P. aeruginosa Metabolome Database: N1-(5-Phospho-a-D-ribosyl)-5,6-dimethylbenzimidazole (PAMDB000527)

Identification Taxonomy Physical Properties Biological Properties Spectra Concentrations Links References Enzymes Transporters

Proteins (3280)

Record Information

Version

1.0

Update Date

1/22/2018 11:54:54 AM

Metabolite ID

PAMDB000527

Identification

Name:

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

Description:

N1-(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

🔍MOL SDF PDB SMILES InChI View Structure

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

Average Molecular Weight:

358.2836

Monoisotopic Molecular Weight:

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

Taxonomy Description

This 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 Class

Nucleosides, nucleotides, and analogues

Class

Benzimidazole ribonucleosides and ribonucleotides

Sub Class

Not Available

Direct Parent

Benzimidazole ribonucleosides and ribonucleotides

Alternative Parents

Substituents

1-ribofuranosylbenzimidazole
N-glycosyl compound
Glycosyl compound
Monosaccharide phosphate
Benzimidazole
Monoalkyl phosphate
Benzenoid
Alkyl phosphate
Phosphoric acid ester
Organic phosphoric acid derivative
Organic phosphate
N-substituted imidazole
Monosaccharide
Saccharide
Heteroaromatic compound
Oxolane
Imidazole
Azole
Secondary alcohol
1,2-diol
Oxacycle
Azacycle
Organoheterocyclic compound
Hydrocarbon derivative
Organooxygen compound
Organonitrogen compound
Alcohol
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

ribose monophosphate (CHEBI:16837 )
1-ribosylbenzimidazole (CHEBI:16837 )
dimethylbenzimidazole (CHEBI:16837 )

Physical Properties

State:

Solid

Charge:

-2

Melting point:

Not Available

Experimental Properties:

Property	Value	Source
LogP:	-0.524	PhysProp

Predicted Properties

Property	Value	Source
Water Solubility	1.53 mg/mL	ALOGPS
logP	-0.32	ALOGPS
logP	-1.5	ChemAxon
logS	-2.4	ALOGPS
pKa (Strongest Acidic)	1.22	ChemAxon
pKa (Strongest Basic)	5.81	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	7	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	134.27 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	82.52 m³·mol^-1	ChemAxon
Polarizability	34.13 Å³	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:

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 > 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

Pathways:

Metabolic pathways pae01100
Porphyrin and chlorophyll metabolism pae00860
Riboflavin metabolism pae00740

Spectra

Spectra:

Spectrum Type	Description	Splash Key
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-0002-0924000000-ca83b2cabb6f848fb606	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0002-1910000000-f1a785d3193f0d8ff5bc	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0002-0900000000-047b40eca213cd9b3d4d	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-0a6s-7709000000-c0797f58260c9a1a6a6c	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-002b-8900000000-1229d2ae6136dbe43637	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-004i-9200000000-e3828a9e7ec68e9998b4	View 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

Synthesis Reference:

Not Available

Material Safety Data Sheet (MSDS)

Not Available

Links

External Links:

Resource	Link
CHEBI ID	16837
HMDB ID	HMDB03882
Pubchem Compound ID	444941
Kegg ID	C04778
ChemSpider ID	392720
Wikipedia ID	Not Available
BioCyc ID	ALPHA-RIBAZOLE-5-P
EcoCyc ID	ALPHA-RIBAZOLE-5-P
Ligand Expo	RIC

N1-(5-Phospho-a-D-ribosyl)-5,6-dimethylbenzimidazole (PAMDB000527)

Structure for N1-(5-Phospho-a-D-ribosyl)-5,6-dimethylbenzimidazole (PAMDB000527)