N1-(alpha-D-ribosyl)-5,6-dimethyl-benzimidazole (PAMDB000805)

IdentificationTaxonomyPhysical PropertiesBiological PropertiesSpectraConcentrationsLinksReferencesEnzymes Transporters
Proteins (3280)
Record Information
Version 1.0
Update Date 1/22/2018 12:54:54 PM
Metabolite IDPAMDB000805
Identification
Name: N1-(alpha-D-ribosyl)-5,6-dimethyl-benzimidazole
Description:N1-(alpha-D-ribosyl)-5,6-dimethyl-benzimidazole is also known as alpha-ribazole. It is converted from N1-(5-Phospho-alpha-D-ribosyl)-5,6-dimethylbenzimidazole via dephosphorylation by the enzyme alpha-ribazole phosphatase (EC 3.1.3.73). It can subsequently be used to synthesize Vitamin B12 coenzyme. (KEGG)
Structure
Thumb
🔍MOLSDFPDBSMILESInChIView Structure
Synonyms:
  • (2S,5R)-2-(5,6 dimethylbenzimidazol-1-yl)-5 (hydroxymethyl)oxolane-3,4-diol
  • 5,6-Dimethyl-1-a-D-ribofuranosyl-1H-benzimidazole
  • 5,6-Dimethyl-1-a-delta-ribofuranosyl-1H-benzimidazole
  • 5,6-Dimethyl-1-a-δ-ribofuranosyl-1H-benzimidazole
  • 5,6-Dimethyl-1-alpha-delta-ribofuranosyl-1H-benzimidazole
  • 5,6-Dimethyl-1-α-δ-ribofuranosyl-1H-benzimidazole
  • A-Ribazole
  • Alpha-Ribazole
  • N1-(α-D-ribosyl)-5,6-dimethylbenzimidazole
  • N1-(a-D-Ribosyl)-5,6-dimethyl-benzimidazole
  • N1-(a-D-Ribosyl)-5,6-dimethylbenzimidazole
  • N1-(a-delta-Ribosyl)-5,6-dimethylbenzimidazole
  • N1-(a-δ-Ribosyl)-5,6-dimethylbenzimidazole
  • N1-(alpha-D-ribosyl)-5,6-dimethylbenzimidazole
  • N1-(alpha-delta-ribosyl)-5,6-dimethylbenzimidazole
  • N1-(α-D-Ribosyl)-5,6-dimethyl-benzimidazole
  • N1-(α-D-Ribosyl)-5,6-dimethylbenzimidazole
  • N1-(α-δ-Ribosyl)-5,6-dimethylbenzimidazole
  • α-Ribazole
Chemical Formula: C14H18N2O4
Average Molecular Weight: 278.3037
Monoisotopic Molecular Weight: 278.126657074
InChI Key: HLRUKOJSWOKCPP-RYSNWHEDSA-N
InChI: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
CAS number: Not Available
IUPAC Name:(2S,5R)-2-(5,6-dimethyl-1H-1,3-benzodiazol-1-yl)-5-(hydroxymethyl)oxolane-3,4-diol
Traditional IUPAC Name: (2S,5R)-2-(5,6-dimethyl-1,3-benzodiazol-1-yl)-5-(hydroxymethyl)oxolane-3,4-diol
SMILES:CC1=CC2=C(C=C1C)N(C=N2)[C@H]1O[C@H](CO)C(O)C1O
Chemical Taxonomy
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.
Kingdom Organic compounds
Super ClassNucleosides, nucleotides, and analogues
Class Benzimidazole ribonucleosides and ribonucleotides
Sub ClassNot Available
Direct Parent Benzimidazole ribonucleosides and ribonucleotides
Alternative Parents
Substituents
  • 1-ribofuranosylbenzimidazole
  • N-glycosyl compound
  • Glycosyl compound
  • Benzimidazole
  • Benzenoid
  • N-substituted imidazole
  • Monosaccharide
  • Saccharide
  • Heteroaromatic compound
  • Oxolane
  • Imidazole
  • Azole
  • Secondary alcohol
  • 1,2-diol
  • Oxacycle
  • Azacycle
  • Organoheterocyclic compound
  • Hydrocarbon derivative
  • Primary alcohol
  • Organooxygen compound
  • Organonitrogen compound
  • Alcohol
  • Aromatic heteropolycyclic compound
Molecular Framework Aromatic heteropolycyclic compounds
External Descriptors Not Available
Physical Properties
State: Solid
Charge:0
Melting point: Not Available
Experimental Properties:
PropertyValueSource
Predicted Properties
PropertyValueSource
Water Solubility4.03 mg/mLALOGPS
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 Å2ChemAxon
Rotatable Bond Count2ChemAxon
Refractivity71.65 m3·mol-1ChemAxon
Polarizability29.38 Å3ChemAxon
Number of Rings3ChemAxon
Bioavailability1ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations: Cytoplasm
Reactions:
Adenosylcobinamide-GDP + N1-(alpha-D-ribosyl)-5,6-dimethyl-benzimidazole > Adenosylcobalamin + Guanosine monophosphate + Hydrogen ion
N1-(5-Phospho-a-D-ribosyl)-5,6-dimethylbenzimidazole + Water <> N1-(alpha-D-ribosyl)-5,6-dimethyl-benzimidazole + Phosphate
Adenosylcobalamin + Guanosine monophosphate <> Adenosylcobinamide-GDP + N1-(alpha-D-ribosyl)-5,6-dimethyl-benzimidazole
Adenosylcobinamide-GDP + N1-(alpha-D-ribosyl)-5,6-dimethyl-benzimidazole + N1-(5-Phospho-a-D-ribosyl)-5,6-dimethylbenzimidazole <> Guanosine monophosphate + Adenosylcobalamin + Adenosylcobalamin 5'-phosphate
Pathways:
Spectra
Spectra:
Spectrum TypeDescriptionSplash Key
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
References
References:
  • Kanehisa, M., Goto, S., Sato, Y., Furumichi, M., Tanabe, M. (2012). "KEGG for integration and interpretation of large-scale molecular data sets." Nucleic Acids Res 40:D109-D114. Pubmed: 22080510
  • Keseler, I. M., Collado-Vides, J., Santos-Zavaleta, A., Peralta-Gil, M., Gama-Castro, S., Muniz-Rascado, L., Bonavides-Martinez, C., Paley, S., Krummenacker, M., Altman, T., Kaipa, P., Spaulding, A., Pacheco, J., Latendresse, M., Fulcher, C., Sarker, M., Shearer, A. G., Mackie, A., Paulsen, I., Gunsalus, R. P., Karp, P. D. (2011). "EcoCyc: a comprehensive database of Escherichia coli biology." Nucleic Acids Res 39:D583-D590. Pubmed: 21097882
  • van der Werf, M. J., Overkamp, K. M., Muilwijk, B., Coulier, L., Hankemeier, T. (2007). "Microbial metabolomics: toward a platform with full metabolome coverage." Anal Biochem 370:17-25. Pubmed: 17765195
  • Winder, C. L., Dunn, W. B., Schuler, S., Broadhurst, D., Jarvis, R., Stephens, G. M., Goodacre, R. (2008). "Global metabolic profiling of Escherichia coli cultures: an evaluation of methods for quenching and extraction of intracellular metabolites." Anal Chem 80:2939-2948. Pubmed: 18331064
Synthesis Reference: Not Available
Material Safety Data Sheet (MSDS) Not Available
External Links:
ResourceLink
CHEBI ID10329
HMDB IDHMDB11112
Pubchem Compound ID440780
Kegg IDC05775
ChemSpider ID389646
Wikipedia IDNot Available
BioCyc IDALPHA-RIBAZOLE
EcoCyc IDALPHA-RIBAZOLE