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Record Information
Version4.0
StatusExpected but not Quantified
Creation Date2008-10-16 22:29:40 UTC
Update Date2017-12-07 02:29:02 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
Thumb
Synonyms
ValueSource
(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
DescriptionThis compound 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:

Physical Properties
StateSolid
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted 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
Bioavailability1ChemAxon
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 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
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
FoodDB IDFDB027894
KNApSAcK IDNot Available
Chemspider ID389646
KEGG Compound IDC05775
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound440780
PDB IDNot Available
ChEBI ID10329
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