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Record Information

Version

5.0

Status

Expected but not Quantified

Creation Date

2006-08-13 16:15:06 UTC

Update Date

2023-02-21 17:16:59 UTC

HMDB ID

HMDB0004291

Secondary Accession Numbers

HMDB04291

Metabolite Identification

Common Name

5-Pyridoxolactone

Description

5-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

MOL 3D MOL SDF 3D SDF PDB 3D PDB SMILES InChI

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

View in JSmol View NMR Assignments View Stereo Labels

Synonyms

Value	Source
5-Pyridoxic acid lactone	ChEBI
5-Pyridoxate lactone	Generator
3-Carboxy-4-(hydroxymethyl)-5-hydroxy-6-methylpyridine lactone	HMDB
5-Pyridoxic acid g-lactone	HMDB
a-Pyracin	HMDB
alpha-Pyracin	HMDB
Pyracin-5	HMDB
Pyridoxic acid gamma-lactone	HMDB

Chemical Formula

C₈H₇NO₃

Average Molecular Weight

165.1461

Monoisotopic Molecular Weight

165.042593095

IUPAC Name

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

Traditional Name

5-pyridoxolactone

CAS Registry Number

4543-56-0

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 Key

PPAXBSPBIWBREI-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.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Pyridines and derivatives

Sub Class

Pyridinecarboxylic acids and derivatives

Direct Parent

Pyridinecarboxylic 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 Framework

Aromatic heteropolycyclic compounds

External Descriptors

phenols (CHEBI:2124 )
lactone (CHEBI:2124 )
furopyridine (CHEBI:2124 )
a small molecule (CPD-9028 )

Ontology

Physiological effect

Not Available

Disposition

Biological location

Cellular substructure

Cytoplasm (HMDB: HMDB0004291)

Source

Endogenous

Endogenous (HMDB: HMDB0004291)

Pheasant (FooDB: FOOD00430)
Squab (FooDB: FOOD00481)
Turkey (FooDB: FOOD00494)
Quail (FooDB: FOOD00541)
Anatidae (FooDB: FOOD00576)
Rock ptarmigan (FooDB: FOOD00597)
Columbidae (Dove, Pigeon) (FooDB: FOOD00610)
Chicken (FooDB: FOOD00329)
Mallard duck (FooDB: FOOD00353)
Emu (FooDB: FOOD00360)
Greylag goose (FooDB: FOOD00368)
Guinea hen (FooDB: FOOD00373)
Ostrich (FooDB: FOOD00422)
Velvet duck (FooDB: FOOD00427)

Lagomorph

Ovis

Sheep (Mutton, Lamb) (FooDB: FOOD00473)

Bovine

Venison

Deer (FooDB: FOOD00524)
Mule deer (FooDB: FOOD00348)
Elk (FooDB: FOOD00359)

Caprae

Domestic goat (FooDB: FOOD00529)

Swine

Domestic pig (FooDB: FOOD00536)
Wild boar (FooDB: FOOD00307)

Equine

Horse (FooDB: FOOD00378)

Process

Not Available

Role

Not Available

Physical Properties

State

Solid

Experimental Molecular 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

Experimental Chromatographic Properties

Not Available

Predicted Molecular Properties

Property	Value	Source
Water Solubility	16.3 g/L	ALOGPS
logP	0.42	ALOGPS
logP	0.14	ChemAxon
logS	-1	ALOGPS
pKa (Strongest Acidic)	7.92	ChemAxon
pKa (Strongest Basic)	4.16	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	3	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	59.42 Å²	ChemAxon
Rotatable Bond Count	0	ChemAxon
Refractivity	41.05 m³·mol⁻¹	ChemAxon
Polarizability	15.44 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

Predicted Chromatographic Properties

Predicted Collision Cross Sections

Predictor	Adduct Type	CCS Value (Å²)	Reference
DarkChem	[M+H]+	136.389	31661259
DarkChem	[M-H]-	132.452	31661259
DeepCCS	[M+H]+	133.445	30932474
DeepCCS	[M-H]-	130.97	30932474
DeepCCS	[M-2H]-	166.839	30932474
DeepCCS	[M+Na]+	141.88	30932474
AllCCS	[M+H]+	133.6	32859911
AllCCS	[M+H-H2O]+	129.0	32859911
AllCCS	[M+NH4]+	137.9	32859911
AllCCS	[M+Na]+	139.1	32859911
AllCCS	[M-H]-	132.7	32859911
AllCCS	[M+Na-2H]-	133.4	32859911
AllCCS	[M+HCOO]-	134.1	32859911

Predicted Retention Times

Underivatized

Chromatographic Method	Retention Time	Reference
Measured using a Waters Acquity ultraperformance liquid chromatography (UPLC) ethylene-bridged hybrid (BEH) C18 column (100 mm × 2.1 mm; 1.7 μmparticle diameter). Predicted by Afia on May 17, 2022. Predicted by Afia on May 17, 2022.	3.19 minutes	32390414
Predicted by Siyang on May 30, 2022	9.5594 minutes	33406817
Predicted by Siyang using ReTip algorithm on June 8, 2022	1.49 minutes	32390414
AjsUoB = Accucore 150 Amide HILIC with 10mM Ammonium Formate, 0.1% Formic Acid	88.1 seconds	40023050
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid	735.9 seconds	40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid	308.1 seconds	40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid	83.8 seconds	40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid	179.0 seconds	40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	57.3 seconds	40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid	275.6 seconds	40023050
BfG_NTS_RP1 =Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) with Water:ACN and 0.1% Formic Acid	441.3 seconds	40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)	427.2 seconds	40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid	639.1 seconds	40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid	53.4 seconds	40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid	974.0 seconds	40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	203.9 seconds	40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	299.1 seconds	40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate	564.9 seconds	40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA	310.6 seconds	40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water	375.4 seconds	40023050

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
5-Pyridoxolactone	CC1=NC=C2C(=O)OCC2=C1O	2688.4	Standard polar	33892256
5-Pyridoxolactone	CC1=NC=C2C(=O)OCC2=C1O	1560.3	Standard non polar	33892256
5-Pyridoxolactone	CC1=NC=C2C(=O)OCC2=C1O	1616.1	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
5-Pyridoxolactone,1TMS,isomer #1	CC1=NC=C2C(=O)OCC2=C1O[Si](C)(C)C	1702.1	Semi standard non polar	33892256
5-Pyridoxolactone,1TBDMS,isomer #1	CC1=NC=C2C(=O)OCC2=C1O[Si](C)(C)C(C)(C)C	1972.7	Semi standard non polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted GC-MS	Predicted GC-MS Spectrum - 5-Pyridoxolactone GC-MS (Non-derivatized) - 70eV, Positive	splash10-0079-2900000000-598ecb7d10dd682a3dcf	2017-09-01	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 5-Pyridoxolactone GC-MS (1 TMS) - 70eV, Positive	splash10-00fu-5950000000-70389cc37e4d8334c996	2017-10-06	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 5-Pyridoxolactone GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum

MS/MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5-Pyridoxolactone 10V, Positive-QTOF	splash10-014i-0900000000-e31be06b2625c73bd5f6	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5-Pyridoxolactone 20V, Positive-QTOF	splash10-014i-0900000000-29db0c2d299c687f5d92	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5-Pyridoxolactone 40V, Positive-QTOF	splash10-0avi-9700000000-6941df81fe970e0f77ea	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5-Pyridoxolactone 10V, Negative-QTOF	splash10-03di-0900000000-faffc018b3d55503a74d	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5-Pyridoxolactone 20V, Negative-QTOF	splash10-0229-0900000000-2778bff0e86a1b588ad5	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5-Pyridoxolactone 40V, Negative-QTOF	splash10-0a4i-7900000000-2287674489aef91fbc24	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5-Pyridoxolactone 10V, Negative-QTOF	splash10-03di-0900000000-65490e650f013cfe115e	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5-Pyridoxolactone 20V, Negative-QTOF	splash10-03di-0900000000-ca0deb64ab0e7aa68bd6	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5-Pyridoxolactone 40V, Negative-QTOF	splash10-0avi-9700000000-96f88c4b6ba8616f8e05	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5-Pyridoxolactone 10V, Positive-QTOF	splash10-014i-0900000000-52879b1c24e4e827f43a	2021-09-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5-Pyridoxolactone 20V, Positive-QTOF	splash10-014i-0900000000-68f7008d86f323185b08	2021-09-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5-Pyridoxolactone 40V, Positive-QTOF	splash10-0fic-9400000000-ff6fdae1aa0cc8c39500	2021-09-24	Wishart Lab	View Spectrum

NMR Spectra

Spectrum Type	Description	Deposition Date	Source	View
Predicted 1D NMR	¹³C NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum

IR Spectra

Spectrum Type	Description	Deposition Date	Source	View
Predicted IR Spectrum	IR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M-H]-)	2023-02-03	FELIX lab	View Spectrum
Predicted IR Spectrum	IR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M+H]+)	2023-02-03	FELIX lab	View Spectrum
Predicted IR Spectrum	IR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M+Na]+)	2023-02-03	FELIX lab	View Spectrum

Biological Properties

Cellular Locations

Cytoplasm (predicted from logP)

Biospecimen Locations

Not Available

Tissue Locations

Not Available

Pathways

Not Available

Name	SMPDB/PathBank	KEGG

Normal Concentrations

Not Available

Abnormal Concentrations

Not Available

Associated Disorders and Diseases

Disease References

None

Associated OMIM IDs

None

External Links

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

FDB023360

KNApSAcK ID

Not Available

Chemspider ID

70672

KEGG Compound ID

C06052

BioCyc ID

CPD-9028

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

78300

PDB ID

Not Available

ChEBI ID

2124

Food Biomarker Ontology

Not Available

VMH ID

Not Available

MarkerDB ID

Not Available

Good Scents ID

Not Available

References

Synthesis Reference

Huff, 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

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 ]

Showing metabocard for 5-Pyridoxolactone (HMDB0004291)

MOL for HMDB0004291 (5-Pyridoxolactone)

3D MOL for HMDB0004291 (5-Pyridoxolactone)

3D SDF for HMDB0004291 (5-Pyridoxolactone)

3D-SDF for HMDB0004291 (5-Pyridoxolactone)

PDB for HMDB0004291 (5-Pyridoxolactone)

3D PDB for HMDB0004291 (5-Pyridoxolactone)

SMILES for HMDB0004291 (5-Pyridoxolactone)

INCHI for HMDB0004291 (5-Pyridoxolactone)

Structure for HMDB0004291 (5-Pyridoxolactone)

3D Structure for HMDB0004291 (5-Pyridoxolactone)

Predicted Collision Cross Sections

Predicted Retention Times

Underivatized

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra

NMR Spectra

IR Spectra