MiMeDB: Showing metabocard for nicotinate beta-D-ribonucleotide (MMDBc0032098)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-11-18 02:02:12 UTC

Update Date

2022-08-31 18:30:07 UTC

Metabolite ID

MMDBc0032098

Metabolite Identification

Common Name

nicotinate beta-D-ribonucleotide

Description

Nicotinate beta-d-ribonucleotide is part of the Cofactor biosynthesis, and Nicotinate and nicotinamide metabolism pathways. It is a substrate for: Nicotinamide riboside kinase 1, and Nicotinamide riboside kinase 2.

Structure

MOL SDF PDB SMILES InChI


  Mrv1572009081517262D          

 26 27  0  0  0  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  1  0  0  0  0  0  0  0  0  0
    0.7145    3.4661    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.0470    2.9812    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.3020    2.1965    0.0000 C   0  0  1  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
    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
   -0.4817   -1.3131    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
    4.3489    3.1939    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.8192    2.1544    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.3093    3.7236    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.7796    2.6841    0.0000 O   0  0  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
    3.5642    2.9390    0.0000 P   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  6  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  6  0  0  0
  8 13  1  1  0  0  0
  9 14  1  1  0  0  0
 15 11  2  0  0  0  0
 16 11  1  0  0  0  0
 20  5  1  0  0  0  0
 21  7  1  0  0  0  0
 21 10  1  0  0  0  0
 22 17  1  0  0  0  0
 22 18  1  0  0  0  0
 22 19  2  0  0  0  0
 22 20  1  0  0  0  0
  7 23  1  1  0  0  0
  8 24  1  6  0  0  0
  9 25  1  6  0  0  0
 10 26  1  1  0  0  0
M  CHG  1  12   1
M  END


  Mrv1572009081517262D          

 26 27  0  0  0  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  1  0  0  0  0  0  0  0  0  0
    0.7145    3.4661    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.0470    2.9812    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.3020    2.1965    0.0000 C   0  0  1  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
    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
   -0.4817   -1.3131    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
    4.3489    3.1939    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.8192    2.1544    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.3093    3.7236    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.7796    2.6841    0.0000 O   0  0  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
    3.5642    2.9390    0.0000 P   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  6  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  6  0  0  0
  8 13  1  1  0  0  0
  9 14  1  1  0  0  0
 15 11  2  0  0  0  0
 16 11  1  0  0  0  0
 20  5  1  0  0  0  0
 21  7  1  0  0  0  0
 21 10  1  0  0  0  0
 22 17  1  0  0  0  0
 22 18  1  0  0  0  0
 22 19  2  0  0  0  0
 22 20  1  0  0  0  0
  7 23  1  1  0  0  0
  8 24  1  6  0  0  0
  9 25  1  6  0  0  0
 10 26  1  1  0  0  0
M  CHG  1  12   1
M  END
> <DATABASE_ID>
MMDBc0032098

> <DATABASE_NAME>
MIME

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

> <INCHI_IDENTIFIER>
InChI=1S/C11H14NO9P/c13-8-7(5-20-22(17,18)19)21-10(9(8)14)12-3-1-2-6(4-12)11(15)16/h1-4,7-10,13-14H,5H2,(H2-,15,16,17,18,19)/p+1/t7-,8-,9-,10-/m0/s1

> <INCHI_KEY>
JOUIQRNQJGXQDC-XKNYDFJKSA-O

> <FORMULA>
C11H15NO9P

> <MOLECULAR_WEIGHT>
336.212

> <EXACT_MASS>
336.047894485

> <JCHEM_ACCEPTOR_COUNT>
8

> <JCHEM_ATOM_COUNT>
37

> <JCHEM_AVERAGE_POLARIZABILITY>
28.827497725441077

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
1

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
3-carboxy-1-[(2S,3S,4R,5S)-3,4-dihydroxy-5-[(phosphonooxy)methyl]oxolan-2-yl]-1λ⁵-pyridin-1-ylium

> <ALOGPS_LOGP>
-0.99

> <JCHEM_LOGP>
-5.437405301471745

> <ALOGPS_LOGS>
-2.34

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
2.769972865112574

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.200840941351724

> <JCHEM_PKA_STRONGEST_BASIC>
-3.7319661030900226

> <JCHEM_POLAR_SURFACE_AREA>
157.63

> <JCHEM_REFRACTIVITY>
69.8852

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.71e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
3-carboxy-1-[(2S,3S,4R,5S)-3,4-dihydroxy-5-[(phosphonooxy)methyl]oxolan-2-yl]-1λ⁵-pyridin-1-ylium

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 08-SEP-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   08-SEP-15         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       1.334   8.010   0.000  0.00  0.00           O+0
HETATM   14  O   UNK     0      -1.377   6.041   0.000  0.00  0.00           O+0
HETATM   15  O   UNK     0      -0.899  -2.451   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       8.118   5.962   0.000  0.00  0.00           O+0
HETATM   18  O   UNK     0       7.129   4.021   0.000  0.00  0.00           O+0
HETATM   19  O   UNK     0       6.177   6.951   0.000  0.00  0.00           O+0
HETATM   20  O   UNK     0       5.189   5.010   0.000  0.00  0.00           O+0
HETATM   21  O   UNK     0       2.104   4.100   0.000  0.00  0.00           O+0
HETATM   22  P   UNK     0       6.653   5.486   0.000  0.00  0.00           P+0
HETATM   23  H   UNK     0       2.820   7.086   0.000  0.00  0.00           H+0
HETATM   24  H   UNK     0      -0.038   7.169   0.000  0.00  0.00           H+0
HETATM   25  H   UNK     0      -1.001   4.476   0.000  0.00  0.00           H+0
HETATM   26  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   20                                                       
CONECT    6    2    4   11                                                  
CONECT    7    5    8   21   23                                             
CONECT    8    7    9   13   24                                             
CONECT    9    8   10   14   25                                             
CONECT   10    9   12   21   26                                             
CONECT   11    6   15   16                                                  
CONECT   12    3    4   10                                                  
CONECT   13    8                                                            
CONECT   14    9                                                            
CONECT   15   11                                                            
CONECT   16   11                                                            
CONECT   17   22                                                            
CONECT   18   22                                                            
CONECT   19   22                                                            
CONECT   20    5   22                                                       
CONECT   21    7   10                                                       
CONECT   22   17   18   19   20                                             
CONECT   23    7                                                            
CONECT   24    8                                                            
CONECT   25    9                                                            
CONECT   26   10                                                            
MASTER        0    0    0    0    0    0    0    0   26    0   54    0
END

Synonyms

Value	Source
Nicotinate b-D-ribonucleotide	Generator
Nicotinate β-D-ribonucleotide	Generator
Nicotinic acid b-D-ribonucleotide	Generator
Nicotinic acid beta-D-ribonucleotide	Generator
Nicotinic acid β-D-ribonucleotide	Generator

Molecular Formula

C₁₁H₁₅NO₉P

Average Mass

336.212

Monoisotopic Mass

336.047894485

IUPAC Name

3-carboxy-1-[(2S,3S,4R,5S)-3,4-dihydroxy-5-[(phosphonooxy)methyl]oxolan-2-yl]-1λ⁵-pyridin-1-ylium

Traditional Name

3-carboxy-1-[(2S,3S,4R,5S)-3,4-dihydroxy-5-[(phosphonooxy)methyl]oxolan-2-yl]-1λ⁵-pyridin-1-ylium

CAS Registry Number

Not Available

SMILES

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

InChI Identifier

InChI=1S/C11H14NO9P/c13-8-7(5-20-22(17,18)19)21-10(9(8)14)12-3-1-2-6(4-12)11(15)16/h1-4,7-10,13-14H,5H2,(H2-,15,16,17,18,19)/p+1/t7-,8-,9-,10-/m0/s1

InChI Key

JOUIQRNQJGXQDC-XKNYDFJKSA-O

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as nicotinic acid nucleotides. These are pyridine nucleotides, in which the pyridine base is nicotinic acid or a derivative thereof.

Kingdom

Organic compounds

Super Class

Nucleosides, nucleotides, and analogues

Class

Pyridine nucleotides

Sub Class

Nicotinic acid nucleotides

Direct Parent

Nicotinic acid nucleotides

Alternative Parents

Substituents

Nicotinic-acid-nucleotide
Pentose phosphate
Pentose-5-phosphate
Glycosyl compound
N-glycosyl compound
Monosaccharide phosphate
Pentose monosaccharide
Pyridine carboxylic acid
Pyridine carboxylic acid or derivatives
Monoalkyl phosphate
Monosaccharide
Organic phosphoric acid derivative
Phosphoric acid ester
Pyridine
Pyridinium
Alkyl phosphate
Vinylogous amide
Oxolane
Heteroaromatic compound
Secondary alcohol
1,2-diol
Organoheterocyclic compound
Carboxylic acid
Carboxylic acid derivative
Azacycle
Oxacycle
Organic nitrogen compound
Organic oxide
Organic oxygen compound
Hydrocarbon derivative
Alcohol
Organonitrogen compound
Organooxygen compound
Organic cation
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

Not Available

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	1.71 g/L	ALOGPS
logP	-0.99	ALOGPS
logP	-5.4	ChemAxon
logS	-2.3	ALOGPS
pKa (Strongest Acidic)	1.2	ChemAxon
pKa (Strongest Basic)	-3.7	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	8	ChemAxon
Hydrogen Donor Count	5	ChemAxon
Polar Surface Area	157.63 Å²	ChemAxon
Rotatable Bond Count	5	ChemAxon
Refractivity	69.89 m³·mol⁻¹	ChemAxon
Polarizability	28.83 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

Spectrum Type	Description	Splash Key	Deposition Date	View
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-000i-1009000000-45cf3b60c4f54fab805e	2015-09-14	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-002b-5239000000-06c5c860a7418e0c306a	2015-09-14	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0007-9500000000-2d068257825e57281eff	2015-09-14	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-000i-1009000000-bb857f4753a96da6b07b	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-002b-9001000000-ca67d776dd7d3f5d4650	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-004i-9000000000-a2c73ccedfb0ecef8b8c	2015-09-15	View Spectrum

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
Bacteria	Proteobacteria	287	Human ; Human feces; Human feces; pleural fluid plaque; bal; Human stool; Pig ; River trout ; Turkey ; Rat	Unknown
Bacteria	Firmicutes	97	Human feces; Human ; Catfish ; Cattle
Bacteria	Bacteroidetes	13	Human ; Human feces
Bacteria	Chloroflexi	10
Bacteria	Chlorobi	11
Bacteria	Actinobacteria	41	Human ; Cattle ; Human feces
Bacteria	Deinococcus-thermus	3
Bacteria	Fusobacteria	1	Human ; Human feces
Bacteria	Spirochaetes	12	Human ; Relapsing fever tick
Archaea/Archaea	Euryarchaeota	7
Bacteria	nah	1
Eukaryota/Fungi	Ascomycota	3
Bacteria	Tenericutes	4	Human
Bacteria	Aquificae	2
Bacteria	Dictyoglomi	2
Bacteria	Elusimicrobia	1
Bacteria	Thermotogae	7
Bacteria	Gemmatimonadetes	1
Bacteria	Cyanobacteria	5
Bacteria	Verrucomicrobia	2
Bacteria	Planctomycetes	1
Bacteria	Acidobacteria	1

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

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

91746275

PDB ID

Not Available

ChEBI ID

Not Available

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 nicotinate beta-D-ribonucleotide (MMDBc0032098)

MOL for #<Metabolite:0x00007fdb4115a008>

3D MOL for #<Metabolite:0x00007fdb4115a008>

3D SDF for #<Metabolite:0x00007fdb4115a008>

3D-SDF for #<Metabolite:0x00007fdb4115a008>

PDB for #<Metabolite:0x00007fdb4115a008>

3D PDB for #<Metabolite:0x00007fdb4115a008>

SMILES for #<Metabolite:0x00007fdb4115a008>

INCHI for #<Metabolite:0x00007fdb4115a008>

Structure for #<Metabolite:0x00007fdb4115a008>

3D Structure for #<Metabolite:0x00007fdb4115a008>