Hmdb loader
Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2021-09-11 22:56:22 UTC
Update Date2022-11-23 22:29:22 UTC
HMDB IDHMDB0259943
Secondary Accession NumbersNone
Metabolite Identification
Common NameXymedon
Description1-(2-hydroxyethyl)-4,6-dimethyl-1,2-dihydropyrimidin-2-one 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 1-(2-hydroxyethyl)-4,6-dimethyl-1,2-dihydropyrimidin-2-one. This compound has been identified in human blood as reported by (PMID: 31557052 ). Xymedon is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically Xymedon 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
Thumb
Synonyms
ValueSource
1-(beta-Hydroxyethyl)-4,6-dimethyl-1,2-dihydro-2-oxopyrimidineMeSH
N-(2-Hydroxyethyl)-4,6-dimethyl-2-dehydropyrimidoneMeSH
XimedonMeSH
XimedoneMeSH
Chemical FormulaC8H12N2O2
Average Molecular Weight168.196
Monoisotopic Molecular Weight168.089877634
IUPAC Name1-(2-hydroxyethyl)-4,6-dimethyl-1,2-dihydropyrimidin-2-one
Traditional Name1-(2-hydroxyethyl)-4,6-dimethylpyrimidin-2-one
CAS Registry NumberNot Available
SMILES
CC1=NC(=O)N(CCO)C(C)=C1
InChI Identifier
InChI=1S/C8H12N2O2/c1-6-5-7(2)10(3-4-11)8(12)9-6/h5,11H,3-4H2,1-2H3
InChI KeyJLKVZOMORMUTDG-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.
KingdomOrganic compounds
Super ClassOrganoheterocyclic compounds
ClassDiazines
Sub ClassPyrimidines and pyrimidine derivatives
Direct ParentPyrimidones
Alternative Parents
Substituents
  • Pyrimidone
  • Hydropyrimidine
  • Heteroaromatic compound
  • Azacycle
  • Alkanolamine
  • Organic nitrogen compound
  • Organic oxygen compound
  • Organopnictogen compound
  • Organic oxide
  • Hydrocarbon derivative
  • Primary alcohol
  • Organooxygen compound
  • Organonitrogen compound
  • Alcohol
  • Aromatic heteromonocyclic compound
Molecular FrameworkAromatic heteromonocyclic compounds
External DescriptorsNot Available
Ontology
Physiological effectNot Available
Disposition
ProcessNot Available
RoleNot Available
Physical Properties
StateNot Available
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
logP-0.62ALOGPS
logP-0.65ChemAxon
logS-1.4ALOGPS
pKa (Strongest Acidic)15.56ChemAxon
pKa (Strongest Basic)-0.49ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count3ChemAxon
Hydrogen Donor Count1ChemAxon
Polar Surface Area52.9 ŲChemAxon
Rotatable Bond Count2ChemAxon
Refractivity46.56 m³·mol⁻¹ChemAxon
Polarizability17.59 ųChemAxon
Number of Rings1ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
AllCCS[M+H]+135.46132859911
AllCCS[M+H-H2O]+131.11332859911
AllCCS[M+Na]+140.6832859911
AllCCS[M+NH4]+139.51232859911
AllCCS[M-H]-137.19332859911
AllCCS[M+Na-2H]-138.43432859911
AllCCS[M+HCOO]-139.86632859911
DeepCCS[M+H]+138.69530932474
DeepCCS[M-H]-134.86830932474
DeepCCS[M-2H]-172.61430932474
DeepCCS[M+Na]+148.15330932474

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
xymedonCC1=NC(=O)N(CCO)C(C)=C12622.7Standard polar33892256
xymedonCC1=NC(=O)N(CCO)C(C)=C11587.4Standard non polar33892256
xymedonCC1=NC(=O)N(CCO)C(C)=C11700.0Semi standard non polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - Xymedon GC-MS (Non-derivatized) - 70eV, Positivesplash10-000i-4900000000-ba332a49eb3a10ba2cd72021-09-23Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Xymedon GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Xymedon GC-MS (TMS_1_1) - 70eV, PositiveNot Available2021-11-05Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Xymedon GC-MS (TBDMS_1_1) - 70eV, PositiveNot Available2021-11-05Wishart LabView Spectrum

NMR Spectra

Spectrum TypeDescriptionDeposition DateSourceView
Predicted 1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-10-27Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-10-27Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-10-27Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-10-27Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-10-27Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-10-27Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-10-27Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-10-27Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-10-27Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-10-27Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-10-27Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-10-27Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-10-27Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-10-27Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-10-27Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-10-27Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-10-27Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-10-27Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-10-27Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-10-27Wishart LabView Spectrum
Biological Properties
Cellular LocationsNot Available
Biospecimen Locations
  • Blood
Tissue LocationsNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodDetected but not QuantifiedNot QuantifiedNot SpecifiedNot SpecifiedNormal details
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDNot Available
KNApSAcK IDNot Available
Chemspider ID108776
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound121931
PDB IDNot Available
ChEBI IDNot Available
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General References
  1. 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 ]