MiMeDB: Showing metabocard for beta-D-ribosylnicotinate (MMDBc0055769)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2022-06-17 20:04:51 UTC

Update Date

2022-08-12 20:09:27 UTC

Metabolite ID

MMDBc0055769

Metabolite Identification

Common Name

beta-D-ribosylnicotinate

Description

nicotinic acid riboside, also known as beta-D-ribosylnicotinate or β-D-ribosylnicotinic acid, belongs to the class of organic compounds known as glycosylamines. Glycosylamines are compounds consisting of an amine with a beta-N-glycosidic bond to a carbohydrate, thus forming a cyclic hemiaminal ether bond (alpha-amino ether). nicotinic acid riboside is a secondary metabolite. Secondary metabolites are metabolically or physiologically non-essential metabolites that may serve a role as defense or signalling molecules. In some cases they are simply molecules that arise from the incomplete metabolism of other secondary metabolites. Based on a literature review a significant number of articles have been published on nicotinic acid riboside.

Structure

MOL SDF PDB SMILES InChI


  Mrv1652306172222042D          

 22 23  0  0  1  0            999 V2000
   -1.4884    0.9479    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1528    0.1942    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0034    1.6153    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1526    0.7754    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1665    3.2361    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3323    0.1080    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3819    2.9812    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.7145    3.4661    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.0470    2.9812    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.3020    2.1965    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.0032   -0.6457    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1830    1.5291    0.0000 N   0  3  0  0  0  0  0  0  0  0  0  0
    2.3381    4.0431    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    4.2911    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7376    3.2361    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8237   -0.7319    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4817   -1.3131    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    1.1270    2.1965    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.5110    3.7960    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0206    3.8406    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5363    2.3978    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6765    1.4614    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  2  0  0  0  0
  3  1  1  0  0  0  0
  6  2  1  0  0  0  0
  6  4  2  0  0  0  0
  7  5  1  1  0  0  0
  8  7  1  0  0  0  0
  9  8  1  0  0  0  0
 10  9  1  0  0  0  0
 11  6  1  0  0  0  0
 12  3  2  0  0  0  0
 12  4  1  0  0  0  0
 10 12  1  1  0  0  0
 13  5  1  0  0  0  0
  8 14  1  6  0  0  0
  9 15  1  6  0  0  0
 16 11  2  0  0  0  0
 17 11  1  0  0  0  0
 18  7  1  0  0  0  0
 18 10  1  0  0  0  0
  7 19  1  6  0  0  0
  8 20  1  1  0  0  0
  9 21  1  1  0  0  0
 10 22  1  6  0  0  0
M  CHG  2  12   1  17  -1
M  END
> <DATABASE_ID>
MMDBc0055769

> <DATABASE_NAME>
MIME

> <SMILES>
[H][C@]1(CO)O[C@@]([H])([N+]2=CC=CC(=C2)C([O-])=O)[C@]([H])(O)[C@]1([H])O

> <INCHI_IDENTIFIER>
InChI=1S/C11H13NO6/c13-5-7-8(14)9(15)10(18-7)12-3-1-2-6(4-12)11(16)17/h1-4,7-10,13-15H,5H2/t7-,8-,9-,10-/m1/s1

> <INCHI_KEY>
PUEDDPCUCPRQNY-ZYUZMQFOSA-N

> <FORMULA>
C11H13NO6

> <MOLECULAR_WEIGHT>
255.226

> <EXACT_MASS>
255.074287143

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
31

> <JCHEM_AVERAGE_POLARIZABILITY>
23.707275559461507

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
1-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-1lambda5-pyridin-1-ylium-3-carboxylate

> <JCHEM_LOGP>
-5.313839270138412

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
11.72231566472464

> <JCHEM_PKA_STRONGEST_ACIDIC>
2.757903592223079

> <JCHEM_PKA_STRONGEST_BASIC>
-2.9841642628693164

> <JCHEM_POLAR_SURFACE_AREA>
113.93

> <JCHEM_REFRACTIVITY>
69.8494

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
1-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-1lambda5-pyridin-1-ylium-3-carboxylate

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 17-JUN-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   17-JUN-22         0                                  
HETATM    1  C   UNK     0      -2.778   1.769   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -2.152   0.363   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -1.873   3.015   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       0.285   1.447   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       4.044   6.041   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -0.620   0.202   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       2.580   5.565   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       1.334   6.470   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       0.088   5.565   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       0.564   4.100   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       0.006  -1.205   0.000  0.00  0.00           C+0
HETATM   12  N   UNK     0      -0.342   2.854   0.000  0.00  0.00           N+1
HETATM   13  O   UNK     0       4.364   7.547   0.000  0.00  0.00           O+0
HETATM   14  O   UNK     0       1.334   8.010   0.000  0.00  0.00           O+0
HETATM   15  O   UNK     0      -1.377   6.041   0.000  0.00  0.00           O+0
HETATM   16  O   UNK     0       1.538  -1.366   0.000  0.00  0.00           O+0
HETATM   17  O   UNK     0      -0.899  -2.451   0.000  0.00  0.00           O-1
HETATM   18  O   UNK     0       2.104   4.100   0.000  0.00  0.00           O+0
HETATM   19  H   UNK     0       2.820   7.086   0.000  0.00  0.00           H+0
HETATM   20  H   UNK     0      -0.038   7.169   0.000  0.00  0.00           H+0
HETATM   21  H   UNK     0      -1.001   4.476   0.000  0.00  0.00           H+0
HETATM   22  H   UNK     0       1.263   2.728   0.000  0.00  0.00           H+0
CONECT    1    2    3                                                       
CONECT    2    1    6                                                       
CONECT    3    1   12                                                       
CONECT    4    6   12                                                       
CONECT    5    7   13                                                       
CONECT    6    2    4   11                                                  
CONECT    7    5    8   18   19                                             
CONECT    8    7    9   14   20                                             
CONECT    9    8   10   15   21                                             
CONECT   10    9   12   18   22                                             
CONECT   11    6   16   17                                                  
CONECT   12    3    4   10                                                  
CONECT   13    5                                                            
CONECT   14    8                                                            
CONECT   15    9                                                            
CONECT   16   11                                                            
CONECT   17   11                                                            
CONECT   18    7   10                                                       
CONECT   19    7                                                            
CONECT   20    8                                                            
CONECT   21    9                                                            
CONECT   22   10                                                            
MASTER        0    0    0    0    0    0    0    0   22    0   46    0
END

Synonyms

Value	Source
beta-D-Ribosylnicotinate	ChEBI
b-D-Ribosylnicotinate	Generator
b-D-Ribosylnicotinic acid	Generator
beta-D-Ribosylnicotinic acid	Generator
Β-D-ribosylnicotinate	Generator
Β-D-ribosylnicotinic acid	Generator
Nicotinate riboside	Generator
Nicotinate ribonucleoside	MeSH
Nicotinate ribose	MeSH
Nicotinic acid ribonucleoside	MeSH

Molecular Formula

C₁₁H₁₃NO₆

Average Mass

255.226

Monoisotopic Mass

255.074287143

IUPAC Name

1-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-1lambda5-pyridin-1-ylium-3-carboxylate

Traditional Name

1-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-1lambda5-pyridin-1-ylium-3-carboxylate

CAS Registry Number

Not Available

SMILES

[H][C@]1(CO)O[C@@]([H])([N+]2=CC=CC(=C2)C([O-])=O)[C@]([H])(O)[C@]1([H])O

InChI Identifier

InChI=1S/C11H13NO6/c13-5-7-8(14)9(15)10(18-7)12-3-1-2-6(4-12)11(16)17/h1-4,7-10,13-15H,5H2/t7-,8-,9-,10-/m1/s1

InChI Key

PUEDDPCUCPRQNY-ZYUZMQFOSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as glycosylamines. Glycosylamines are compounds consisting of an amine with a beta-N-glycosidic bond to a carbohydrate, thus forming a cyclic hemiaminal ether bond (alpha-amino ether).

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Carbohydrates and carbohydrate conjugates

Direct Parent

Glycosylamines

Alternative Parents

Substituents

N-glycosyl compound
Pentose monosaccharide
Pyridine carboxylic acid
Pyridine carboxylic acid or derivatives
Alkaloid or derivatives
Monosaccharide
Pyridine
Pyridinium
Vinylogous amide
Tetrahydrofuran
Heteroaromatic compound
Secondary alcohol
Carboxylic acid salt
Organoheterocyclic compound
Oxacycle
Azacycle
Carboxylic acid derivative
Carboxylic acid
Monocarboxylic acid or derivatives
Organic salt
Organopnictogen compound
Organonitrogen compound
Alcohol
Primary alcohol
Organic nitrogen compound
Organic oxide
Hydrocarbon derivative
Organic zwitterion
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

ammonium betaine (CHEBI:58527 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
logP	-5.3	ChemAxon
pKa (Strongest Acidic)	2.76	ChemAxon
pKa (Strongest Basic)	-3	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	6	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	113.93 Å²	ChemAxon
Rotatable Bond Count	3	ChemAxon
Refractivity	69.85 m³·mol⁻¹	ChemAxon
Polarizability	23.71 Å³	ChemAxon
Number of Rings	2	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Spectra

Not Available

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Not Available

Tissue Locations

Not Available

Associated OMIM IDs

114500 (Colorectal cancer)
610247 (Eosinophilic esophagitis)

Human Proteins and Enzymes

Protein ID	Protein Name	Protein Type	Uniprot ID	Species

Human Pathways

Pathways

Name	SMPDB/PathBank

Metabolic Reactions

Reactions

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference

Health Effects and Bioactivity

Health Outcome/Bioactivity	Metabolite Response/Effect	Evidence Type	Host and Biospecimen	Data Source	Reference

Microbial Sources

Superkingdom/Kingdom	Phylum	Total species	Hosts and Body Sites	Microbial Links
Eukaryota/Fungi	Ascomycota	3

Exposure Sources

Host Biospecimen and Location

Host and Biospecimen	Status	Mean	Std	Min	Max	Units	Age	Sex	Health Condition	Data Source	Reference

External Links

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

141635

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

161233

PDB ID

Not Available

ChEBI ID

58527

Food Biomarker Ontology

Not Available

References

Synthesis Reference

Not Available

General References

Bansal P, Morgat A, Axelsen KB, Muthukrishnan V, Coudert E, Aimo L, Hyka-Nouspikel N, Gasteiger E, Kerhornou A, Neto TB, Pozzato M, Blatter MC, Ignatchenko A, Redaschi N, Bridge A: Rhea, the reaction knowledgebase in 2022. Nucleic Acids Res. 2022 Jan 7;50(D1):D693-D700. doi: 10.1093/nar/gkab1016. [PubMed:34755880 ]

Showing metabocard for beta-D-ribosylnicotinate (MMDBc0055769)

MOL for #<Metabolite:0x00007fdb4c4130f0>

3D MOL for #<Metabolite:0x00007fdb4c4130f0>

3D SDF for #<Metabolite:0x00007fdb4c4130f0>

3D-SDF for #<Metabolite:0x00007fdb4c4130f0>

PDB for #<Metabolite:0x00007fdb4c4130f0>

3D PDB for #<Metabolite:0x00007fdb4c4130f0>

SMILES for #<Metabolite:0x00007fdb4c4130f0>

INCHI for #<Metabolite:0x00007fdb4c4130f0>

Structure for #<Metabolite:0x00007fdb4c4130f0>

3D Structure for #<Metabolite:0x00007fdb4c4130f0>