N1-(5-Phospho-a-D-ribosyl)-5,6-dimethylbenzimidazole (ECMDB03882) (M2MDB000527)

IdentificationTaxonomyPhysical PropertiesBiological PropertiesSpectraConcentrationsLinksReferencesEnzymes (3)XML
Proteins (338)
Record Information
Version2.0
Creation Date2012-05-31 14:00:30 -0600
Update Date2015-06-03 15:54:32 -0600
Secondary Accession Numbers
  • ECMDB03882
Identification
Name:N1-(5-Phospho-a-D-ribosyl)-5,6-dimethylbenzimidazole
DescriptionN1-(5-Phospho-alpha-D-ribosyl)-5,6-dimethylbenzimidazole (or alpha-ribazole-5'-Phosphate) is an intermediate in Riboflavin metabolism. In particular, alpha-Ribazole 5'-phosphate is converted from Dimethylbenzimidazole via the enzyme nicotinate-nucleotide-dimethylbenzimidazole
Structure
Thumb
MOLSDFPDBSMILESInChI
Synonyms:
  • α-ribazole-5'-P
  • a-Ribazole 5'-phosphate
  • a-Ribazole 5'-phosphoric acid
  • a-Ribazole-5'-P
  • a-Ribazole-5'-PO4
  • Alpha-Ribazole 5'-phosphate
  • alpha-Ribazole 5'-phosphoric acid
  • Alpha-Ribazole-5'-P
  • Alpha-Ribazole-5'-PO4
  • DMB-ribose-5'-P
  • N1-(5'-phospho-α-D-ribosyl)-5,6-dimethylbenzimidazole
  • N1-(5'-phospho-a-D-Ribosyl)-5,6-dimethylbenzimidazole
  • N1-(5'-phospho-alpha-D-ribosyl)-5,6-dimethylbenzimidazole
  • N1-(5'-phospho-α-D-Ribosyl)-5,6-dimethylbenzimidazole
  • N1-(5-phospho-a-delta-Ribosyl)-5,6-dimethylbenzimidazole
  • N1-(5-phospho-a-δ-Ribosyl)-5,6-dimethylbenzimidazole
  • N1-(5-Phospho-alpha-D-ribosyl)-5,6-dimethylbenzimidazole
  • N1-(5-Phospho-alpha-delta-ribosyl)-5,6-dimethylbenzimidazole
  • N1-(5-phospho-α-D-Ribosyl)-5,6-dimethylbenzimidazole
  • N1-(5-phospho-α-δ-Ribosyl)-5,6-dimethylbenzimidazole
  • Ribazole5'P
  • α-Ribazole 5'-phosphate
  • α-Ribazole 5'-phosphoric acid
  • α-Ribazole-5'-P
  • α-Ribazole-5'-PO4
Chemical Formula:C14H19N2O7P
Weight:Average: 358.2836
Monoisotopic: 358.092987484
InChI Key:ZMRGXEJKZPRBPJ-SYQHCUMBSA-N
InChI:InChI=1S/C14H19N2O7P/c1-7-3-9-10(4-8(7)2)16(6-15-9)14-13(18)12(17)11(23-14)5-22-24(19,20)21/h3-4,6,11-14,17-18H,5H2,1-2H3,(H2,19,20,21)/t11-,12-,13-,14+/m1/s1
CAS number:Not Available
IUPAC Name:{[(2R,3S,4R,5S)-5-(5,6-dimethyl-1H-1,3-benzodiazol-1-yl)-3,4-dihydroxyoxolan-2-yl]methoxy}phosphonic acid
Traditional IUPAC Name:α-ribazole-5'-P
SMILES:CC1=CC2=C(C=C1C)N(C=N2)[C@H]1O[C@H](COP(O)(O)=O)[C@@H](O)[C@H]1O
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
  • Pentose phosphate
  • Pentose-5-phosphate
  • Glycosyl compound
  • N-glycosyl compound
  • Monosaccharide phosphate
  • Pentose monosaccharide
  • Benzimidazole
  • Monoalkyl phosphate
  • Monosaccharide
  • N-substituted imidazole
  • Organic phosphoric acid derivative
  • Phosphoric acid ester
  • Alkyl phosphate
  • Benzenoid
  • Azole
  • Tetrahydrofuran
  • Imidazole
  • Heteroaromatic compound
  • 1,2-diol
  • Secondary alcohol
  • Oxacycle
  • Organoheterocyclic compound
  • Azacycle
  • Hydrocarbon derivative
  • Organonitrogen compound
  • Organooxygen compound
  • Organic oxygen compound
  • Organic nitrogen compound
  • Organopnictogen compound
  • Organic oxide
  • Alcohol
  • Aromatic heteropolycyclic compound
Molecular FrameworkAromatic heteropolycyclic compounds
External Descriptors
Physical Properties
State:Solid
Charge:-2
Melting point:Not Available
Experimental Properties:
PropertyValueSource
LogP:-0.524PhysProp
Predicted Properties
PropertyValueSource
Water Solubility1.53 g/LALOGPS
logP-0.32ALOGPS
logP-1.5ChemAxon
logS-2.4ALOGPS
pKa (Strongest Acidic)1.22ChemAxon
pKa (Strongest Basic)5.81ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count7ChemAxon
Hydrogen Donor Count4ChemAxon
Polar Surface Area134.27 ŲChemAxon
Rotatable Bond Count4ChemAxon
Refractivity82.52 m³·mol⁻¹ChemAxon
Polarizability34.13 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
Dimethylbenzimidazole + Nicotinamide ribotide <> N1-(5-Phospho-a-D-ribosyl)-5,6-dimethylbenzimidazole + Hydrogen ion + Nicotinic acid
N1-(5-Phospho-a-D-ribosyl)-5,6-dimethylbenzimidazole + Water <> N1-(alpha-D-ribosyl)-5,6-dimethyl-benzimidazole + Phosphate
Adenosylcobinamide-GDP + N1-(5-Phospho-a-D-ribosyl)-5,6-dimethylbenzimidazole > adenosylcobalamin 5'-phosphate + Guanosine monophosphate + Hydrogen ion
Nicotinamide ribotide + Dimethylbenzimidazole > Hydrogen ion + Nicotinic acid + N1-(5-Phospho-a-D-ribosyl)-5,6-dimethylbenzimidazole
N1-(5-Phospho-a-D-ribosyl)-5,6-dimethylbenzimidazole + Water > alpha-ribazole + Inorganic phosphate
Nicotinamide ribotide + Dimethylbenzimidazole > Nicotinic acid + N1-(5-Phospho-a-D-ribosyl)-5,6-dimethylbenzimidazole
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
Dimethylbenzimidazole + nicotinate beta-D-ribonucleotide + Nicotinamide ribotide > Hydrogen ion + Nicotinic acid + N1-(5-Phospho-a-D-ribosyl)-5,6-dimethylbenzimidazole
N1-(5-Phospho-a-D-ribosyl)-5,6-dimethylbenzimidazole + Adenosylcobinamide-GDP + Adenosylcobinamide-GDP > Hydrogen ion + GMP + 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:
adenosylcobalamin salvage from cobinamidePW001884 ThumbThumb?image type=greyscaleThumb?image type=simple
KEGG Pathways:
EcoCyc Pathways:
Concentrations
Not Available
Spectra
Spectra:
Spectrum TypeDescriptionSplash Key
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-0002-9612000000-fb21cfa813df9fff3f0dView in MoNA
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (2 TMS) - 70eV, Positivesplash10-01vk-5943100000-cb128df76b1b27f96534View 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, Positivesplash10-0002-0924000000-ca83b2cabb6f848fb606View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-0002-1910000000-f1a785d3193f0d8ff5bcView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-0002-0900000000-047b40eca213cd9b3d4dView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0a6s-7709000000-c0797f58260c9a1a6a6cView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-002b-8900000000-1229d2ae6136dbe43637View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-004i-9200000000-e3828a9e7ec68e9998b4View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0a4i-3009000000-6535ffb46debd0ae1f34View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-004i-9001000000-578749d5ff31e4fab5eaView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-004i-9100000000-d4ee221347b2259634d2View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-0a4j-0719000000-2538d2d5f670e5ddcec9View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-0002-0923000000-40c17e787a25cabb848eView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-0002-4900000000-6c85eaa5dbac4013d383View 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
Synthesis Reference:Not Available
Material Safety Data Sheet (MSDS)Not Available
External Links:
ResourceLink
CHEBI ID16837
HMDB IDHMDB03882
Pubchem Compound ID444941
Kegg IDC04778
ChemSpider ID392720
Wikipedia IDNot Available
BioCyc IDALPHA-RIBAZOLE-5-P
EcoCyc IDALPHA-RIBAZOLE-5-P
Ligand ExpoRIC

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. Nicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase
General function:
Involved in nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase activity
Specific function:
Catalyzes the synthesis of alpha-ribazole-5'-phosphate from nicotinate mononucleotide (NAMN) and 5,6- dimethylbenzimidazole (DMB)
Gene Name:
cobT
Uniprot ID:
P36562
Molecular weight:
36987
Reactions
Beta-nicotinate D-ribonucleotide + 5,6-dimethylbenzimidazole = nicotinate + alpha-ribazole 5'-phosphate.
Protein Details
3. 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.