb392170cb323	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0006-9000000000-3cf6f9fc3ab6890266ac	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-03di-4900000000-67a3d94ab649e28bda13	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-0006-9100000000-bbf50de54fc413b6588e	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0006-9000000000-98042b91f1087b0c2563	Spectrum
MS	Mass Spectrum (Electron Ionization)	splash10-03xu-9400000000-d7ffe72f606f1af3349b	Spectrum
1D NMR	13C NMR Spectrum	Not Available	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
1D NMR	1H NMR Spectrum	Not Available	Spectrum
1D NMR	13C NMR Spectrum	Not Available	Spectrum
1D NMR	1H NMR Spectrum	Not Available	Spectrum
1D NMR	13C NMR Spectrum	Not Available	Spectrum
1D NMR	1H NMR Spectrum	Not Available	Spectrum
1D NMR	13C NMR Spectrum	Not Available	Spectrum
1D NMR	1H NMR Spectrum	Not Available	Spectrum
1D NMR	13C NMR Spectrum	Not Available	Spectrum
1D NMR	1H NMR Spectrum	Not Available	Spectrum
1D NMR	13C NMR Spectrum	Not Available	Spectrum
1D NMR	1H NMR Spectrum	Not Available	Spectrum
1D NMR	13C NMR Spectrum	Not Available	Spectrum
1D NMR	1H NMR Spectrum	Not Available	Spectrum
1D NMR	13C NMR Spectrum	Not Available	Spectrum
1D NMR	1H NMR Spectrum	Not Available	Spectrum
1D NMR	13C NMR Spectrum	Not Available	Spectrum
1D NMR	1H NMR Spectrum	Not Available	Spectrum
1D NMR	13C NMR Spectrum	Not Available	Spectrum
1D NMR	1H NMR Spectrum	Not Available	Spectrum
1D NMR	13C NMR Spectrum	Not Available	Spectrum
1D NMR	1H NMR Spectrum	Not Available	Spectrum
2D NMR	[1H,1H] 2D NMR Spectrum	Not Available	Spectrum
2D NMR	[1H,13C] 2D NMR Spectrum	Not Available	Spectrum

Biological Properties

Cellular Locations

Not Available

Biofluid Locations and Tissue Locations

Brain
Feces
Jejunum
Kidney
Kidney perfusate
Liver
Milk
Plasma
Ruminal Fluid

Concentrations

Biofluid	Status	Value	Condition	Species	Reference	Details
Brain	Detected but not Quantified	Not Applicable	Not Available	Ovine	25959287	details
Feces	Detected but not Quantified	Not Applicable	Not Available	Equine	E. E. Escalona, J...	details
Feces	Detected but not Quantified	Not Applicable	Not Available	Ovine	17249687	details
Feces	Detected but not Quantified	Not Applicable	Not Available	Ovine	17249687	details
Jejunum	Detected but not Quantified	Not Applicable	Not Available	Porcine	21584308	details
Kidney	Detected but not Quantified	Not Applicable	Not Available	Porcine	21761043	details
Kidney perfusate	Detected but not Quantified	Not Applicable	Not Available	Porcine	25502759	details
Liver	Detected but not Quantified	Not Applicable	Not Available	Porcine	21761043	details
Milk	Detected but not Quantified	Not Applicable	Not Available	Bovine	Kurt J. Boudonck,...	details
Milk	Detected but not Quantified	Not Applicable	Not Available	Bovine	23438684	details
Plasma	Detected but not Quantified	Not Applicable	Not Available	Ovine	17249687	details
Plasma	Detected but not Quantified	Not Applicable	Not Available	Ovine	17249687	details
Ruminal Fluid	Detected and Quantified	234.6 uM	Not Available	Bovine	22959937	details
Ruminal Fluid	Detected and Quantified	270.2 uM	Not Available	Bovine	22959937	details
Ruminal Fluid	Detected and Quantified	92.6 uM	Not Available	Bovine	Burim NA, Qendrim...	details
Ruminal Fluid	Detected and Quantified	149 uM	Not Available	Bovine	Burim NA, Qendrim...	details
Ruminal Fluid	Detected and Quantified	193 uM	Not Available	Bovine	Burim NA, Qendrim...	details
Ruminal Fluid	Detected and Quantified	224 uM	Not Available	Bovine	Burim NA, Qendrim...	details
Ruminal Fluid	Detected and Quantified	104 +/- 25 uM	Not Available	Bovine	Saleem F, Bouatra...	details
Ruminal Fluid	Detected and Quantified	104 +/- 25 uM	Not Available	Bovine	Saleem F, Bouatra...	details
Ruminal Fluid	Detected and Quantified	121 +/- 40 uM	Not Available	Bovine	Saleem F, Bouatra...	details
Ruminal Fluid	Detected and Quantified	122 +/- 127 uM	Not Available	Bovine	Saleem F, Bouatra...	details
Ruminal Fluid	Detected and Quantified	199 +/- 91 uM	Not Available	Bovine	Saleem F, Bouatra...	details
Ruminal Fluid	Detected and Quantified	246 +/- 48 uM	Not Available	Bovine	Saleem F, Bouatra...	details
Ruminal Fluid	Detected but not Quantified	Not Applicable	Not Available	Bovine	25599412	details
Ruminal Fluid	Detected and Quantified	113.2 uM	Not Available	Bovine	22959937	details
Ruminal Fluid	Detected and Quantified	142.5 uM	Not Available	Bovine	22959937	details