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Showing NP-Card for 5-Pyridoxolactone (NP0087172)

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Record Information
Version2.0
Created at2022-05-11 16:42:08 UTC
Updated at2022-05-11 16:42:08 UTC
NP-MRD IDNP0087172
Secondary Accession NumbersNone
Natural Product Identification
Common Name5-Pyridoxolactone
Description5-Pyridoxolactone, also known as a-pyracin, belongs to the class of organic compounds known as pyridinecarboxylic acids. Pyridinecarboxylic acids are compounds containing a pyridine ring bearing a carboxylic acid group. 5-Pyridoxolactone is found in Apis cerana. 5-Pyridoxolactone was first documented in 1986 (PMID: 3771565). 5-Pyridoxolactone is a strong basic compound (based on its pKa) (PMID: 9211301).
Structure
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MOL3D MOLSDFPDBSMILESInChI

MOL for NP0087172 (5-Pyridoxolactone)


  Mrv0541 02231219552D          

 12 13  0  0  0  0            999 V2000
   13.4676   -7.8461    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   15.4442   -9.4965    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   15.2191  -10.9445    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   12.7529   -9.9089    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   12.0384   -8.6712    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.9627   -8.8323    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.9627  -10.1603    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.7529   -9.0839    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.4676   -8.6712    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.1820   -9.0839    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.1820   -9.9089    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.4676  -10.3215    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  9  1  0  0  0  0
  2  6  1  0  0  0  0
  2  7  1  0  0  0  0
  3  7  2  0  0  0  0
  4  8  2  0  0  0  0
  4 12  1  0  0  0  0
  5  8  1  0  0  0  0
  6 10  1  0  0  0  0
  7 11  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  2  0  0  0  0
 10 11  1  0  0  0  0
 11 12  2  0  0  0  0
M  END
Download

3D MOL for NP0087172 (5-Pyridoxolactone)

     RDKit          3D

 19 20  0  0  0  0  0  0  0  0999 V2000
    2.9470    0.0404   -0.3706 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5020    0.3459   -0.1666 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1101    1.6464   -0.0234 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1999    1.9635    0.1645 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1719    0.9799    0.2160 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7526   -0.3166    0.0697 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5692   -0.6650   -0.1219 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9929   -1.9746   -0.2698 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9293   -1.1898    0.1550 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0194   -0.3284    0.3544 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6108    0.9858    0.3978 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3564    1.9768    0.5632 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.1812   -0.8698    0.2432 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2006   -0.1030   -1.4412 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5950    0.8565    0.0351 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4980    3.0074    0.2773 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2610   -2.6984   -0.2298 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0061   -1.7299   -0.8364 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8144   -1.9273    0.9835 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  0
  3  4  1  0
  4  5  2  0
  5 11  1  0
 11 12  2  0
 11 10  1  0
 10  9  1  0
  9  6  1  0
  6  7  2  0
  7  8  1  0
  7  2  1  0
  6  5  1  0
  1 13  1  0
  1 14  1  0
  1 15  1  0
  4 16  1  0
  9 18  1  0
  9 19  1  0
  8 17  1  0
M  END
Download

3D SDF for NP0087172 (5-Pyridoxolactone)


  Mrv0541 02231219552D          

 12 13  0  0  0  0            999 V2000
   13.4676   -7.8461    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   15.4442   -9.4965    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   15.2191  -10.9445    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   12.7529   -9.9089    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   12.0384   -8.6712    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.9627   -8.8323    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.9627  -10.1603    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.7529   -9.0839    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.4676   -8.6712    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.1820   -9.0839    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.1820   -9.9089    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.4676  -10.3215    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  9  1  0  0  0  0
  2  6  1  0  0  0  0
  2  7  1  0  0  0  0
  3  7  2  0  0  0  0
  4  8  2  0  0  0  0
  4 12  1  0  0  0  0
  5  8  1  0  0  0  0
  6 10  1  0  0  0  0
  7 11  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  2  0  0  0  0
 10 11  1  0  0  0  0
 11 12  2  0  0  0  0
M  END
> <DATABASE_ID>
NP0087172

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC1=NC=C2C(=O)OCC2=C1O

> <INCHI_IDENTIFIER>
InChI=1S/C8H7NO3/c1-4-7(10)6-3-12-8(11)5(6)2-9-4/h2,10H,3H2,1H3

> <INCHI_KEY>
PPAXBSPBIWBREI-UHFFFAOYSA-N

> <FORMULA>
C8H7NO3

> <MOLECULAR_WEIGHT>
165.1461

> <EXACT_MASS>
165.042593095

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_AVERAGE_POLARIZABILITY>
15.443728031042546

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
7-hydroxy-6-methyl-1H,3H-furo[3,4-c]pyridin-3-one

> <ALOGPS_LOGP>
0.42

> <JCHEM_LOGP>
0.13808250166666675

> <ALOGPS_LOGS>
-1.01

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
15.08733239763994

> <JCHEM_PKA_STRONGEST_ACIDIC>
7.9163967050474975

> <JCHEM_PKA_STRONGEST_BASIC>
4.1647683898220595

> <JCHEM_POLAR_SURFACE_AREA>
59.42

> <JCHEM_REFRACTIVITY>
41.0534

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.63e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
5-pyridoxolactone

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for NP0087172 (5-Pyridoxolactone)

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PDB for NP0087172 (5-Pyridoxolactone)
HEADER    PROTEIN                                 23-FEB-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   23-FEB-12         0                                  
HETATM    1  O   UNK     0      25.140 -14.646   0.000  0.00  0.00           O+0
HETATM    2  O   UNK     0      28.829 -17.727   0.000  0.00  0.00           O+0
HETATM    3  O   UNK     0      28.409 -20.430   0.000  0.00  0.00           O+0
HETATM    4  N   UNK     0      23.805 -18.497   0.000  0.00  0.00           N+0
HETATM    5  C   UNK     0      22.472 -16.186   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      27.930 -16.487   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      27.930 -18.966   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      23.805 -16.957   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      25.140 -16.186   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      26.473 -16.957   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      26.473 -18.497   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      25.140 -19.267   0.000  0.00  0.00           C+0
CONECT    1    9                                                            
CONECT    2    6    7                                                       
CONECT    3    7                                                            
CONECT    4    8   12                                                       
CONECT    5    8                                                            
CONECT    6    2   10                                                       
CONECT    7    2    3   11                                                  
CONECT    8    4    5    9                                                  
CONECT    9    1    8   10                                                  
CONECT   10    6    9   11                                                  
CONECT   11    7   10   12                                                  
CONECT   12    4   11                                                       
MASTER        0    0    0    0    0    0    0    0   12    0   26    0
END

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3D PDB for NP0087172 (5-Pyridoxolactone)
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SMILES for NP0087172 (5-Pyridoxolactone)
CC1=NC=C2C(=O)OCC2=C1O
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INCHI for NP0087172 (5-Pyridoxolactone)
InChI=1S/C8H7NO3/c1-4-7(10)6-3-12-8(11)5(6)2-9-4/h2,10H,3H2,1H3
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View in JSmol
Synonyms
ValueSource
5-Pyridoxic acid lactoneChEBI
5-Pyridoxate lactoneGenerator
3-Carboxy-4-(hydroxymethyl)-5-hydroxy-6-methylpyridine lactoneHMDB
5-Pyridoxic acid g-lactoneHMDB
a-PyracinHMDB
alpha-PyracinHMDB
Pyracin-5HMDB
Pyridoxic acid gamma-lactoneHMDB
Chemical FormulaC8H7NO3
Average Mass165.1461 Da
Monoisotopic Mass165.04259 Da
IUPAC Name7-hydroxy-6-methyl-1H,3H-furo[3,4-c]pyridin-3-one
Traditional Name5-pyridoxolactone
CAS Registry NumberNot Available
SMILES
CC1=NC=C2C(=O)OCC2=C1O
InChI Identifier
InChI=1S/C8H7NO3/c1-4-7(10)6-3-12-8(11)5(6)2-9-4/h2,10H,3H2,1H3
InChI KeyPPAXBSPBIWBREI-UHFFFAOYSA-N
Experimental Spectra
Not Available
Predicted Spectra
Spectrum TypeDescriptionDepositor IDDepositor OrganizationDepositorDeposition DateView
1D NMR13C NMR Spectrum (1D, 25 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 252 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 1000 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 50 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 200 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 75 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 300 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 101 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 126 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 151 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 600 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 176 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 700 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 201 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 800 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 226 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
Chemical Shift Submissions
Not Available
Species
Species of Origin
Species NameSourceReference
Anas platyrhynchosFooDB
AnatidaeFooDB
Anser anserFooDB
Apis ceranaLOTUS Database
Bison bisonFooDB
Bos taurusFooDB
Bos taurus X Bison bisonFooDB
Bubalus bubalisFooDB
Capra aegagrus hircusFooDB
CervidaeFooDB
Cervus canadensisFooDB
ColumbaFooDB
ColumbidaeFooDB
Dromaius novaehollandiaeFooDB
Equus caballusFooDB
Gallus gallusFooDB
Lagopus mutaFooDB
LeporidaeFooDB
Lepus timidusFooDB
Melanitta fuscaFooDB
Meleagris gallopavoFooDB
Numida meleagrisFooDB
OdocoileusFooDB
OryctolagusFooDB
Ovis ariesFooDB
PhasianidaeFooDB
Phasianus colchicusFooDB
Struthio camelusFooDB
Sus scrofaFooDB
Sus scrofa domesticaFooDB
Chemical Taxonomy
Description Belongs to the class of organic compounds known as pyridinecarboxylic acids. Pyridinecarboxylic acids are compounds containing a pyridine ring bearing a carboxylic acid group.
KingdomOrganic compounds  
Super ClassOrganoheterocyclic compounds  
ClassPyridines and derivatives  
Sub ClassPyridinecarboxylic acids and derivatives  
Direct ParentPyridinecarboxylic acids  
Alternative Parents
Substituents
  • Pyridine carboxylic acid
    • 

  • Methylpyridine
    • 

  • Hydroxypyridine
    • 

  • Heteroaromatic compound
    • 

  • Carboxylic acid ester
    • 

  • Lactone
    • 

  • Carboxylic acid derivative
    • 

  • Monocarboxylic acid or derivatives
    • 

  • Azacycle
    • 

  • Oxacycle
    • 

  • Organopnictogen compound
    • 

  • Organooxygen compound
    • 

  • Organonitrogen compound
    • 

  • Organic nitrogen compound
    • 

  • Organic oxygen compound
    • 

  • Organic oxide
    • 

  • Hydrocarbon derivative
    • 

  • Aromatic heteropolycyclic compound
Molecular FrameworkAromatic heteropolycyclic compounds
External Descriptors
Physical Properties
StateNot Available
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
logP0.42ALOGPS
logP0.14ChemAxon
logS-1ALOGPS
pKa (Strongest Acidic)7.92ChemAxon
pKa (Strongest Basic)4.16ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count3ChemAxon
Hydrogen Donor Count1ChemAxon
Polar Surface Area59.42 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity41.05 m³·mol⁻¹ChemAxon
Polarizability15.44 ųChemAxon
Number of Rings2ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDHMDB0004291  
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDFDB023360  
KNApSAcK IDNot Available
Chemspider ID70672  
KEGG Compound IDC06052  
BioCyc IDCPD-9028  
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound78300  
PDB IDNot Available
ChEBI ID2124  
Good Scents IDNot Available
References
General References
  1. Mahuren JD, Coburn SP: Determination of 5-pyridoxic acid, 5-pyridoxic acid lactone, and other vitamin B6 compounds by cation-exchange high-performance liquid chromatography. Methods Enzymol. 1997;280:22-9. doi: 10.1016/s0076-6879(97)80097-3. [PubMed:9211301  ] 
  2. Jong YJ, Snell EE: Enzymes of vitamin B6 degradation. Purification and properties of 4- and 5-pyridoxolactonases. J Biol Chem. 1986 Nov 15;261(32):15112-4. [PubMed:3771565  ]