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Showing metabocard for 5-Pyridoxolactone (HMDB0004291)

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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2006-08-13 16:15:06 UTC
Update Date2023-02-21 17:16:59 UTC
HMDB IDHMDB0004291
Secondary Accession Numbers
  • HMDB04291
Metabolite Identification
Common Name5-Pyridoxolactone
Description5-Pyridoxolactone 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 has been detected, but not quantified in, a few different foods, such as anatidaes (Anatidae), chickens (Gallus gallus), and domestic pigs (Sus scrofa domestica). This could make 5-pyridoxolactone a potential biomarker for the consumption of these foods. 5-Pyridoxolactone is a primary metabolite. Primary metabolites are metabolically or physiologically essential metabolites. They are directly involved in an organism’s growth, development or reproduction. Based on a literature review a significant number of articles have been published on 5-Pyridoxolactone.
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0004291 (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
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3D MOL for HMDB0004291 (5-Pyridoxolactone)

HMDB0004291
     RDKit          3D
5-Pyridoxolactone
 19 20  0  0  0  0  0  0  0  0999 V2000
    2.9853    0.0453   -0.2682 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5035    0.3241   -0.2670 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0587    1.4967   -0.7539 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2552    1.7764   -0.7674 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2015    0.8795   -0.2857 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7352   -0.3161    0.2096 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6286   -0.6151    0.2276 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0829   -1.8214    0.7287 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9110   -1.0847    0.6535 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0216   -0.2913    0.3927 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6502    0.8997   -0.1717 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4321    1.8129   -0.5139 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.4859    0.9250    0.2251 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3844    0.0201   -1.3068 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1613   -0.8931    0.2711 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6607    2.7107   -1.1510 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3928   -2.4715    1.0782 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8330   -1.4057    1.7161 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9829   -1.9914   -0.0174 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  6  1  0
  6  7  2  0
  7  8  1  0
  6  9  1  0
  9 10  1  0
 10 11  1  0
 11 12  2  0
  7  2  1  0
 11  5  1  0
  1 13  1  0
  1 14  1  0
  1 15  1  0
  4 16  1  0
  8 17  1  0
  9 18  1  0
  9 19  1  0
M  END
Download

3D SDF for HMDB0004291 (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>
HMDB0004291

> <DATABASE_NAME>
hmdb

> <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

$$$$
Download

3D-SDF for HMDB0004291 (5-Pyridoxolactone)

HMDB0004291
     RDKit          3D
5-Pyridoxolactone
 19 20  0  0  0  0  0  0  0  0999 V2000
    2.9853    0.0453   -0.2682 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5035    0.3241   -0.2670 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0587    1.4967   -0.7539 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2552    1.7764   -0.7674 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2015    0.8795   -0.2857 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7352   -0.3161    0.2096 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6286   -0.6151    0.2276 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0829   -1.8214    0.7287 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9110   -1.0847    0.6535 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0216   -0.2913    0.3927 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6502    0.8997   -0.1717 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4321    1.8129   -0.5139 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.4859    0.9250    0.2251 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3844    0.0201   -1.3068 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1613   -0.8931    0.2711 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6607    2.7107   -1.1510 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3928   -2.4715    1.0782 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8330   -1.4057    1.7161 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9829   -1.9914   -0.0174 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  6  1  0
  6  7  2  0
  7  8  1  0
  6  9  1  0
  9 10  1  0
 10 11  1  0
 11 12  2  0
  7  2  1  0
 11  5  1  0
  1 13  1  0
  1 14  1  0
  1 15  1  0
  4 16  1  0
  8 17  1  0
  9 18  1  0
  9 19  1  0
M  END
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PDB for HMDB0004291 (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 HMDB0004291 (5-Pyridoxolactone)

COMPND    HMDB0004291
HETATM    1  C1  UNL     1       2.985   0.045  -0.268  1.00  0.00           C  
HETATM    2  C2  UNL     1       1.503   0.324  -0.267  1.00  0.00           C  
HETATM    3  N1  UNL     1       1.059   1.497  -0.754  1.00  0.00           N  
HETATM    4  C3  UNL     1      -0.255   1.776  -0.767  1.00  0.00           C  
HETATM    5  C4  UNL     1      -1.201   0.879  -0.286  1.00  0.00           C  
HETATM    6  C5  UNL     1      -0.735  -0.316   0.210  1.00  0.00           C  
HETATM    7  C6  UNL     1       0.629  -0.615   0.228  1.00  0.00           C  
HETATM    8  O1  UNL     1       1.083  -1.821   0.729  1.00  0.00           O  
HETATM    9  C7  UNL     1      -1.911  -1.085   0.653  1.00  0.00           C  
HETATM   10  O2  UNL     1      -3.022  -0.291   0.393  1.00  0.00           O  
HETATM   11  C8  UNL     1      -2.650   0.900  -0.172  1.00  0.00           C  
HETATM   12  O3  UNL     1      -3.432   1.813  -0.514  1.00  0.00           O  
HETATM   13  H1  UNL     1       3.486   0.925   0.225  1.00  0.00           H  
HETATM   14  H2  UNL     1       3.384   0.020  -1.307  1.00  0.00           H  
HETATM   15  H3  UNL     1       3.161  -0.893   0.271  1.00  0.00           H  
HETATM   16  H4  UNL     1      -0.661   2.711  -1.151  1.00  0.00           H  
HETATM   17  H5  UNL     1       0.393  -2.472   1.078  1.00  0.00           H  
HETATM   18  H6  UNL     1      -1.833  -1.406   1.716  1.00  0.00           H  
HETATM   19  H7  UNL     1      -1.983  -1.991  -0.017  1.00  0.00           H  
CONECT    1    2   13   14   15
CONECT    2    3    3    7
CONECT    3    4
CONECT    4    5    5   16
CONECT    5    6   11
CONECT    6    7    7    9
CONECT    7    8
CONECT    8   17
CONECT    9   10   18   19
CONECT   10   11
CONECT   11   12   12
END
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SMILES for HMDB0004291 (5-Pyridoxolactone)

CC1=NC=C2C(=O)OCC2=C1O
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INCHI for HMDB0004291 (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 JSmolView NMR AssignmentsView Stereo Labels
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 Molecular Weight165.1461
Monoisotopic Molecular Weight165.042593095
IUPAC Name7-hydroxy-6-methyl-1H,3H-furo[3,4-c]pyridin-3-one
Traditional Name5-pyridoxolactone
CAS Registry Number4543-56-0
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
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
Ontology
Physiological effectNot Available
Disposition
Biological locationSource
ProcessNot Available
RoleNot Available
Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
Predicted Chromatographic Properties
Spectra
Biological Properties
Cellular Locations
  • Cytoplasm (predicted from logP)
Biospecimen LocationsNot Available
Tissue LocationsNot Available
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB 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
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceHuff, Jesse W.; Perlzweig, Wm. A. A product of oxidative metabolism of pyridoxine, 2-methyl-3-hydroxy-4-carboxy-5-hydroxymethylpyridine (4-pyridoxic acid). I. Isolation from urine, structure, and synthesis. Journal of Biological Chemistry (1944), 155 345-55.
Material Safety Data Sheet (MSDS)Not Available
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. [PubMed:9211301 ]