NP-MRD: Showing NP-Card for Nicotinate D-ribonucleoside (NP0087643)

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Record Information

Version

2.0

Created at

2022-05-11 16:55:37 UTC

Updated at

2022-05-11 16:55:37 UTC

NP-MRD ID

NP0087643

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Nicotinate D-ribonucleoside

Description

Nicotinate D-ribonucleoside, also known as nicotinic acid riboside or beta-D-ribosylnicotinate, 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). Nicotinate D-ribonucleoside is an extremely weak basic (essentially neutral) compound (based on its pKa). Nicotinate D-ribonucleoside exists in all living species, ranging from bacteria to humans. Within humans, nicotinate D-ribonucleoside participates in a number of enzymatic reactions. In particular, nicotinate D-ribonucleoside can be converted into nicotinic acid mononucleotide; which is catalyzed by the enzyme nicotinamide riboside kinase 1. In addition, nicotinate D-ribonucleoside can be biosynthesized from nicotinic acid mononucleotide; which is mediated by the enzyme cytosolic purine 5'-nucleotidase. A pyridine nucleoside consisting of nicotinic acid with a beta-D-ribofuranosyl moiety at the 1-position. Nicotinate D-ribonucleoside is found in Arabidopsis thaliana and Mus musculus. In humans, nicotinate D-ribonucleoside is involved in nicotinate and nicotinamide metabolism.

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 32 33  0  0  0  0  0  0  0  0999 V2000
    5.0439    1.0507   -0.2318 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.8144    1.1783   -0.0569 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2920    2.3942    0.3378 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.9269    0.0612   -0.2642 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4586   -1.1595   -0.6613 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6367   -2.2321   -0.8638 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2872   -2.0403   -0.6576 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7485   -0.8695   -0.2734 N   0  0  0  0  0  4  0  0  0  0  0  0
   -0.6873   -0.7507   -0.0776 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.1185    0.3541   -0.8044 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3868    0.6061   -0.2468 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.7813    1.9887   -0.6633 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8175    2.0034   -2.0681 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2391    0.4422    1.2357 C   0  0  1  0  0  0  0  0  0  0  0  0
   -3.3646   -0.1074    1.8182 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0696   -0.5175    1.3467 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.4679   -1.7433    1.8901 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.5540    0.1680   -0.0788 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3979    3.2448   -0.2070 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.5169   -1.2659   -0.8109 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0513   -3.1840   -1.1735 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6066   -2.8639   -0.8075 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1760   -1.6435   -0.5164 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1271   -0.1217   -0.6306 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7476    2.3187   -0.2467 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9615    2.6848   -0.3778 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1243    1.1080   -2.3893 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9656    1.3903    1.7270 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2550   -1.0519    2.0952 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2707   -0.1057    1.9747 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9293   -2.4620    1.4512 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1545    1.1256    0.2307 H   0  0  0  0  0  0  0  0  0  0  0  0
 13 12  1  0
 12 11  1  0
 11 10  1  0
 10  9  1  0
  9 16  1  0
 16 17  1  0
 16 14  1  0
 14 15  1  0
  9  8  1  0
  8  7  2  0
  7  6  1  0
  6  5  2  0
  5  4  1  0
  4 18  2  0
  4  2  1  0
  2  3  1  0
  2  1  2  0
 14 11  1  0
 18  8  1  0
 13 27  1  0
 12 25  1  0
 12 26  1  0
 11 24  1  6
  9 23  1  6
 16 30  1  1
 17 31  1  0
 14 28  1  1
 15 29  1  0
  7 22  1  0
  6 21  1  0
  5 20  1  0
 18 32  1  0
  3 19  1  0
M  CHG  1   8   1
M  END


  Mrv1652307172022202D          

 18 19  0  0  0  0            999 V2000
10000.197910001.5537    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10001.986010001.5454    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10002.4541 9999.6947    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10003.169810000.1059    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9997.544510000.1059    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9996.8301 9999.6947    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9997.544510000.9308    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9998.974710000.1069    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9998.2603 9999.6944    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9998.2603 9998.8693    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9998.9747 9998.4568    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9999.6892 9998.8693    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9999.6892 9999.6944    0.0000 N   0  3  0  0  0  0  0  0  0  0  0  0
10001.0744 9999.6119    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10000.407010000.0969    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
10000.661910000.8815    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
10001.486910000.8815    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
10001.741810000.0969    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
  3  4  1  0  0  0  0
  5  6  1  0  0  0  0
  5  7  2  0  0  0  0
  8  9  2  0  0  0  0
  9 10  1  0  0  0  0
 10 11  2  0  0  0  0
 11 12  1  0  0  0  0
 12 13  2  0  0  0  0
 13  8  1  0  0  0  0
  9  5  1  0  0  0  0
 15 16  1  0  0  0  0
 16 17  1  0  0  0  0
 17 18  1  0  0  0  0
 14 15  1  0  0  0  0
 14 18  1  0  0  0  0
 16  1  1  6  0  0  0
 15 13  1  1  0  0  0
 17  2  1  6  0  0  0
 18  3  1  1  0  0  0
M  CHG  1  13   1
M  END
> <DATABASE_ID>
NP0087643

> <DATABASE_NAME>
NP-MRD

> <SMILES>
OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)[N+]1=CC=CC(=C1)C(O)=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/p+1/t7-,8-,9-,10-/m1/s1

> <INCHI_KEY>
PUEDDPCUCPRQNY-ZYUZMQFOSA-O

> <FORMULA>
C11H14NO6

> <MOLECULAR_WEIGHT>
256.232

> <EXACT_MASS>
256.082112185

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
32

> <JCHEM_AVERAGE_POLARIZABILITY>
24.20731172269263

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
1

> <JCHEM_GHOSE_FILTER>
0

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

> <ALOGPS_LOGP>
-1.87

> <JCHEM_LOGP>
-5.313839270138412

> <ALOGPS_LOGS>
-1.74

> <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>
111.10000000000002

> <JCHEM_REFRACTIVITY>
59.012299999999996

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
5.34e+00 g/l

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

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 17-JUL-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   17-JUL-20         0                                  
HETATM    1  O   UNK     0    8667.0368669.567   0.000  0.00  0.00           O+0
HETATM    2  O   UNK     0    8670.3748669.551   0.000  0.00  0.00           O+0
HETATM    3  C   UNK     0    8671.2488666.097   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0    8672.5848666.864   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0    8662.0838666.864   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0    8660.7508666.097   0.000  0.00  0.00           O+0
HETATM    7  O   UNK     0    8662.0838668.404   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0    8664.7538666.866   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0    8663.4198666.096   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0    8663.4198664.556   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0    8664.7538663.786   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0    8666.0878664.556   0.000  0.00  0.00           C+0
HETATM   13  N   UNK     0    8666.0878666.096   0.000  0.00  0.00           N+1
HETATM   14  O   UNK     0    8668.6728665.942   0.000  0.00  0.00           O+0
HETATM   15  C   UNK     0    8667.4268666.848   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0    8667.9028668.312   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0    8669.4428668.312   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0    8669.9188666.848   0.000  0.00  0.00           C+0
CONECT    1   16                                                            
CONECT    2   17                                                            
CONECT    3    4   18                                                       
CONECT    4    3                                                            
CONECT    5    6    7    9                                                  
CONECT    6    5                                                            
CONECT    7    5                                                            
CONECT    8    9   13                                                       
CONECT    9    8   10    5                                                  
CONECT   10    9   11                                                       
CONECT   11   10   12                                                       
CONECT   12   11   13                                                       
CONECT   13   12    8   15                                                  
CONECT   14   15   18                                                       
CONECT   15   16   14   13                                                  
CONECT   16   15   17    1                                                  
CONECT   17   16   18    2                                                  
CONECT   18   17   14    3                                                  
MASTER        0    0    0    0    0    0    0    0   18    0   38    0
END

View in JSmol

Synonyms

Value	Source
Nicotinic acid riboside	ChEBI
beta-D-Ribosylnicotinate	Kegg
Nicotinate riboside	Generator
b-D-Ribosylnicotinate	Generator
b-D-Ribosylnicotinic acid	Generator
beta-D-Ribosylnicotinic acid	Generator
Β-D-ribosylnicotinate	Generator
Β-D-ribosylnicotinic acid	Generator
Nicotinic acid D-ribonucleoside	Generator
D-Ribosylnicotinate	HMDB
Nicotinic acid ribose	HMDB
Ribosylnicotinate	HMDB
Nicotinate ribonucleoside	HMDB
Nicotinate ribose	HMDB
Nicotinic acid ribonucleoside	HMDB
3-Carboxy-1-beta-D-ribofuranosylpyridinium	HMDB
3-Carboxy-1-β-D-ribofuranosylpyridinium	HMDB
Nicotinic riboside	HMDB

Chemical Formula

C₁₁H₁₄NO₆

Average Mass

256.2320 Da

Monoisotopic Mass

256.08211 Da

IUPAC Name

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

Traditional Name

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

CAS Registry Number

Not Available

SMILES

OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)[N+]1=CC=CC(=C1)C(O)=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/p+1/t7-,8-,9-,10-/m1/s1

InChI Key

PUEDDPCUCPRQNY-ZYUZMQFOSA-O

Experimental Spectra

Not Available

Predicted Spectra

Spectrum Type	Description	Depositor ID	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹³C NMR Spectrum (1D, 25 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Anas platyrhynchos	FooDB	FooDB
Anatidae	FooDB	FooDB
Anser anser	FooDB	FooDB
Arabidopsis thaliana	LOTUS Database	35616633
Bison bison	FooDB	FooDB
Bos taurus	FooDB	FooDB
Bos taurus X Bison bison	FooDB	FooDB
Bubalus bubalis	FooDB	FooDB
Capra aegagrus hircus	FooDB	FooDB
Cervidae	FooDB	FooDB
Cervus canadensis	FooDB	FooDB
Columba	FooDB	FooDB
Columbidae	FooDB	FooDB
Dromaius novaehollandiae	FooDB	FooDB
Equus caballus	FooDB	FooDB
Gallus gallus	FooDB	FooDB
Lagopus muta	FooDB	FooDB
Leporidae	FooDB	FooDB
Lepus timidus	FooDB	FooDB
Melanitta fusca	FooDB	FooDB
Meleagris gallopavo	FooDB	FooDB
Mus musculus	LOTUS Database	35616633
Numida meleagris	FooDB	FooDB
Odocoileus	FooDB	FooDB
Oryctolagus	FooDB	FooDB
Ovis aries	FooDB	FooDB
Phasianidae	FooDB	FooDB
Phasianus colchicus	FooDB	FooDB
Struthio camelus	FooDB	FooDB
Sus scrofa	FooDB	FooDB
Sus scrofa domestica	FooDB	FooDB

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
Monosaccharide
Pyridine
Pyridinium
Vinylogous amide
Heteroaromatic compound
Tetrahydrofuran
Secondary alcohol
Organoheterocyclic compound
Carboxylic acid derivative
Oxacycle
Azacycle
Carboxylic acid
Monocarboxylic acid or derivatives
Hydrocarbon derivative
Organic oxide
Organopnictogen compound
Organonitrogen compound
Alcohol
Primary alcohol
Organic nitrogen compound
Organic cation
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

pyridine nucleoside (CHEBI:27748 )

Physical Properties

State

Not Available

Experimental Properties

Property	Value	Reference
Melting Point	Not Available	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	Not Available	Not Available
LogP	Not Available	Not Available

Predicted Properties

Property	Value	Source
logP	-1.9	ALOGPS
logP	-5.3	ChemAxon
logS	-1.7	ALOGPS
pKa (Strongest Acidic)	2.76	ChemAxon
pKa (Strongest Basic)	-3	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	6	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	111.1 Å²	ChemAxon
Rotatable Bond Count	3	ChemAxon
Refractivity	59.01 m³·mol⁻¹	ChemAxon
Polarizability	24.21 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