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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2008-10-16 22:29:40 UTC
Update Date2021-09-14 14:58:36 UTC
HMDB IDHMDB0011112
Secondary Accession Numbers
  • HMDB11112
Metabolite Identification
Common NameN1-(alpha-D-ribosyl)-5,6-dimethyl-benzimidazole
DescriptionN1-(alpha-D-ribosyl)-5,6-dimethyl-benzimidazole is an intermediate in riboflavin metabolism. It is converted from N1-(5-Phospho-alpha-D-ribosyl)-5,6-dimethylbenzimidazole via dephosphorylation by the enzyme phosphohistidine phosphatase 1 (EC 3.1.3.-). Humans do not have all the enzymes needed to synthesize or metabolize riboflavin. However, gut microflora do have the necessary enzymatic machinery to produce and metabolize this vitamin. Riboflavin (or vitamin B2) is an easily absorbed micronutrient with a key role in maintaining health in humans and animals. It is the central component of the cofactors FAD and FMN, and is therefore required by all flavoproteins. Riboflavin is yellow or yellow-orange in color and in addition to being used as a food coloring it is also used to fortify some foods including baby foods, breakfast cereals, pastas, sauces, processed cheese, fruit drinks, vitamin-enriched milk products, some energy drinks, and vitamin supplements.
Structure
Data?1582752869
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
Disposition

Source

Route of exposure

Physical Properties
StateSolid
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
Water Solubility4.03 g/LALOGPS
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 RuleNoChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
DarkChem[M+H]+165.0231661259
DarkChem[M-H]-160.53631661259
DeepCCS[M+H]+163.10530932474
DeepCCS[M-H]-160.74730932474
DeepCCS[M-2H]-194.71130932474
DeepCCS[M+Na]+169.89830932474

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
N1-(alpha-D-ribosyl)-5,6-dimethyl-benzimidazoleCC1=CC2=C(C=C1C)N(C=N2)[C@H]1O[C@H](CO)C(O)C1O3909.4Standard polar33892256
N1-(alpha-D-ribosyl)-5,6-dimethyl-benzimidazoleCC1=CC2=C(C=C1C)N(C=N2)[C@H]1O[C@H](CO)C(O)C1O1580.4Standard non polar33892256
N1-(alpha-D-ribosyl)-5,6-dimethyl-benzimidazoleCC1=CC2=C(C=C1C)N(C=N2)[C@H]1O[C@H](CO)C(O)C1O2681.6Semi standard non polar33892256

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
N1-(alpha-D-ribosyl)-5,6-dimethyl-benzimidazole,1TMS,isomer #1CC1=CC2=C(C=C1C)N([C@H]1O[C@H](CO[Si](C)(C)C)C(O)C1O)C=N22655.0Semi standard non polar33892256
N1-(alpha-D-ribosyl)-5,6-dimethyl-benzimidazole,1TMS,isomer #2CC1=CC2=C(C=C1C)N([C@H]1O[C@H](CO)C(O[Si](C)(C)C)C1O)C=N22662.3Semi standard non polar33892256
N1-(alpha-D-ribosyl)-5,6-dimethyl-benzimidazole,1TMS,isomer #3CC1=CC2=C(C=C1C)N([C@H]1O[C@H](CO)C(O)C1O[Si](C)(C)C)C=N22637.5Semi standard non polar33892256
N1-(alpha-D-ribosyl)-5,6-dimethyl-benzimidazole,2TMS,isomer #1CC1=CC2=C(C=C1C)N([C@H]1O[C@H](CO[Si](C)(C)C)C(O[Si](C)(C)C)C1O)C=N22629.2Semi standard non polar33892256
N1-(alpha-D-ribosyl)-5,6-dimethyl-benzimidazole,2TMS,isomer #2CC1=CC2=C(C=C1C)N([C@H]1O[C@H](CO[Si](C)(C)C)C(O)C1O[Si](C)(C)C)C=N22615.7Semi standard non polar33892256
N1-(alpha-D-ribosyl)-5,6-dimethyl-benzimidazole,2TMS,isomer #3CC1=CC2=C(C=C1C)N([C@H]1O[C@H](CO)C(O[Si](C)(C)C)C1O[Si](C)(C)C)C=N22613.5Semi standard non polar33892256
N1-(alpha-D-ribosyl)-5,6-dimethyl-benzimidazole,3TMS,isomer #1CC1=CC2=C(C=C1C)N([C@H]1O[C@H](CO[Si](C)(C)C)C(O[Si](C)(C)C)C1O[Si](C)(C)C)C=N22614.4Semi standard non polar33892256
N1-(alpha-D-ribosyl)-5,6-dimethyl-benzimidazole,1TBDMS,isomer #1CC1=CC2=C(C=C1C)N([C@H]1O[C@H](CO[Si](C)(C)C(C)(C)C)C(O)C1O)C=N22914.3Semi standard non polar33892256
N1-(alpha-D-ribosyl)-5,6-dimethyl-benzimidazole,1TBDMS,isomer #2CC1=CC2=C(C=C1C)N([C@H]1O[C@H](CO)C(O[Si](C)(C)C(C)(C)C)C1O)C=N22914.4Semi standard non polar33892256
N1-(alpha-D-ribosyl)-5,6-dimethyl-benzimidazole,1TBDMS,isomer #3CC1=CC2=C(C=C1C)N([C@H]1O[C@H](CO)C(O)C1O[Si](C)(C)C(C)(C)C)C=N22895.5Semi standard non polar33892256
N1-(alpha-D-ribosyl)-5,6-dimethyl-benzimidazole,2TBDMS,isomer #1CC1=CC2=C(C=C1C)N([C@H]1O[C@H](CO[Si](C)(C)C(C)(C)C)C(O[Si](C)(C)C(C)(C)C)C1O)C=N23110.1Semi standard non polar33892256
N1-(alpha-D-ribosyl)-5,6-dimethyl-benzimidazole,2TBDMS,isomer #2CC1=CC2=C(C=C1C)N([C@H]1O[C@H](CO[Si](C)(C)C(C)(C)C)C(O)C1O[Si](C)(C)C(C)(C)C)C=N23098.8Semi standard non polar33892256
N1-(alpha-D-ribosyl)-5,6-dimethyl-benzimidazole,2TBDMS,isomer #3CC1=CC2=C(C=C1C)N([C@H]1O[C@H](CO)C(O[Si](C)(C)C(C)(C)C)C1O[Si](C)(C)C(C)(C)C)C=N23105.6Semi standard non polar33892256
N1-(alpha-D-ribosyl)-5,6-dimethyl-benzimidazole,3TBDMS,isomer #1CC1=CC2=C(C=C1C)N([C@H]1O[C@H](CO[Si](C)(C)C(C)(C)C)C(O[Si](C)(C)C(C)(C)C)C1O[Si](C)(C)C(C)(C)C)C=N23318.2Semi standard non polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - N1-(alpha-D-ribosyl)-5,6-dimethyl-benzimidazole GC-MS (Non-derivatized) - 70eV, Positivesplash10-0c01-9330000000-689525590087845886d02017-09-01Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - N1-(alpha-D-ribosyl)-5,6-dimethyl-benzimidazole GC-MS (3 TMS) - 70eV, Positivesplash10-05dr-6967600000-599f6974301e18e156c82017-10-06Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - N1-(alpha-D-ribosyl)-5,6-dimethyl-benzimidazole GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - N1-(alpha-D-ribosyl)-5,6-dimethyl-benzimidazole GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart LabView Spectrum

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - N1-(alpha-D-ribosyl)-5,6-dimethyl-benzimidazole 10V, Positive-QTOFsplash10-002b-0960000000-caf2068534b445ebedc92015-09-15Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - N1-(alpha-D-ribosyl)-5,6-dimethyl-benzimidazole 20V, Positive-QTOFsplash10-0002-1910000000-d37ce3a70cce736343f02015-09-15Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - N1-(alpha-D-ribosyl)-5,6-dimethyl-benzimidazole 40V, Positive-QTOFsplash10-0002-1900000000-df05b1aea7df1fbcf30a2015-09-15Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - N1-(alpha-D-ribosyl)-5,6-dimethyl-benzimidazole 10V, Negative-QTOFsplash10-004j-0690000000-77b436d3918c437841c72015-09-15Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - N1-(alpha-D-ribosyl)-5,6-dimethyl-benzimidazole 20V, Negative-QTOFsplash10-0002-0900000000-2a72e9c715cb7e187a0c2015-09-15Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - N1-(alpha-D-ribosyl)-5,6-dimethyl-benzimidazole 40V, Negative-QTOFsplash10-0002-1900000000-d0b6a5aa908f50a2969b2015-09-15Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - N1-(alpha-D-ribosyl)-5,6-dimethyl-benzimidazole 10V, Positive-QTOFsplash10-0002-0900000000-ec86bad39756964675dc2021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - N1-(alpha-D-ribosyl)-5,6-dimethyl-benzimidazole 20V, Positive-QTOFsplash10-0002-0900000000-c514f16784cfa467b6ec2021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - N1-(alpha-D-ribosyl)-5,6-dimethyl-benzimidazole 40V, Positive-QTOFsplash10-000t-0900000000-f8563f3a5ea022479f4a2021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - N1-(alpha-D-ribosyl)-5,6-dimethyl-benzimidazole 10V, Negative-QTOFsplash10-0002-0910000000-481df73ff3b8689b95282021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - N1-(alpha-D-ribosyl)-5,6-dimethyl-benzimidazole 20V, Negative-QTOFsplash10-0002-0900000000-8f3a4e497c02cd33d0972021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - N1-(alpha-D-ribosyl)-5,6-dimethyl-benzimidazole 40V, Negative-QTOFsplash10-0002-2900000000-d54bc813eef1d7fc515a2021-09-24Wishart LabView Spectrum

NMR Spectra

Spectrum TypeDescriptionDeposition DateSourceView
Predicted 1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Biological Properties
Cellular LocationsNot Available
Biospecimen LocationsNot Available
Tissue LocationsNot Available
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
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
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 ReferencesNot Available

Enzymes

General function:
Involved in phosphohistidine phosphatase activity
Specific function:
Exhibits phosphohistidine phosphatase activity.
Gene Name:
PHPT1
Uniprot ID:
Q9NRX4
Molecular weight:
Not Available