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Showing Compound hydroxymethylpyrimidine (FDB030912)

Record Information
Version1.0
Creation date2015-05-07 20:30:18 UTC
Update date2025-11-19 03:02:29 UTC
Primary IDFDB030912
Secondary Accession NumbersNot Available
Chemical Information
FooDB Namehydroxymethylpyrimidine
DescriptionHydroxymethylpyrimidine, also known as pyramine or toxopyrimidine, is a member of the class of compounds known as hydropyrimidines. Hydropyrimidines are compounds containing a hydrogenated pyrimidine ring (i.e. containing less than the maximum number of double bonds.). Hydroxymethylpyrimidine is soluble (in water) and a very weakly acidic compound (based on its pKa). Hydroxymethylpyrimidine can be found in a number of food items such as mexican oregano, sugar apple, tronchuda cabbage, and cinnamon, which makes hydroxymethylpyrimidine a potential biomarker for the consumption of these food products. Hydroxymethylpyrimidine exists in E.coli (prokaryote) and yeast (eukaryote).
CAS Number73-67-6
Structure
Thumb
MOLSDFPDBSMILESInChI
Synonyms
SynonymSource
2-Methyl-4-amino-5-hydroxymethylpyrimidineChEBI
4-Amino-2-methyl-5-hydroxymethylpyrimidineChEBI
4-Amino-2-methyl-5-pyrimidinemethanolChEBI
AtoxopyrimidineChEBI
PyraminChEBI
PyramineChEBI
ToxopyrimidineChEBI
HMPKegg
HMP CPDHMDB
Predicted Properties
PropertyValueSource
Water Solubility12 g/LALOGPS
logP-0.26ALOGPS
logP-0.36ChemAxon
logS-1.1ALOGPS
pKa (Strongest Acidic)14.41ChemAxon
pKa (Strongest Basic)6.17ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count4ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area72.03 ŲChemAxon
Rotatable Bond Count1ChemAxon
Refractivity39.18 m³·mol⁻¹ChemAxon
Polarizability14.2 ųChemAxon
Number of Rings1ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Chemical FormulaC6H9N3O
IUPAC name(4-amino-2-methylpyrimidin-5-yl)methanol
InChI IdentifierInChI=1S/C6H9N3O/c1-4-8-2-5(3-10)6(7)9-4/h2,10H,3H2,1H3,(H2,7,8,9)
InChI KeyVUTBELPREDJDDH-UHFFFAOYSA-N
Isomeric SMILESCC1=NC=C(CO)C(N)=N1
Average Molecular Weight139.1552
Monoisotopic Molecular Weight139.074561925
Classification
Description Belongs to the class of organic compounds known as hydropyrimidines. Hydropyrimidines are compounds containing a hydrogenated pyrimidine ring (i.E. Containing less than the maximum number of double bonds.).
KingdomOrganic compounds
Super ClassOrganoheterocyclic compounds
ClassDiazines
Sub ClassPyrimidines and pyrimidine derivatives
Direct ParentHydropyrimidines
Alternative Parents
Substituents
  • Imidolactam
  • Hydropyrimidine
  • Heteroaromatic compound
  • Azacycle
  • Organic nitrogen compound
  • Organic oxygen compound
  • Organopnictogen compound
  • Hydrocarbon derivative
  • Aromatic alcohol
  • Primary alcohol
  • Organooxygen compound
  • Organonitrogen compound
  • Alcohol
  • Aromatic heteromonocyclic compound
Molecular FrameworkAromatic heteromonocyclic compounds
External Descriptors
Ontology
OntologyNo ontology term
Physico-Chemical Properties
Physico-Chemical Properties - Experimental
PropertyValueReference
Physical stateNot Available
Physical DescriptionNot Available
Mass CompositionNot Available
Melting PointNot Available
Boiling PointNot Available
Experimental Water SolubilityNot Available
Experimental logPNot Available
Experimental pKaNot Available
Isoelectric pointNot Available
ChargeNot Available
Optical RotationNot Available
Spectroscopic UV DataNot Available
DensityNot Available
Refractive IndexNot Available
Spectra
Spectra
EI-MS/GC-MS
TypeDescriptionSplash KeyView
Predicted GC-MShydroxymethylpyrimidine, non-derivatized, Predicted GC-MS Spectrum - 70eV, Positivesplash10-0abi-1900000000-e3106b1f3a699dcbb5cfSpectrum
Predicted GC-MShydroxymethylpyrimidine, non-derivatized, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MShydroxymethylpyrimidine, TMS_1_1, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MShydroxymethylpyrimidine, TMS_1_2, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MShydroxymethylpyrimidine, TBDMS_1_1, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MShydroxymethylpyrimidine, TBDMS_1_2, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
MS/MS
TypeDescriptionSplash KeyView
Predicted MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-006x-0900000000-1464721132642f06c7632015-05-27View Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-00di-1900000000-ffcb98d194c46375afed2015-05-27View Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-007k-9200000000-146c29035e7732b4a3862015-05-27View Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-000i-0900000000-a6fee6edf0aa915e501a2015-05-27View Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-0a4r-4900000000-7fb22624813fc7a882082015-05-27View Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-0006-9000000000-fd0e2a1b16eb26493e892015-05-27View Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-00dl-0900000000-bcee92b22282400d9aa92021-10-12View Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-00e9-7900000000-c3b2ba29d4a3384fbf9f2021-10-12View Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-00lu-9000000000-cecde0be355431a2920b2021-10-12View Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-000i-0900000000-cfc1d884f8ea3db6b6a62021-10-12View Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-006x-8900000000-bb08081d11c0ce9935372021-10-12View Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-014l-9000000000-f27a78acaec6ce8759832021-10-12View Spectrum
NMRNot Available
ChemSpider IDNot Available
ChEMBL IDNot Available
KEGG Compound IDC01279
Pubchem Compound ID777
Pubchem Substance IDNot Available
ChEBI IDNot Available
Phenol-Explorer IDNot Available
DrugBank IDNot Available
HMDB IDNot Available
CRC / DFC (Dictionary of Food Compounds) IDNot Available
EAFUS IDNot Available
Dr. Duke IDNot Available
BIGG IDNot Available
KNApSAcK IDC00007494
HET IDNot Available
Food Biomarker OntologyNot Available
VMH IDNot Available
Flavornet IDNot Available
GoodScent IDNot Available
SuperScent IDNot Available
Wikipedia IDNot Available
Phenol-Explorer Metabolite IDNot Available
Duplicate IDSNot Available
Old DFC IDSNot Available
Associated Foods
FoodContent Range AverageReference
FoodReference
Biological Effects and Interactions
Health Effects / BioactivitiesNot Available
EnzymesNot Available
PathwaysNot Available
MetabolismNot Available
BiosynthesisNot Available
Organoleptic Properties
FlavoursNot Available
Files
MSDSNot Available
References
Synthesis ReferenceNot Available
General ReferenceNot Available
Content Reference