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

Record Information

Version

5.0

Status

Detected but not Quantified

Creation Date

2021-09-10 23:51:10 UTC

Update Date

2021-09-26 22:56:09 UTC

HMDB ID

HMDB0246840

Secondary Accession Numbers

None

Metabolite Identification

Common Name

5-Propynyluracil

Description

5-Propynyluracil 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. Based on a literature review very few articles have been published on 5-Propynyluracil. This compound has been identified in human blood as reported by (PMID: 31557052 ). 5-propynyluracil is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically 5-Propynyluracil is part of the human exposome. The exposome can be defined as the collection of all the exposures of an individual in a lifetime and how those exposures relate to health. An individual's exposure begins before birth and includes insults from environmental and occupational sources.

Structure

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

View in JSmol View Stereo Labels

Synonyms

Not Available

Chemical Formula

C₇H₆N₂O₂

Average Molecular Weight

150.137

Monoisotopic Molecular Weight

150.042927441

IUPAC Name

5-(prop-1-yn-1-yl)-1,2,3,4-tetrahydropyrimidine-2,4-dione

Traditional Name

5-(prop-1-yn-1-yl)-1,3-dihydropyrimidine-2,4-dione

CAS Registry Number

Not Available

SMILES

CC#CC1=CNC(=O)NC1=O

InChI Identifier

InChI=1S/C7H6N2O2/c1-2-3-5-4-8-7(11)9-6(5)10/h4H,1H3,(H2,8,9,10,11)

InChI Key

UJBCLAXPPIDQEE-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

Not Available

Ontology

Physiological effect

Not Available

Disposition

Biological location

Non-excretory biofluid

Biofluid or Excreta

Blood (PMID: 31557052)

Source

Exogenous

Exogenous (PMID: 31557052)

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	0.08	ALOGPS
logP	0.014	ChemAxon
logS	-2.5	ALOGPS
pKa (Strongest Acidic)	8.54	ChemAxon
pKa (Strongest Basic)	-6.1	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	1	ChemAxon
Refractivity	38.89 m³·mol⁻¹	ChemAxon
Polarizability	14.41 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
DeepCCS	[M+H]+	120.358	30932474
DeepCCS	[M-H]-	116.545	30932474
DeepCCS	[M-2H]-	153.341	30932474
DeepCCS	[M+Na]+	128.915	30932474

Predicted Retention Times

Underivatized

Chromatographic Method	Retention Time	Reference
Predicted by Siyang on May 30, 2022	9.1856 minutes	33406817
Predicted by Siyang using ReTip algorithm on June 8, 2022	2.09 minutes	32390414
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid	715.7 seconds	40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid	323.5 seconds	40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid	94.2 seconds	40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid	206.7 seconds	40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	58.6 seconds	40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid	280.5 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	327.5 seconds	40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)	92.5 seconds	40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid	622.6 seconds	40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid	260.7 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	760.9 seconds	40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	215.5 seconds	40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	223.8 seconds	40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate	503.6 seconds	40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA	254.8 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	136.5 seconds	40023050

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
5-Propynyluracil	CC#CC1=CNC(=O)NC1=O	2330.8	Standard polar	33892256
5-Propynyluracil	CC#CC1=CNC(=O)NC1=O	1527.7	Standard non polar	33892256
5-Propynyluracil	CC#CC1=CNC(=O)NC1=O	1872.7	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
5-Propynyluracil,1TMS,isomer #1	CC#CC1=CN([Si](C)(C)C)C(=O)[NH]C1=O	1793.0	Semi standard non polar	33892256
5-Propynyluracil,1TMS,isomer #1	CC#CC1=CN([Si](C)(C)C)C(=O)[NH]C1=O	1732.2	Standard non polar	33892256
5-Propynyluracil,1TMS,isomer #1	CC#CC1=CN([Si](C)(C)C)C(=O)[NH]C1=O	2366.3	Standard polar	33892256
5-Propynyluracil,1TMS,isomer #2	CC#CC1=C[NH]C(=O)N([Si](C)(C)C)C1=O	1726.7	Semi standard non polar	33892256
5-Propynyluracil,1TMS,isomer #2	CC#CC1=C[NH]C(=O)N([Si](C)(C)C)C1=O	1725.6	Standard non polar	33892256
5-Propynyluracil,1TMS,isomer #2	CC#CC1=C[NH]C(=O)N([Si](C)(C)C)C1=O	2355.8	Standard polar	33892256
5-Propynyluracil,2TMS,isomer #1	CC#CC1=CN([Si](C)(C)C)C(=O)N([Si](C)(C)C)C1=O	1867.3	Semi standard non polar	33892256
5-Propynyluracil,2TMS,isomer #1	CC#CC1=CN([Si](C)(C)C)C(=O)N([Si](C)(C)C)C1=O	1884.4	Standard non polar	33892256
5-Propynyluracil,2TMS,isomer #1	CC#CC1=CN([Si](C)(C)C)C(=O)N([Si](C)(C)C)C1=O	2147.1	Standard polar	33892256
5-Propynyluracil,1TBDMS,isomer #1	CC#CC1=CN([Si](C)(C)C(C)(C)C)C(=O)[NH]C1=O	2049.1	Semi standard non polar	33892256
5-Propynyluracil,1TBDMS,isomer #1	CC#CC1=CN([Si](C)(C)C(C)(C)C)C(=O)[NH]C1=O	1978.4	Standard non polar	33892256
5-Propynyluracil,1TBDMS,isomer #1	CC#CC1=CN([Si](C)(C)C(C)(C)C)C(=O)[NH]C1=O	2451.8	Standard polar	33892256
5-Propynyluracil,1TBDMS,isomer #2	CC#CC1=C[NH]C(=O)N([Si](C)(C)C(C)(C)C)C1=O	1950.0	Semi standard non polar	33892256
5-Propynyluracil,1TBDMS,isomer #2	CC#CC1=C[NH]C(=O)N([Si](C)(C)C(C)(C)C)C1=O	1964.6	Standard non polar	33892256
5-Propynyluracil,1TBDMS,isomer #2	CC#CC1=C[NH]C(=O)N([Si](C)(C)C(C)(C)C)C1=O	2403.8	Standard polar	33892256
5-Propynyluracil,2TBDMS,isomer #1	CC#CC1=CN([Si](C)(C)C(C)(C)C)C(=O)N([Si](C)(C)C(C)(C)C)C1=O	2279.0	Semi standard non polar	33892256
5-Propynyluracil,2TBDMS,isomer #1	CC#CC1=CN([Si](C)(C)C(C)(C)C)C(=O)N([Si](C)(C)C(C)(C)C)C1=O	2344.5	Standard non polar	33892256
5-Propynyluracil,2TBDMS,isomer #1	CC#CC1=CN([Si](C)(C)C(C)(C)C)C(=O)N([Si](C)(C)C(C)(C)C)C1=O	2284.1	Standard polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted GC-MS	Predicted GC-MS Spectrum - 5-Propynyluracil GC-MS (Non-derivatized) - 70eV, Positive	splash10-0zor-3900000000-12f318c67e4c50dee234	2021-09-24	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 5-Propynyluracil GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum

MS/MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5-Propynyluracil 10V, Positive-QTOF	splash10-0udi-0900000000-df9aa8d2c0dabf6ab72f	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5-Propynyluracil 20V, Positive-QTOF	splash10-0udi-4900000000-97accd4c45139ded6d6d	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5-Propynyluracil 40V, Positive-QTOF	splash10-0w29-9000000000-28ba08959835ae190086	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5-Propynyluracil 10V, Negative-QTOF	splash10-0002-3900000000-ce85c1314d33074b55d3	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5-Propynyluracil 20V, Negative-QTOF	splash10-0006-9300000000-a0806aa862a21f0036b2	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5-Propynyluracil 40V, Negative-QTOF	splash10-0006-9000000000-0994285a5b6da6dc7cc5	2021-10-12	Wishart Lab	View Spectrum

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Blood

Tissue Locations

Not Available

Pathways

Not Available

Name	SMPDB/PathBank	KEGG

Normal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Blood	Detected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	31557052	details

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

Not Available

KNApSAcK ID

Not Available

Chemspider ID

116452

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

131813

PDB ID

Not Available

ChEBI ID

Not Available

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

Barupal DK, Fiehn O: Generating the Blood Exposome Database Using a Comprehensive Text Mining and Database Fusion Approach. Environ Health Perspect. 2019 Sep;127(9):97008. doi: 10.1289/EHP4713. Epub 2019 Sep 26. [PubMed:31557052 ]

Showing metabocard for 5-Propynyluracil (HMDB0246840)

MOL for HMDB0246840 (5-Propynyluracil)

3D MOL for HMDB0246840 (5-Propynyluracil)

3D SDF for HMDB0246840 (5-Propynyluracil)

3D-SDF for HMDB0246840 (5-Propynyluracil)

PDB for HMDB0246840 (5-Propynyluracil)

3D PDB for HMDB0246840 (5-Propynyluracil)

SMILES for HMDB0246840 (5-Propynyluracil)

INCHI for HMDB0246840 (5-Propynyluracil)

Structure for HMDB0246840 (5-Propynyluracil)

3D Structure for HMDB0246840 (5-Propynyluracil)

Predicted Collision Cross Sections

Predicted Retention Times

Underivatized

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra