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Record Information

Version

5.0

Status

Expected but not Quantified

Creation Date

2021-09-23 22:52:29 UTC

Update Date

2021-09-23 22:52:30 UTC

HMDB ID

HMDB0303045

Secondary Accession Numbers

None

Metabolite Identification

Common Name

5-Hydroxyuracil

Description

5-hydroxyuracil, also known as dihydropyrimidine-2,4,5(3h)-trione or isobarbituric acid, is a member of the class of compounds known as hydroxypyrimidines. Hydroxypyrimidines are organic compounds containing a hydroxyl group attached to a pyrimidine ring. Pyrimidine is a 6-membered ring consisting of four carbon atoms and two nitrogen centers at the 1- and 3- ring positions. 5-hydroxyuracil is slightly soluble (in water) and a very weakly acidic compound (based on its pKa). 5-hydroxyuracil can be found in broad bean, which makes 5-hydroxyuracil a potential biomarker for the consumption of this food product. 5-hydroxyuracil is an oxidized form of cytosine that is produced by the oxidative deamination of cytosines by reactive oxygen species. It does not distort the DNA molecule and is bypassed by replicative DNA polymerases. It can miscode for adenine and is potentially mutagenic .

Structure

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

View in JSmol View Stereo Labels

Synonyms

Value	Source
Dihydropyrimidine-2,4,5(3H)-trione	ChEBI
Isobarbituric acid	ChEBI
Isobarbitate	Generator
Isobarbitic acid	Generator

Chemical Formula

C₄H₄N₂O₃

Average Molecular Weight

128.0862

Monoisotopic Molecular Weight

128.022192004

IUPAC Name

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

Traditional Name

5-hydroxyuracil

CAS Registry Number

Not Available

SMILES

OC1=CNC(=O)NC1=O

InChI Identifier

InChI=1S/C4H4N2O3/c7-2-1-5-4(9)6-3(2)8/h1,7H,(H2,5,6,8,9)

InChI Key

OFJNVANOCZHTMW-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as hydroxypyrimidines. These are organic compounds containing a hydroxyl group attached to a pyrimidine ring. 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

Hydroxypyrimidines

Alternative Parents

Substituents

Hydroxypyrimidine
Heteroaromatic compound
Azacycle
Polyol
Organic nitrogen compound
Organic oxygen compound
Organopnictogen compound
Hydrocarbon derivative
Organooxygen compound
Organonitrogen compound
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

hydroxypyrimidine (CHEBI:29115 )

Ontology

Not Available

Exogenous (HMDB: HMDB0303045)

Food

Pulse

Bean

Broad bean (FooDB: FOOD00197)

Process

Not Available

Role

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	-1.4	ALOGPS
logP	-1.1	ChemAxon
logS	-1.2	ALOGPS
pKa (Strongest Acidic)	8.8	ChemAxon
pKa (Strongest Basic)	-4.9	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	3	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	78.43 Å²	ChemAxon
Rotatable Bond Count	0	ChemAxon
Refractivity	27.94 m³·mol⁻¹	ChemAxon
Polarizability	10.27 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]+	127.375	32859911
AllCCS	[M+H-H2O]+	122.586	32859911
AllCCS	[M+Na]+	133.135	32859911
AllCCS	[M+NH4]+	131.845	32859911
AllCCS	[M-H]-	120.652	32859911
AllCCS	[M+Na-2H]-	122.722	32859911
AllCCS	[M+HCOO]-	125.033	32859911
DeepCCS	[M+H]+	119.921	30932474
DeepCCS	[M-H]-	116.913	30932474
DeepCCS	[M-2H]-	153.286	30932474
DeepCCS	[M+Na]+	128.479	30932474

Predicted Retention Times

Underivatized

Chromatographic Method	Retention Time	Reference
Predicted by Siyang on May 30, 2022	9.1315 minutes	33406817
Predicted by Siyang using ReTip algorithm on June 8, 2022	4.03 minutes	32390414
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid	539.9 seconds	40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid	348.7 seconds	40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid	80.5 seconds	40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid	244.6 seconds	40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	56.3 seconds	40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid	278.2 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	281.6 seconds	40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)	452.4 seconds	40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid	602.2 seconds	40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid	131.3 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	704.8 seconds	40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	211.1 seconds	40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	264.4 seconds	40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate	670.1 seconds	40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA	317.5 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	332.8 seconds	40023050

Predicted Kovats Retention Indices

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
5-Hydroxyuracil,2TMS,isomer #1	C[Si](C)(C)OC1=CN([Si](C)(C)C)C(=O)[NH]C1=O	1729.7	Semi standard non polar	33892256
5-Hydroxyuracil,2TMS,isomer #1	C[Si](C)(C)OC1=CN([Si](C)(C)C)C(=O)[NH]C1=O	1753.8	Standard non polar	33892256
5-Hydroxyuracil,2TMS,isomer #1	C[Si](C)(C)OC1=CN([Si](C)(C)C)C(=O)[NH]C1=O	1982.2	Standard polar	33892256
5-Hydroxyuracil,2TMS,isomer #2	C[Si](C)(C)OC1=C[NH]C(=O)N([Si](C)(C)C)C1=O	1672.5	Semi standard non polar	33892256
5-Hydroxyuracil,2TMS,isomer #2	C[Si](C)(C)OC1=C[NH]C(=O)N([Si](C)(C)C)C1=O	1732.7	Standard non polar	33892256
5-Hydroxyuracil,2TMS,isomer #2	C[Si](C)(C)OC1=C[NH]C(=O)N([Si](C)(C)C)C1=O	1907.1	Standard polar	33892256
5-Hydroxyuracil,2TMS,isomer #3	C[Si](C)(C)N1C=C(O)C(=O)N([Si](C)(C)C)C1=O	1693.8	Semi standard non polar	33892256
5-Hydroxyuracil,2TMS,isomer #3	C[Si](C)(C)N1C=C(O)C(=O)N([Si](C)(C)C)C1=O	1741.7	Standard non polar	33892256
5-Hydroxyuracil,2TMS,isomer #3	C[Si](C)(C)N1C=C(O)C(=O)N([Si](C)(C)C)C1=O	2020.2	Standard polar	33892256
5-Hydroxyuracil,3TMS,isomer #1	C[Si](C)(C)OC1=CN([Si](C)(C)C)C(=O)N([Si](C)(C)C)C1=O	1858.3	Semi standard non polar	33892256
5-Hydroxyuracil,3TMS,isomer #1	C[Si](C)(C)OC1=CN([Si](C)(C)C)C(=O)N([Si](C)(C)C)C1=O	1823.9	Standard non polar	33892256
5-Hydroxyuracil,3TMS,isomer #1	C[Si](C)(C)OC1=CN([Si](C)(C)C)C(=O)N([Si](C)(C)C)C1=O	1836.9	Standard polar	33892256
5-Hydroxyuracil,2TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC1=CN([Si](C)(C)C(C)(C)C)C(=O)[NH]C1=O	2198.0	Semi standard non polar	33892256
5-Hydroxyuracil,2TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC1=CN([Si](C)(C)C(C)(C)C)C(=O)[NH]C1=O	2193.1	Standard non polar	33892256
5-Hydroxyuracil,2TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC1=CN([Si](C)(C)C(C)(C)C)C(=O)[NH]C1=O	2172.6	Standard polar	33892256
5-Hydroxyuracil,2TBDMS,isomer #2	CC(C)(C)[Si](C)(C)OC1=C[NH]C(=O)N([Si](C)(C)C(C)(C)C)C1=O	2127.8	Semi standard non polar	33892256
5-Hydroxyuracil,2TBDMS,isomer #2	CC(C)(C)[Si](C)(C)OC1=C[NH]C(=O)N([Si](C)(C)C(C)(C)C)C1=O	2157.6	Standard non polar	33892256
5-Hydroxyuracil,2TBDMS,isomer #2	CC(C)(C)[Si](C)(C)OC1=C[NH]C(=O)N([Si](C)(C)C(C)(C)C)C1=O	2096.5	Standard polar	33892256
5-Hydroxyuracil,2TBDMS,isomer #3	CC(C)(C)[Si](C)(C)N1C=C(O)C(=O)N([Si](C)(C)C(C)(C)C)C1=O	2134.8	Semi standard non polar	33892256
5-Hydroxyuracil,2TBDMS,isomer #3	CC(C)(C)[Si](C)(C)N1C=C(O)C(=O)N([Si](C)(C)C(C)(C)C)C1=O	2160.6	Standard non polar	33892256
5-Hydroxyuracil,2TBDMS,isomer #3	CC(C)(C)[Si](C)(C)N1C=C(O)C(=O)N([Si](C)(C)C(C)(C)C)C1=O	2151.1	Standard polar	33892256
5-Hydroxyuracil,3TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC1=CN([Si](C)(C)C(C)(C)C)C(=O)N([Si](C)(C)C(C)(C)C)C1=O	2398.9	Semi standard non polar	33892256
5-Hydroxyuracil,3TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC1=CN([Si](C)(C)C(C)(C)C)C(=O)N([Si](C)(C)C(C)(C)C)C1=O	2456.2	Standard non polar	33892256
5-Hydroxyuracil,3TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC1=CN([Si](C)(C)C(C)(C)C)C(=O)N([Si](C)(C)C(C)(C)C)C1=O	2180.3	Standard polar	33892256

Spectra

MS/MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5-Hydroxyuracil 10V, Positive-QTOF	splash10-004i-2900000000-7c98db209af74a35673f	2016-06-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5-Hydroxyuracil 20V, Positive-QTOF	splash10-06vr-9700000000-5f609d5f41d3ad58ca81	2016-06-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5-Hydroxyuracil 40V, Positive-QTOF	splash10-0ab9-9000000000-e8b1bac36c23b484e8fc	2016-06-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5-Hydroxyuracil 10V, Negative-QTOF	splash10-004l-9800000000-47afce14571a38f0a313	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5-Hydroxyuracil 20V, Negative-QTOF	splash10-0006-9100000000-b393d7ba3fdf523f21a5	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5-Hydroxyuracil 40V, Negative-QTOF	splash10-0006-9000000000-ca85a1bf1d20542f3ae5	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5-Hydroxyuracil 10V, Positive-QTOF	splash10-004i-0900000000-29b0b53134d035b235ae	2021-10-21	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5-Hydroxyuracil 20V, Positive-QTOF	splash10-004i-9800000000-82c2f9c5476ae42d70ba	2021-10-21	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5-Hydroxyuracil 40V, Positive-QTOF	splash10-0aou-9000000000-c010103cfa38919d0321	2021-10-21	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5-Hydroxyuracil 10V, Negative-QTOF	splash10-004l-6900000000-c1f4383276e3eda60a68	2021-10-21	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5-Hydroxyuracil 20V, Negative-QTOF	splash10-0006-9000000000-b21221b06476df9dd12b	2021-10-21	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5-Hydroxyuracil 40V, Negative-QTOF	splash10-0006-9000000000-90726b17dc36e29c5299	2021-10-21	Wishart Lab	View Spectrum

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Not Available

Tissue Locations

Not Available

Pathways

Not Available

Name	SMPDB/PathBank	KEGG

Normal Concentrations

Not Available

Abnormal Concentrations

Not Available

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

FDB007481

KNApSAcK ID

Not Available

Chemspider ID

66014

KEGG Compound ID

Not Available

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

29115

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-Hydroxyuracil (HMDB0303045)

MOL for HMDB0303045 (5-Hydroxyuracil)

3D MOL for HMDB0303045 (5-Hydroxyuracil)

3D SDF for HMDB0303045 (5-Hydroxyuracil)

3D-SDF for HMDB0303045 (5-Hydroxyuracil)

PDB for HMDB0303045 (5-Hydroxyuracil)

3D PDB for HMDB0303045 (5-Hydroxyuracil)

SMILES for HMDB0303045 (5-Hydroxyuracil)

INCHI for HMDB0303045 (5-Hydroxyuracil)

Structure for HMDB0303045 (5-Hydroxyuracil)

3D Structure for HMDB0303045 (5-Hydroxyuracil)

Predicted Collision Cross Sections

Predicted Retention Times

Underivatized

Predicted Kovats Retention Indices

Derivatized

MS/MS Spectra