Hmdb loader
Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2021-09-11 00:12:42 UTC
Update Date2021-09-26 22:56:44 UTC
HMDB IDHMDB0247200
Secondary Accession NumbersNone
Metabolite Identification
Common Name1-(2-Hydroxyethoxy)methyl-5-methyluracil
Description1-(2-Hydroxyethoxy)methyl-5-methyluracil, also known as acyclothymidine, 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-Hydroxyethoxy)methyl-5-methyluracil. This compound has been identified in human blood as reported by (PMID: 31557052 ). 1-(2-hydroxyethoxy)methyl-5-methyluracil is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically 1-(2-Hydroxyethoxy)methyl-5-methyluracil 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
N-(2-(Hydroxyethoxy)methyl)-5-methyluracilHMDB
AcyclothymidineHMDB
Chemical FormulaC8H12N2O4
Average Molecular Weight200.194
Monoisotopic Molecular Weight200.079706874
IUPAC Name1-[(2-hydroxyethoxy)methyl]-5-methyl-1,2,3,4-tetrahydropyrimidine-2,4-dione
Traditional Name1-[(2-hydroxyethoxy)methyl]-5-methyl-3H-pyrimidine-2,4-dione
CAS Registry NumberNot Available
SMILES
CC1=CN(COCCO)C(=O)NC1=O
InChI Identifier
InChI=1S/C8H12N2O4/c1-6-4-10(5-14-3-2-11)8(13)9-7(6)12/h4,11H,2-3,5H2,1H3,(H,9,12,13)
InChI KeyATKOZYBRBNGECU-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
  • Vinylogous amide
  • Heteroaromatic compound
  • Lactam
  • Urea
  • Azacycle
  • Alcohol
  • Hydrocarbon derivative
  • Organic oxide
  • Organopnictogen compound
  • Primary alcohol
  • Organooxygen compound
  • Organonitrogen compound
  • Organic oxygen compound
  • Organic nitrogen compound
  • 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-0.92ALOGPS
logP-0.86ChemAxon
logS-0.82ALOGPS
pKa (Strongest Acidic)9.97ChemAxon
pKa (Strongest Basic)-2.7ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count4ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area78.87 ŲChemAxon
Rotatable Bond Count4ChemAxon
Refractivity47.37 m³·mol⁻¹ChemAxon
Polarizability19.6 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
DeepCCS[M+H]+137.36230932474
DeepCCS[M-H]-133.52930932474
DeepCCS[M-2H]-170.84630932474
DeepCCS[M+Na]+146.38630932474
AllCCS[M+H]+142.932859911
AllCCS[M+H-H2O]+139.032859911
AllCCS[M+NH4]+146.632859911
AllCCS[M+Na]+147.632859911
AllCCS[M-H]-144.132859911
AllCCS[M+Na-2H]-145.032859911
AllCCS[M+HCOO]-146.032859911

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
1-(2-Hydroxyethoxy)methyl-5-methyluracilCC1=CN(COCCO)C(=O)NC1=O2892.7Standard polar33892256
1-(2-Hydroxyethoxy)methyl-5-methyluracilCC1=CN(COCCO)C(=O)NC1=O1836.8Standard non polar33892256
1-(2-Hydroxyethoxy)methyl-5-methyluracilCC1=CN(COCCO)C(=O)NC1=O1953.3Semi standard non polar33892256

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
1-(2-Hydroxyethoxy)methyl-5-methyluracil,2TMS,isomer #1CC1=CN(COCCO[Si](C)(C)C)C(=O)N([Si](C)(C)C)C1=O2024.4Semi standard non polar33892256
1-(2-Hydroxyethoxy)methyl-5-methyluracil,2TMS,isomer #1CC1=CN(COCCO[Si](C)(C)C)C(=O)N([Si](C)(C)C)C1=O2101.4Standard non polar33892256
1-(2-Hydroxyethoxy)methyl-5-methyluracil,2TMS,isomer #1CC1=CN(COCCO[Si](C)(C)C)C(=O)N([Si](C)(C)C)C1=O2414.0Standard polar33892256
1-(2-Hydroxyethoxy)methyl-5-methyluracil,2TBDMS,isomer #1CC1=CN(COCCO[Si](C)(C)C(C)(C)C)C(=O)N([Si](C)(C)C(C)(C)C)C1=O2459.8Semi standard non polar33892256
1-(2-Hydroxyethoxy)methyl-5-methyluracil,2TBDMS,isomer #1CC1=CN(COCCO[Si](C)(C)C(C)(C)C)C(=O)N([Si](C)(C)C(C)(C)C)C1=O2517.1Standard non polar33892256
1-(2-Hydroxyethoxy)methyl-5-methyluracil,2TBDMS,isomer #1CC1=CN(COCCO[Si](C)(C)C(C)(C)C)C(=O)N([Si](C)(C)C(C)(C)C)C1=O2553.3Standard polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - 1-(2-Hydroxyethoxy)methyl-5-methyluracil GC-MS (Non-derivatized) - 70eV, Positivesplash10-004u-8900000000-ff833170cbb700fb1b602021-09-23Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 1-(2-Hydroxyethoxy)methyl-5-methyluracil GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 1-(2-Hydroxyethoxy)methyl-5-methyluracil GC-MS (TMS_1_1) - 70eV, PositiveNot Available2021-11-03Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 1-(2-Hydroxyethoxy)methyl-5-methyluracil GC-MS (TMS_1_2) - 70eV, PositiveNot Available2021-11-03Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 1-(2-Hydroxyethoxy)methyl-5-methyluracil GC-MS (TBDMS_1_1) - 70eV, PositiveNot Available2021-11-03Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 1-(2-Hydroxyethoxy)methyl-5-methyluracil GC-MS (TBDMS_1_2) - 70eV, PositiveNot Available2021-11-03Wishart LabView Spectrum

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 1-(2-Hydroxyethoxy)methyl-5-methyluracil 10V, Positive-QTOFsplash10-0f79-0930000000-1788371aadb096cbe6d82021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 1-(2-Hydroxyethoxy)methyl-5-methyluracil 20V, Positive-QTOFsplash10-004i-2900000000-f3cbabf2b50f8a57095c2021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 1-(2-Hydroxyethoxy)methyl-5-methyluracil 40V, Positive-QTOFsplash10-0pec-9300000000-784e3746ccbae42a76592021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 1-(2-Hydroxyethoxy)methyl-5-methyluracil 10V, Negative-QTOFsplash10-000i-0900000000-e99ad76ed0da1b60386e2021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 1-(2-Hydroxyethoxy)methyl-5-methyluracil 20V, Negative-QTOFsplash10-004i-4900000000-e999600a32b728e056252021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 1-(2-Hydroxyethoxy)methyl-5-methyluracil 40V, Negative-QTOFsplash10-002f-9400000000-05f23ab13233ba447b6e2021-10-12Wishart LabView Spectrum

NMR Spectra

Spectrum TypeDescriptionDeposition DateSourceView
Predicted 1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-10-13Wishart 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 ID65295
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound72358
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 ]