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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2021-09-12 00:34:52 UTC
Update Date2021-09-26 23:18:27 UTC
HMDB IDHMDB0260369
Secondary Accession NumbersNone
Metabolite Identification
Common Name6-[(2R,4S,5R)-4-Hydroxy-5-(hydroxymethyl)oxolan-2-yl]-7,8-dihydroimidazo[1,2-c]pyrimidin-5-one
Description6-[4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]-5H,6H,7H,8H-imidazo[1,2-c]pyrimidin-5-one belongs to the class of organic compounds known as pentoses. These are monosaccharides in which the carbohydrate moiety contains five carbon atoms. Based on a literature review very few articles have been published on 6-[4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]-5H,6H,7H,8H-imidazo[1,2-c]pyrimidin-5-one. This compound has been identified in human blood as reported by (PMID: 31557052 ). 6-[(2r,4s,5r)-4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]-7,8-dihydroimidazo[1,2-c]pyrimidin-5-one is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically 6-[(2R,4S,5R)-4-Hydroxy-5-(hydroxymethyl)oxolan-2-yl]-7,8-dihydroimidazo[1,2-c]pyrimidin-5-one 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
SynonymsNot Available
Chemical FormulaC11H15N3O4
Average Molecular Weight253.258
Monoisotopic Molecular Weight253.106255975
IUPAC Name6-[4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]-5H,6H,7H,8H-imidazo[1,2-c]pyrimidin-5-one
Traditional Name6-[4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]-7H,8H-imidazo[1,2-c]pyrimidin-5-one
CAS Registry NumberNot Available
SMILES
OCC1OC(CC1O)N1CCC2=NC=CN2C1=O
InChI Identifier
InChI=1S/C11H15N3O4/c15-6-8-7(16)5-10(18-8)14-3-1-9-12-2-4-13(9)11(14)17/h2,4,7-8,10,15-16H,1,3,5-6H2
InChI KeyDKGALSINFDGMOW-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as pentoses. These are monosaccharides in which the carbohydrate moiety contains five carbon atoms.
KingdomOrganic compounds
Super ClassOrganic oxygen compounds
ClassOrganooxygen compounds
Sub ClassCarbohydrates and carbohydrate conjugates
Direct ParentPentoses
Alternative Parents
Substituents
  • Pentose monosaccharide
  • Imidazopyrimidinone
  • Pyrimidone
  • Pyrimidine
  • N-substituted imidazole
  • Heteroaromatic compound
  • Tetrahydrofuran
  • Imidazole
  • Azole
  • Urea
  • Secondary alcohol
  • Carbonic acid derivative
  • Oxacycle
  • Azacycle
  • Organoheterocyclic compound
  • Organic nitrogen compound
  • Organopnictogen compound
  • Organic oxide
  • Hydrocarbon derivative
  • Primary alcohol
  • Organonitrogen compound
  • Alcohol
  • Aromatic heteropolycyclic compound
Molecular FrameworkAromatic heteropolycyclic compounds
External DescriptorsNot Available
Ontology
Not 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-1.2ALOGPS
logP-1.5ChemAxon
logS-0.94ALOGPS
pKa (Strongest Acidic)13.9ChemAxon
pKa (Strongest Basic)2.31ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count5ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area87.82 ŲChemAxon
Rotatable Bond Count2ChemAxon
Refractivity59.52 m³·mol⁻¹ChemAxon
Polarizability25.2 ųChemAxon
Number of Rings3ChemAxon
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]+158.00432859911
AllCCS[M+H-H2O]+154.32832859911
AllCCS[M+Na]+162.39832859911
AllCCS[M+NH4]+161.41732859911
AllCCS[M-H]-158.47832859911
AllCCS[M+Na-2H]-158.15532859911
AllCCS[M+HCOO]-157.90832859911
DeepCCS[M+H]+150.8630932474
DeepCCS[M-H]-148.50230932474
DeepCCS[M-2H]-183.30930932474
DeepCCS[M+Na]+159.18930932474

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
6-[(2R,4S,5R)-4-Hydroxy-5-(hydroxymethyl)oxolan-2-yl]-7,8-dihydroimidazo[1,2-c]pyrimidin-5-oneOCC1OC(CC1O)N1CCC2=NC=CN2C1=O3585.2Standard polar33892256
6-[(2R,4S,5R)-4-Hydroxy-5-(hydroxymethyl)oxolan-2-yl]-7,8-dihydroimidazo[1,2-c]pyrimidin-5-oneOCC1OC(CC1O)N1CCC2=NC=CN2C1=O2069.1Standard non polar33892256
6-[(2R,4S,5R)-4-Hydroxy-5-(hydroxymethyl)oxolan-2-yl]-7,8-dihydroimidazo[1,2-c]pyrimidin-5-oneOCC1OC(CC1O)N1CCC2=NC=CN2C1=O2537.2Semi standard non polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - 6-[(2R,4S,5R)-4-Hydroxy-5-(hydroxymethyl)oxolan-2-yl]-7,8-dihydroimidazo[1,2-c]pyrimidin-5-one GC-MS (Non-derivatized) - 70eV, Positivesplash10-0006-9340000000-c2e5a81980c8c922226c2021-09-23Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 6-[(2R,4S,5R)-4-Hydroxy-5-(hydroxymethyl)oxolan-2-yl]-7,8-dihydroimidazo[1,2-c]pyrimidin-5-one GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 6-[(2R,4S,5R)-4-Hydroxy-5-(hydroxymethyl)oxolan-2-yl]-7,8-dihydroimidazo[1,2-c]pyrimidin-5-one GC-MS (TMS_1_1) - 70eV, PositiveNot Available2021-11-05Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 6-[(2R,4S,5R)-4-Hydroxy-5-(hydroxymethyl)oxolan-2-yl]-7,8-dihydroimidazo[1,2-c]pyrimidin-5-one GC-MS (TMS_1_2) - 70eV, PositiveNot Available2021-11-05Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 6-[(2R,4S,5R)-4-Hydroxy-5-(hydroxymethyl)oxolan-2-yl]-7,8-dihydroimidazo[1,2-c]pyrimidin-5-one GC-MS (TMS_2_1) - 70eV, PositiveNot Available2021-11-05Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 6-[(2R,4S,5R)-4-Hydroxy-5-(hydroxymethyl)oxolan-2-yl]-7,8-dihydroimidazo[1,2-c]pyrimidin-5-one GC-MS (TBDMS_1_1) - 70eV, PositiveNot Available2021-11-05Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 6-[(2R,4S,5R)-4-Hydroxy-5-(hydroxymethyl)oxolan-2-yl]-7,8-dihydroimidazo[1,2-c]pyrimidin-5-one GC-MS (TBDMS_1_2) - 70eV, PositiveNot Available2021-11-05Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 6-[(2R,4S,5R)-4-Hydroxy-5-(hydroxymethyl)oxolan-2-yl]-7,8-dihydroimidazo[1,2-c]pyrimidin-5-one GC-MS (TBDMS_2_1) - 70eV, PositiveNot Available2021-11-05Wishart LabView Spectrum

NMR Spectra

Spectrum TypeDescriptionDeposition DateSourceView
Predicted 1D NMR13C NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-10-27Wishart LabView Spectrum
Predicted 1D NMR1H 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 NMR13C NMR Spectrum (1D, 200 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, 300 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 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 NMR13C NMR Spectrum (1D, 500 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, 600 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, 700 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 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 NMR13C NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-10-27Wishart LabView Spectrum
Predicted 1D NMR1H 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 IDNot Available
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem CompoundNot Available
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 ]