Showing metabocard for 5-Hydroxymethyl-4-methyluracil (BMDB0000544)

IdentificationTaxonomyPhysical propertiesPathwaysSpectraConcentrationsLinksReferencesXML
Record Information
Version1.0
Creation Date2016-09-30 22:32:30 UTC
Update Date2020-04-22 15:04:05 UTC
BMDB IDBMDB0000544
Secondary Accession Numbers
  • BMDB00544
Metabolite Identification
Common Name5-Hydroxymethyl-4-methyluracil
Description5-Hydroxymethyl-4-methyluracil, also known as pentoxyl or 4-methyl-5-hydroxymethyluracil, 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 a significant number of articles have been published on 5-Hydroxymethyl-4-methyluracil.
Structure
Thumb
MOLSDF3D-SDFPDBSMILESInChI View 3D Structure
Synonyms
ValueSource
PentoxylHMDB
4-Methyl-5-hydroxymethyluracilHMDB
5-Hydroxymethyl-6-methyluracilHMDB
PentoxilHMDB
Chemical FormulaC6H8N2O3
Average Molecular Weight156.1393
Monoisotopic Molecular Weight156.053492132
IUPAC Name5-(hydroxymethyl)-6-methyl-1,2,3,4-tetrahydropyrimidine-2,4-dione
Traditional Name5-hydroxymethyl-6-methyluracil
CAS Registry Number147-61-5
SMILES
CC1=C(CO)C(=O)NC(=O)N1
InChI Identifier
InChI=1S/C6H8N2O3/c1-3-4(2-9)5(10)8-6(11)7-3/h9H,2H2,1H3,(H2,7,8,10,11)
InChI KeyXBAVGYMDOXCWQU-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
  • Aromatic alcohol
  • 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
StatusExpected but not Quantified
Origin
  • Endogenous
BiofunctionNot Available
ApplicationNot Available
Cellular locations
  • Cytoplasm
Physical Properties
StateSolid
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
logP-0.95ALOGPS
logP-1.5ChemAxon
logS-1.2ALOGPS
pKa (Strongest Acidic)8.97ChemAxon
pKa (Strongest Basic)-2.8ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count3ChemAxon
Hydrogen Donor Count3ChemAxon
Polar Surface Area78.43 ŲChemAxon
Rotatable Bond Count1ChemAxon
Refractivity37.92 m³·mol⁻¹ChemAxon
Polarizability14.31 ųChemAxon
Number of Rings1ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Spectra
Spectra
Biological Properties
Cellular Locations
  • Cytoplasm
Biospecimen LocationsNot Available
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
Not Available
HMDB IDHMDB0000544
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB022107
KNApSAcK IDNot Available
Chemspider ID8635
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN ID5529
PubChem Compound8983
PDB IDNot Available
ChEBI IDNot Available
References
Synthesis ReferenceCannon-Carlson S V; Gokhale H; Teebor G W Purification and characterization of 5-hydroxymethyluracil-DNA glycosylase from calf thymus. Its possible role in the maintenance of methylated cytosine residues. The Journal of biological chemistry (1989), 264(22), 13306-12.
Material Safety Data Sheet (MSDS)Not Available
General ReferencesNot Available