N1-(alpha-D-ribosyl)-5,6-dimethyl-benzimidazole (ECMDB11112) (M2MDB000805)

IdentificationTaxonomyPhysical PropertiesBiological PropertiesSpectraConcentrationsLinksReferencesEnzymes (2)XML
Proteins (347)
Record Information
Version2.0
Creation Date2012-05-31 14:19:49 -0600
Update Date2015-06-03 17:19:00 -0600
Secondary Accession Numbers
  • ECMDB11112
Identification
Name:N1-(alpha-D-ribosyl)-5,6-dimethyl-benzimidazole
DescriptionN1-(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
MOLSDF3D-SDFPDBSMILESInChI View 3D 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
Weight:Average: 278.3037
Monoisotopic: 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
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
Physical Properties
State:Solid
Charge:0
Melting point:Not Available
Experimental Properties:
PropertyValueSource
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
Biological Properties
Cellular Locations:Cytoplasm
Reactions:
N1-(5-Phospho-a-D-ribosyl)-5,6-dimethylbenzimidazole + Water > Phosphate + N1-(alpha-D-ribosyl)-5,6-dimethyl-benzimidazole
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 Hydrogen ion + Adenosylcobalamin + Guanosine monophosphate
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
N1-(5-Phospho-a-D-ribosyl)-5,6-dimethylbenzimidazole + Water > Phosphate + N1-(alpha-D-ribosyl)-5,6-dimethyl-benzimidazole
N1-(5-Phospho-a-D-ribosyl)-5,6-dimethylbenzimidazole + Water > Phosphate + N1-(alpha-D-ribosyl)-5,6-dimethyl-benzimidazole
SMPDB Pathways:Not Available
KEGG Pathways:
EcoCyc Pathways:Not Available
Concentrations
Not Available
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 SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
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

Enzymes

Protein Details
1. Cobalamin synthase
General function:
Involved in cobalamin 5'-phosphate synthase activity
Specific function:
Joins Ado-cobinamide-GDP and alpha-ribazole to generate adenosylcobalamin (Ado-cobalamin)
Gene Name:
cobS
Uniprot ID:
P36561
Molecular weight:
26385
Reactions
GDP-cobinamide + alpha-ribazole = cobalamin + GMP.
Protein Details
2. Alpha-ribazole phosphatase
General function:
Involved in catalytic activity
Specific function:
Converts N1-(5-phospho-alpha-D-ribosyl)-5,6- dimethylbenzimidazole into N1-alpha-D-ribosyl-5,6- dimethylbenzimidazole; involved in the assembly of the nucleotide loop of cobalamin
Gene Name:
cobC
Uniprot ID:
P52086
Molecular weight:
23308
Reactions
Adenosylcobalamin 5'-phosphate + H(2)O = coenzyme B12 + phosphate.
Alpha-ribazole 5'-phosphate + H(2)O = alpha-ribazole + phosphate.