Cannabis Compound Database: Showing Compound Card for Uracil (CDB004843)

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Identification Taxonomy Ontology Physical properties Spectra Protein target Pathways Concentrations Links References enzymes (7) Show 10 proteins XML

Record Information

Version

1.0

Created at

2020-04-17 18:42:31 UTC

Updated at

2020-12-07 19:11:05 UTC

CannabisDB ID

CDB004843

Secondary Accession Numbers

Not Available

Cannabis Compound 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. Uracil is expected to be in Cannabis as all living plants are known to produce and metabolize it.

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

112.09

Monoisotopic Molecular Weight

112.0273

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

Uremia

Vascular disorders:

Hypertension

Metabolism and nutrition disorders:

Dihydropyrimidine dehydrogenase deficiency

Disposition

Route of exposure:

Enteral:

Ingestion

Source:

Biological:

Animal

Plant:

Biological location:

Tissue and substructures:

Organ and components:

Prostate

Biofluid and excreta:

Cell and elements:

Extracellular

Role

Industrial application:

Prodrug

Pharmaceutical industry:

Pharmaceutical

Physical Properties

State

Solid

Experimental Properties

Property	Value	Reference
Melting Point	330 °C	Not Available
Boiling Point	137 °C	Wikipedia
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	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Spectra

EI-MS/GC-MS

Type	Description	Splash Key	View
EI-MS	Mass Spectrum (Electron Ionization)	splash10-03xu-9400000000-d7ffe72f606f1af3349b	2014-09-20	View Spectrum
GC-MS	Uracil, non-derivatized, GC-MS Spectrum	splash10-0002-5950000000-18425875415ad150c4fc	Spectrum
GC-MS	Uracil, 2 TMS, GC-MS Spectrum	splash10-006t-9740000000-e884a4b98e7e9dc75e5f	Spectrum
GC-MS	Uracil, 2 TMS, GC-MS Spectrum	splash10-052e-7790000000-026cb6beb5cde6a61b80	Spectrum
GC-MS	Uracil, non-derivatized, GC-MS Spectrum	splash10-02tc-9200000000-4a57c4e06fd552d6a9bf	Spectrum
GC-MS	Uracil, non-derivatized, GC-MS Spectrum	splash10-03xu-9400000000-1c29f070a8135b06f88b	Spectrum
GC-MS	Uracil, non-derivatized, GC-MS Spectrum	splash10-0002-5950000000-18425875415ad150c4fc	Spectrum
GC-MS	Uracil, non-derivatized, GC-MS Spectrum	splash10-006t-9740000000-e884a4b98e7e9dc75e5f	Spectrum
GC-MS	Uracil, non-derivatized, GC-MS Spectrum	splash10-052e-7790000000-026cb6beb5cde6a61b80	Spectrum
GC-MS	Uracil, non-derivatized, GC-MS Spectrum	splash10-0002-6940000000-a726178341f6443e60cc	Spectrum
Predicted GC-MS	Uracil, non-derivatized, Predicted GC-MS Spectrum - 70eV, Positive	splash10-03xu-9300000000-6a96f6ce1ef731689107	Spectrum
Predicted GC-MS	Uracil, non-derivatized, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum

MS/MS

Type	Description	Splash Key	View
MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 10V, Positive (Annotated)	splash10-03di-3900000000-e422eda255a4b6414f86	2012-07-24	View Spectrum
MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 25V, Positive (Annotated)	splash10-006y-9000000000-130eb5f4414426e03667	2012-07-24	View Spectrum
MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 40V, Positive (Annotated)	splash10-0006-9100000000-c096d08ca715d97cd732	2012-07-24	View Spectrum
MS/MS	LC-MS/MS Spectrum - EI-B (HITACHI M-60) , Positive	splash10-02tc-9200000000-83a0a6ad4fc1b407e570	2012-08-31	View Spectrum
MS/MS	LC-MS/MS Spectrum - EI-B (HITACHI M-80) , Positive	splash10-03xu-9400000000-acd0cfd54af7d6a55283	2012-08-31	View Spectrum
MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 10V, Negative	splash10-03di-0900000000-309fe212c929f3c6a930	2012-08-31	View Spectrum
MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 20V, Negative	splash10-03di-6900000000-55a7de75a40eab61da8b	2012-08-31	View Spectrum
MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 30V, Negative	splash10-0006-9000000000-1c3caab26eb7e359db92	2012-08-31	View Spectrum
MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 40V, Negative	splash10-0006-9000000000-7494d4e611a73ecb79ea	2012-08-31	View Spectrum
MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 50V, Negative	splash10-0006-9000000000-ed4046b040337db620d8	2012-08-31	View Spectrum
MS/MS	LC-MS/MS Spectrum - LC-ESI-QTOF (UPLC Q-Tof Premier, Waters) , Positive	splash10-03di-0900000000-ff54f3083ce4ccccfd95	2012-08-31	View Spectrum
MS/MS	LC-MS/MS Spectrum - LC-ESI-QTOF (UPLC Q-Tof Premier, Waters) , Negative	splash10-03di-0900000000-6728c1eb6f68b40c09f8	2012-08-31	View Spectrum
MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ , negative	splash10-03di-0900000000-309fe212c929f3c6a930	2017-09-14	View Spectrum
MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ , negative	splash10-03di-6900000000-55a7de75a40eab61da8b	2017-09-14	View Spectrum
MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ , negative	splash10-0006-9000000000-1c3caab26eb7e359db92	2017-09-14	View Spectrum
MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ , negative	splash10-0006-9000000000-7494d4e611a73ecb79ea	2017-09-14	View Spectrum
MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ , negative	splash10-0006-9000000000-ed4046b040337db620d8	2017-09-14	View Spectrum
MS/MS	LC-MS/MS Spectrum - LC-ESI-QTOF , negative	splash10-03di-0900000000-6728c1eb6f68b40c09f8	2017-09-14	View Spectrum
MS/MS	LC-MS/MS Spectrum - , negative	splash10-03di-0900000000-a21102c708f8d5eaf262	2017-09-14	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-03di-1900000000-0029cbdcaa1377a4d03e	2015-05-26	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0229-9400000000-c227e1deb392170cb323	2015-05-26	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0006-9000000000-3cf6f9fc3ab6890266ac	2015-05-26	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-03di-4900000000-67a3d94ab649e28bda13	2015-05-27	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-0006-9100000000-bbf50de54fc413b6588e	2015-05-27	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0006-9000000000-98042b91f1087b0c2563	2015-05-27	View Spectrum

NMR

Type	Description	View
1D NMR	¹³C NMR Spectrum (1D, 125 MHz, H₂O, experimental)	Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, experimental)	Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, DMSO-d6, experimental)	Spectrum
1D NMR	¹³C NMR Spectrum (1D, 100.72 MHz, DMSO-d6, experimental)	Spectrum
1D NMR	¹H NMR Spectrum (1D, D₂O, experimental)	Spectrum
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, D₂O, predicted)	Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	Spectrum
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, D₂O, predicted)	Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	Spectrum
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, D₂O, predicted)	Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, D₂O, predicted)	Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	Spectrum
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, predicted)	Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	Spectrum
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, D₂O, predicted)	Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	Spectrum
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, D₂O, predicted)	Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	Spectrum
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, D₂O, predicted)	Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, predicted)	Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	Spectrum
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)	Spectrum
2D NMR	[¹H, ¹³C]-HSQC NMR Spectrum (2D, 600 MHz, H₂O, experimental)	Spectrum

Pathways

Name	SMPDB/Pathwhiz	KEGG
Pyrimidine Metabolism
Beta-Alanine Metabolism
GABA-Transaminase Deficiency		Not Available
Ureidopropionase Deficiency		Not Available
Carnosinuria, carnosinemia		Not Available

Protein Targets

Enzymes

Protein Name	Gene Name	Locus	Uniprot ID	Details
Dihydropyrimidine dehydrogenase [NADP(+)]	DPYD	1p22	Q12882	details
Purine nucleoside phosphorylase	PNP	14q13.1	P00491	details
Thymidine phosphorylase	TYMP	22q13.33	P19971	details
Uridine phosphorylase 1	UPP1	7p12.3	Q16831	details
Uridine phosphorylase 2	UPP2	2q24.1	O95045	details
Uridine-cytidine kinase-like 1	UCKL1	20q13.33	Q9NWZ5	details
Uracil phosphoribosyltransferase homolog	UPRT		Q96BW1	details

Transporters

Not Available

Metal Bindings

Protein Name	Gene Name	Locus	Uniprot ID	Details
Dihydropyrimidine dehydrogenase [NADP(+)]	DPYD	1p22	Q12882	details

Receptors

Protein Name	Gene Name	Locus	Uniprot ID	Details
Thymidine phosphorylase	TYMP	22q13.33	P19971	details
Uracil nucleotide/cysteinyl leukotriene receptor	GPR17	2q21	Q13304	details

Transcriptional Factors

Not Available

Concentrations Data

Not Available

External Links

HMDB ID

HMDB0000300

DrugBank ID

DB03419

Phenol Explorer Compound ID

Not Available

FoodDB 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

General References

Not Available

Enzymes

Enzyme Details

1. Dihydropyrimidine dehydrogenase [NADP(+)]

General function:: Involved in electron carrier activity
Specific function:: Involved in pyrimidine base degradation. Catalyzes the reduction of uracil and thymine. Also involved the degradation of the chemotherapeutic drug 5-fluorouracil.
Gene Name:: DPYD
Uniprot ID:: Q12882
Molecular weight:: 111400.32

Enzyme Details

2. Purine nucleoside phosphorylase

General function:: Involved in purine-nucleoside phosphorylase activity
Specific function:: The purine nucleoside phosphorylases catalyze the phosphorolytic breakdown of the N-glycosidic bond in the beta-(deoxy)ribonucleoside molecules, with the formation of the corresponding free purine bases and pentose-1-phosphate.
Gene Name:: PNP
Uniprot ID:: P00491
Molecular weight:: 32117.69

Enzyme Details

3. Thymidine phosphorylase

General function:: Involved in transferase activity, transferring glycosyl groups
Specific function:: May have a role in maintaining the integrity of the blood vessels. Has growth promoting activity on endothelial cells, angiogenic activity in vivo and chemotactic activity on endothelial cells in vitro. Catalyzes the reversible phosphorolysis of thymidine. The produced molecules are then utilized as carbon and energy sources or in the rescue of pyrimidine bases for nucleotide synthesis.
Gene Name:: TYMP
Uniprot ID:: P19971
Molecular weight:: 49954.965

Enzyme Details

4. Uridine phosphorylase 1

General function:: Involved in transferase activity, transferring pentosyl groups
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:: UPP1
Uniprot ID:: Q16831
Molecular weight:: 33934.005

Enzyme Details

5. Uridine phosphorylase 2

General function:: Involved in transferase activity, transferring pentosyl groups
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. Shows substrate specificity and accept uridine, deoxyuridine, and thymidine as well as the two pyrimidine nucleoside analogs 5-fluorouridine and 5-fluoro-2(')-deoxyuridine as substrates.
Gene Name:: UPP2
Uniprot ID:: O95045
Molecular weight:: 41601.795

Enzyme Details

6. Uridine-cytidine kinase-like 1

General function:: Involved in ATP binding
Specific function:: May contribute to UTP accumulation needed for blast transformation and proliferation.
Gene Name:: UCKL1
Uniprot ID:: Q9NWZ5
Molecular weight:: 59465.77

Enzyme Details

7. Uracil phosphoribosyltransferase homolog

General function:: Involved in nucleoside metabolic process
Specific function:: Not Available
Gene Name:: UPRT
Uniprot ID:: Q96BW1
Molecular weight:: Not Available

Showing Compound Card for Uracil (CDB004843)

Structure for CDB004843 (Uracil)

Enzymes