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Record Information
Version	2.0
Creation Date	2012-05-31 14:19:49 -0600
Update Date	2015-06-03 17:19:00 -0600
Secondary Accession Numbers	ECMDB11112
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	MOLSDF3D-SDFPDBSMILESInChI View 3D Structure × Structure for #<Compound:0xacd8f868> Close
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.
Kingdom	Organic compounds
Super Class	Nucleosides, nucleotides, and analogues
Class	Benzimidazole ribonucleosides and ribonucleotides
Sub Class	Not Available
Direct Parent	Benzimidazole ribonucleosides and ribonucleotides
Alternative Parents	Glycosylamines Pentoses Benzimidazoles N-substituted imidazoles Benzenoids Tetrahydrofurans Heteroaromatic compounds Secondary alcohols Oxacyclic compounds Azacyclic compounds Primary alcohols Organopnictogen compounds Organonitrogen compounds Hydrocarbon derivatives
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 Framework	Aromatic heteropolycyclic compounds
External Descriptors	Not Available
Physical Properties
State:	Solid
Charge:	0
Melting point:	Not Available
Experimental Properties:	Property Value Source
Predicted Properties	Property Value Source Water Solubility 4.03 g/L ALOGPS logP 0.35 ALOGPS logP 0.73 ChemAxon logS -1.8 ALOGPS pKa (Strongest Acidic) 12.46 ChemAxon pKa (Strongest Basic) 6 ChemAxon Physiological Charge 0 ChemAxon Hydrogen Acceptor Count 5 ChemAxon Hydrogen Donor Count 3 ChemAxon Polar Surface Area 87.74 Ų ChemAxon Rotatable Bond Count 2 ChemAxon Refractivity 71.65 m³·mol⁻¹ ChemAxon Polarizability 29.38 ų ChemAxon Number of Rings 3 ChemAxon Bioavailability 1 ChemAxon Rule of Five Yes ChemAxon Ghose Filter Yes ChemAxon Veber's Rule Yes ChemAxon MDDR-like Rule Yes ChemAxon
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:	Metabolic pathways eco01100 Porphyrin and chlorophyll metabolism ec00860
EcoCyc Pathways:	Not Available
Concentrations
	Not Available
Spectra
Spectra:	Spectrum Type Description Splash Key Predicted GC-MS Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive splash10-0c01-9330000000-689525590087845886d0 View in MoNA Predicted GC-MS Predicted GC-MS Spectrum - GC-MS (3 TMS) - 70eV, Positive splash10-05dr-6967600000-599f6974301e18e156c8 View in MoNA Predicted GC-MS Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive Not Available View in JSpectraViewer Predicted GC-MS Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive Not Available View in JSpectraViewer Predicted LC-MS/MS Predicted LC-MS/MS Spectrum - 10V, Positive splash10-002b-0960000000-caf2068534b445ebedc9 View in MoNA Predicted LC-MS/MS Predicted LC-MS/MS Spectrum - 20V, Positive splash10-0002-1910000000-d37ce3a70cce736343f0 View in MoNA Predicted LC-MS/MS Predicted LC-MS/MS Spectrum - 40V, Positive splash10-0002-1900000000-df05b1aea7df1fbcf30a View in MoNA Predicted LC-MS/MS Predicted LC-MS/MS Spectrum - 10V, Negative splash10-004j-0690000000-77b436d3918c437841c7 View in MoNA Predicted LC-MS/MS Predicted LC-MS/MS Spectrum - 20V, Negative splash10-0002-0900000000-2a72e9c715cb7e187a0c View in MoNA Predicted LC-MS/MS Predicted LC-MS/MS Spectrum - 40V, Negative splash10-0002-1900000000-d0b6a5aa908f50a2969b View in MoNA Predicted LC-MS/MS Predicted LC-MS/MS Spectrum - 10V, Positive splash10-0002-0900000000-ec86bad39756964675dc View in MoNA Predicted LC-MS/MS Predicted LC-MS/MS Spectrum - 20V, Positive splash10-0002-0900000000-c514f16784cfa467b6ec View in MoNA Predicted LC-MS/MS Predicted LC-MS/MS Spectrum - 40V, Positive splash10-000t-0900000000-f8563f3a5ea022479f4a View in MoNA Predicted LC-MS/MS Predicted LC-MS/MS Spectrum - 10V, Negative splash10-0002-0910000000-481df73ff3b8689b9528 View in MoNA Predicted LC-MS/MS Predicted LC-MS/MS Spectrum - 20V, Negative splash10-0002-0900000000-8f3a4e497c02cd33d097 View in MoNA Predicted LC-MS/MS Predicted LC-MS/MS Spectrum - 40V, Negative splash10-0002-2900000000-d54bc813eef1d7fc515a View in MoNA 1D NMR 1H NMR Spectrum Not Available View in JSpectraViewer 1D NMR 13C NMR Spectrum Not Available View in JSpectraViewer 1D NMR 1H NMR Spectrum Not Available View in JSpectraViewer 1D NMR 13C NMR Spectrum Not Available View in JSpectraViewer 1D NMR 1H NMR Spectrum Not Available View in JSpectraViewer 1D NMR 13C NMR Spectrum Not Available View in JSpectraViewer 1D NMR 1H NMR Spectrum Not Available View in JSpectraViewer 1D NMR 13C NMR Spectrum Not Available View in JSpectraViewer 1D NMR 1H NMR Spectrum Not Available View in JSpectraViewer 1D NMR 13C NMR Spectrum Not Available View in JSpectraViewer 1D NMR 1H NMR Spectrum Not Available View in JSpectraViewer 1D NMR 13C NMR Spectrum Not Available View in JSpectraViewer 1D NMR 1H NMR Spectrum Not Available View in JSpectraViewer 1D NMR 13C NMR Spectrum Not Available View in JSpectraViewer 1D NMR 1H NMR Spectrum Not Available View in JSpectraViewer 1D NMR 13C NMR Spectrum Not Available View in JSpectraViewer 1D NMR 1H NMR Spectrum Not Available View in JSpectraViewer 1D NMR 13C NMR Spectrum Not Available View in JSpectraViewer 1D NMR 1H NMR Spectrum Not Available View in JSpectraViewer 1D NMR 13C NMR Spectrum Not Available View 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
Links
External Links:	Resource Link CHEBI ID 10329 HMDB ID HMDB11112 Pubchem Compound ID 440780 Kegg ID C05775 ChemSpider ID 389646 Wikipedia ID Not Available BioCyc ID ALPHA-RIBAZOLE EcoCyc ID ALPHA-RIBAZOLE

Enzymes