Showing metabocard for N1-(alpha-D-ribosyl)-5,6-dimethyl-benzimidazole (BMDB0011112)

IdentificationTaxonomyPhysical propertiesPathwaysSpectraConcentrationsLinksReferencesXML
Record Information
Version1.0
Creation Date2016-10-03 18:13:00 UTC
Update Date2020-04-22 15:42:44 UTC
BMDB IDBMDB0011112
Secondary Accession Numbers
  • BMDB11112
Metabolite Identification
Common NameN1-(alpha-D-ribosyl)-5,6-dimethyl-benzimidazole
DescriptionN1-(alpha-D-ribosyl)-5,6-dimethyl-benzimidazole belongs to the class of organic compounds known as benzimidazole ribonucleosides and ribonucleotides. These are nucleosides with a structure that consists of an imidazole moiety of benzimidazole is N-linked to a ribose (or deoxyribose). Nucleotides have a phosphate group linked to the C5 carbon of the ribose (or deoxyribose) moiety. N1-(alpha-D-ribosyl)-5,6-dimethyl-benzimidazole is a very strong basic compound (based on its pKa). N1-(alpha-D-ribosyl)-5,6-dimethyl-benzimidazole exists in all living organisms, ranging from bacteria to humans.
Structure
Thumb
MOLSDF3D-SDFPDBSMILESInChI View 3D Structure
Synonyms
ValueSource
N1-(a-D-Ribosyl)-5,6-dimethyl-benzimidazoleGenerator
N1-(Α-D-ribosyl)-5,6-dimethyl-benzimidazoleGenerator
(2S,5R)-2-(5,6 Dimethylbenzimidazol-1-yl)-5 (hydroxymethyl)oxolane-3,4-diolHMDB
5,6-Dimethyl-1-a-D-ribofuranosyl-1H-benzimidazoleHMDB
5,6-Dimethyl-1-alpha-delta-ribofuranosyl-1H-benzimidazoleHMDB
a-RibazoleHMDB
alpha-RibazoleHMDB
N1-(alpha-D-Ribosyl)-5,6-dimethylbenzimidazoleHMDB
N1-(alpha-delta-Ribosyl)-5,6-dimethylbenzimidazoleHMDB
Chemical FormulaC14H18N2O4
Average Molecular Weight278.3037
Monoisotopic Molecular Weight278.126657074
IUPAC Name(2S,5R)-2-(5,6-dimethyl-1H-1,3-benzodiazol-1-yl)-5-(hydroxymethyl)oxolane-3,4-diol
Traditional Name(2S,5R)-2-(5,6-dimethyl-1,3-benzodiazol-1-yl)-5-(hydroxymethyl)oxolane-3,4-diol
CAS Registry NumberNot Available
SMILES
CC1=CC2=C(C=C1C)N(C=N2)[C@H]1O[C@H](CO)C(O)C1O
InChI Identifier
InChI=1S/C14H18N2O4/c1-7-3-9-10(4-8(7)2)16(6-15-9)14-13(19)12(18)11(5-17)20-14/h3-4,6,11-14,17-19H,5H2,1-2H3/t11-,12?,13?,14+/m1/s1
InChI KeyHLRUKOJSWOKCPP-RYSNWHEDSA-N
Chemical Taxonomy
Description belongs to the class of organic compounds known as benzimidazole ribonucleosides and ribonucleotides. These are nucleosides with a structure that consists of an imidazole moiety of benzimidazole is N-linked to a ribose (or deoxyribose). Nucleotides have a phosphate group linked to the C5 carbon of the ribose (or deoxyribose) moiety.
KingdomOrganic compounds
Super ClassNucleosides, nucleotides, and analogues
ClassBenzimidazole ribonucleosides and ribonucleotides
Sub ClassNot Available
Direct ParentBenzimidazole ribonucleosides and ribonucleotides
Alternative Parents
Substituents
  • 1-ribofuranosylbenzimidazole
  • Glycosyl compound
  • N-glycosyl compound
  • Pentose monosaccharide
  • Benzimidazole
  • Monosaccharide
  • N-substituted imidazole
  • Benzenoid
  • Azole
  • Heteroaromatic compound
  • Imidazole
  • Tetrahydrofuran
  • Secondary alcohol
  • Oxacycle
  • Azacycle
  • Organoheterocyclic compound
  • Organic nitrogen compound
  • Alcohol
  • Hydrocarbon derivative
  • Organopnictogen compound
  • Organic oxygen compound
  • Organonitrogen compound
  • Organooxygen compound
  • Primary alcohol
  • Aromatic heteropolycyclic compound
Molecular FrameworkAromatic heteropolycyclic compounds
External DescriptorsNot Available
Ontology
StatusExpected but not Quantified
Origin
  • Endogenous
BiofunctionNot Available
ApplicationNot Available
Cellular locationsNot Available
Physical Properties
StateSolid
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
logP0.35ALOGPS
logP0.73ChemAxon
logS-1.8ALOGPS
pKa (Strongest Acidic)12.46ChemAxon
pKa (Strongest Basic)6ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count5ChemAxon
Hydrogen Donor Count3ChemAxon
Polar Surface Area87.74 ŲChemAxon
Rotatable Bond Count2ChemAxon
Refractivity71.65 m³·mol⁻¹ChemAxon
Polarizability29.38 ųChemAxon
Number of Rings3ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Spectra
Spectra
Spectrum TypeDescriptionSplash Key
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-0c01-9330000000-689525590087845886d0View in MoNA
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (3 TMS) - 70eV, Positivesplash10-05dr-6967600000-599f6974301e18e156c8View in MoNA
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, PositiveNot AvailableView in JSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, PositiveNot AvailableView in JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-002b-0960000000-caf2068534b445ebedc9View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-0002-1910000000-d37ce3a70cce736343f0View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-0002-1900000000-df05b1aea7df1fbcf30aView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-004j-0690000000-77b436d3918c437841c7View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-0002-0900000000-2a72e9c715cb7e187a0cView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-0002-1900000000-d0b6a5aa908f50a2969bView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-0002-0900000000-ec86bad39756964675dcView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-0002-0900000000-c514f16784cfa467b6ecView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-000t-0900000000-f8563f3a5ea022479f4aView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0002-0910000000-481df73ff3b8689b9528View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-0002-0900000000-8f3a4e497c02cd33d097View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-0002-2900000000-d54bc813eef1d7fc515aView in MoNA
1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 100 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 1000 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 1000 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 200 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 200 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 300 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 300 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 400 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 500 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 600 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 600 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 700 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 700 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 800 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 800 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 900 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
Biological Properties
Cellular LocationsNot Available
Biospecimen LocationsNot Available
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
Not Available
HMDB IDHMDB0011112
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB027894
KNApSAcK IDNot Available
Chemspider IDNot Available
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound440780
PDB IDNot Available
ChEBI IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General ReferencesNot Available