NP-MRD: Showing NP-Card for β-D-ribosylnicotinate (NP0339965)

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Record Information

Version

2.0

Created at

2024-09-12 00:30:15 UTC

Updated at

2024-09-12 00:30:15 UTC

NP-MRD ID

NP0339965

Secondary Accession Numbers

None

Natural Product Identification

Common Name

β-D-ribosylnicotinate

Description

β-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). Based on a literature review very few articles have been published on β-D-ribosylnicotinate.

Structure

MOL SDF PDB SMILES InChI


  Mrv2104 05272303022D          

 18 19  0  0  0  0            999 V2000
    0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3819   -1.7224    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1665   -1.4675    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1270   -2.5070    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6119   -3.1745    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3020   -2.5070    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0470   -1.7224    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1830   -3.1745    0.0000 N   0  3  0  0  0  0  0  0  0  0  0  0
    0.1526   -3.9282    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3323   -4.5956    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1528   -4.5094    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4884   -3.7557    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3088   -3.6695    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7938   -4.3369    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6444   -2.9158    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
   -1.0034   -3.0882    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  4  6  1  0  0  0  0
  6  7  1  0  0  0  0
  6  8  1  0  0  0  0
  8  9  1  0  0  0  0
  3  9  1  0  0  0  0
  8 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  2  0  0  0  0
 12 13  1  0  0  0  0
 13 14  2  0  0  0  0
 14 15  1  0  0  0  0
 15 16  2  0  0  0  0
 15 17  1  0  0  0  0
 14 18  1  0  0  0  0
 10 18  2  0  0  0  0
M  CHG  2  10   1  17  -1
M  END
> <DATABASE_ID>
NP0339965

> <DATABASE_NAME>
NP-MRD

> <SMILES>
OCC1OC(C(O)C1O)[N+]1=CC(=CC=C1)C([O-])=O

> <INCHI_IDENTIFIER>
InChI=1/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

> <INCHI_KEY>
PUEDDPCUCPRQNY-UHFFFAOYNA-N

> <FORMULA>
C11H13NO6

> <MOLECULAR_WEIGHT>
255.226

> <EXACT_MASS>
255.074287143

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
31

> <JCHEM_AVERAGE_POLARIZABILITY>
24.138732244167745

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
1-[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>
11.722315684546466

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.3579035741619463

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

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 27-MAY-23   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   27-MAY-23         0                                  
HETATM    1  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    2  O   UNK     0       2.667  -0.000   0.000  0.00  0.00           O+0
HETATM    3  C   UNK     0       1.334  -2.310   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       2.580  -3.215   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0       4.044  -2.739   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0       2.104  -4.680   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       3.009  -5.926   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0       0.564  -4.680   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0       0.088  -3.215   0.000  0.00  0.00           O+0
HETATM   10  N   UNK     0      -0.342  -5.926   0.000  0.00  0.00           N+1
HETATM   11  C   UNK     0       0.285  -7.333   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      -0.620  -8.578   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      -2.152  -8.417   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      -2.778  -7.011   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      -4.310  -6.850   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0      -5.215  -8.096   0.000  0.00  0.00           O+0
HETATM   17  O   UNK     0      -4.936  -5.443   0.000  0.00  0.00           O-1
HETATM   18  C   UNK     0      -1.873  -5.765   0.000  0.00  0.00           C+0
CONECT    1    2    3                                                       
CONECT    2    1                                                            
CONECT    3    1    4    9                                                  
CONECT    4    3    5    6                                                  
CONECT    5    4                                                            
CONECT    6    4    7    8                                                  
CONECT    7    6                                                            
CONECT    8    6    9   10                                                  
CONECT    9    8    3                                                       
CONECT   10    8   11   18                                                  
CONECT   11   10   12                                                       
CONECT   12   11   13                                                       
CONECT   13   12   14                                                       
CONECT   14   13   15   18                                                  
CONECT   15   14   16   17                                                  
CONECT   16   15                                                            
CONECT   17   15                                                            
CONECT   18   14   10                                                       
MASTER        0    0    0    0    0    0    0    0   18    0   38    0
END

View in JSmol

Synonyms

Value	Source
Β-D-ribosylnicotinic acid	Generator

Chemical Formula

C₁₁H₁₃NO₆

Average Mass

255.2260 Da

Monoisotopic Mass

255.07429 Da

IUPAC Name

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

Traditional Name

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

CAS Registry Number

Not Available

SMILES

OCC1OC(C(O)C1O)[N+]1=CC(=CC=C1)C([O-])=O

InChI Identifier

InChI=1/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

InChI Key

PUEDDPCUCPRQNY-UHFFFAOYNA-N

Experimental Spectra

Not Available

Predicted Spectra

Not Available

Chemical Shift Submissions

Not Available

Species

Species of Origin

Not Available

Chemical Taxonomy

Description

This compound belongs to the class of organic compounds known as glycosylamines. These 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

a small molecule (CPD-8259 )

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	-5.3	ChemAxon
pKa (Strongest Acidic)	3.36	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	24.14 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

External Links

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

Not Available

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

Not Available

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Not Available

Showing NP-Card for β-D-ribosylnicotinate (NP0339965)

MOL for NP0339965 (β-D-ribosylnicotinate)

3D MOL for NP0339965 (β-D-ribosylnicotinate)

3D SDF for NP0339965 (β-D-ribosylnicotinate)

3D-SDF for NP0339965 (β-D-ribosylnicotinate)

PDB for NP0339965 (β-D-ribosylnicotinate)

3D PDB for NP0339965 (β-D-ribosylnicotinate)

SMILES for NP0339965 (β-D-ribosylnicotinate)

INCHI for NP0339965 (β-D-ribosylnicotinate)

Structure for NP0339965 (β-D-ribosylnicotinate)

3D Structure for NP0339965 (β-D-ribosylnicotinate)