AFCDB: Pyridoxine (FDB000574)

Record Information

Version

1.0

Creation date

2010-04-08 22:04:37 UTC

Update date

2020-09-17 15:41:38 UTC

Primary ID

FDB000574

Secondary Accession Numbers

Not Available

Chemical Information

FooDB Name

Pyridoxine

Description

Pyridoxine, also known as pyridoxol or vitamin B6, belongs to the class of organic compounds known as pyridoxines. These are pyridoxal derivatives in which the carbaldehyde group at position 2 of the pyridoxal moiety is replaced by a hydroxymethyl group. Pyridoxine is a very strong basic compound (based on its pKa). Pyridoxine exists in all living species, ranging from bacteria to humans. Within humans, pyridoxine participates in a number of enzymatic reactions. In particular, pyridoxine can be converted into pyridoxal; which is catalyzed by the enzyme pyridoxine-5'-phosphate oxidase. In addition, pyridoxine can be converted into pyridoxine 5'-phosphate through its interaction with the enzyme pyridoxal kinase. In humans, pyridoxine is involved in vitamin B6 metabolism. Outside of the human body, Pyridoxine is found, on average, in the highest concentration within a few different foods, such as common sages, tarragons, and summer savories and in a lower concentration in hushpuppies, alaska pollocks, and clupeinae (herring, sardine, sprat). Pyridoxine has also been detected, but not quantified in, several different foods, such as ucuhuba, pikeperchs, whiskies, fruit gums, and ginsengs. This could make pyridoxine a potential biomarker for the consumption of these foods. Pyridoxine is a potentially toxic compound.

CAS Number

65-23-6

Structure

MOL SDF PDB SMILES InChI

Synonyms

Synonym	Source
Not Available	Not Available

Predicted Properties

Property	Value	Source
Water Solubility	16.1 g/L	ALOGPS
logP	-0.57	ALOGPS
logP	-0.95	ChemAxon
logS	-1	ALOGPS
pKa (Strongest Acidic)	9.4	ChemAxon
pKa (Strongest Basic)	5.58	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	73.58 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	44.11 m³·mol⁻¹	ChemAxon
Polarizability	17.11 Å³	ChemAxon
Number of Rings	1	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Chemical Formula

C8H11NO3

IUPAC name

4,5-bis(hydroxymethyl)-2-methylpyridin-3-ol

InChI Identifier

InChI=1S/C8H11NO3/c1-5-8(12)7(4-11)6(3-10)2-9-5/h2,10-12H,3-4H2,1H3

InChI Key

LXNHXLLTXMVWPM-UHFFFAOYSA-N

Isomeric SMILES

CC1=C(O)C(CO)=C(CO)C=N1

Average Molecular Weight

169.1778

Monoisotopic Molecular Weight

169.073893223

Classification

Description

Belongs to the class of organic compounds known as pyridoxines. These are pyridoxal derivatives in which the carbaldehyde group at position 2 of the pyridoxal moiety is replaced by a hydroxymethyl group.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Pyridines and derivatives

Sub Class

Pyridoxines

Direct Parent

Pyridoxines

Alternative Parents

Substituents

Pyridoxine
Methylpyridine
Hydroxypyridine
Heteroaromatic compound
Azacycle
Organic nitrogen compound
Organic oxygen compound
Organopnictogen compound
Hydrocarbon derivative
Aromatic alcohol
Primary alcohol
Organooxygen compound
Organonitrogen compound
Alcohol
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

monohydroxypyridine (CHEBI:16709 )
methylpyridines (CHEBI:16709 )
vitamin B6 (CHEBI:16709 )
hydroxymethylpyridine (CHEBI:16709 )
Water-soluble vitamins (C00314 )
a vitamin B6 (PYRIDOXINE )

Ontology

Physiological effect

Health effect:

Health condition:

Homozygous sickle cell disease

Gastrointestinal disorders:

Diarrhea

Musculoskeletal and connective tissue disorders:

Muscle weakness

Intramuscular

Source:

Synthetic:

Personal care product

Biological:

Animal

Plant:

Biological location:

Organ and components:

Liver

Cell and elements:

Extracellular

Biofluid and excreta:

Role

Industrial application:

Pharmaceutical industry:

Pharmaceutical

Physico-Chemical Properties

Physico-Chemical Properties - Experimental

Property	Value	Reference
Physical state	Solid
Physical Description	Not Available
Mass Composition	C 56.80%; H 6.55%; N 8.28%; O 28.37%	DFC
Melting Point	Mp 160°	DFC
Boiling Point	Not Available
Experimental Water Solubility	Not Available
Experimental logP	-0.77	SANGSTER (1993)
Experimental pKa	pKa2 8.96 (25°, 0.15M NaCl)	DFC
Isoelectric point	Not Available
Charge	0
Optical Rotation	Not Available
Spectroscopic UV Data	Not Available
Density	Not Available
Refractive Index	Not Available

Spectra

EI-MS/GC-MS

Type	Description	Splash Key	View
EI-MS	Mass Spectrum (Electron Ionization)	splash10-1003-6900000000-1237eaf82dfadfd54d4b	2014-09-20	View Spectrum
GC-MS	Pyridoxine, 3 TMS, GC-MS Spectrum	splash10-000t-0940000000-30b4702623a6d8fcb4bb	Spectrum
GC-MS	Pyridoxine, non-derivatized, GC-MS Spectrum	splash10-001j-0690000000-0581e2b42fa48c1ea498	Spectrum
GC-MS	Pyridoxine, 3 TMS, GC-MS Spectrum	splash10-00di-9330000000-32929ff06762b9f5887f	Spectrum
GC-MS	Pyridoxine, 3 TMS, GC-MS Spectrum	splash10-001i-0490000000-34a09ddbbb462aeb02a6	Spectrum
GC-MS	Pyridoxine, non-derivatized, GC-MS Spectrum	splash10-0f6x-9400000000-486db54a30b61c2eb9d4	Spectrum
GC-MS	Pyridoxine, non-derivatized, GC-MS Spectrum	splash10-000t-0940000000-30b4702623a6d8fcb4bb	Spectrum
GC-MS	Pyridoxine, non-derivatized, GC-MS Spectrum	splash10-001j-0690000000-0581e2b42fa48c1ea498	Spectrum
GC-MS	Pyridoxine, non-derivatized, GC-MS Spectrum	splash10-00di-9330000000-32929ff06762b9f5887f	Spectrum
GC-MS	Pyridoxine, non-derivatized, GC-MS Spectrum	splash10-001i-0490000000-34a09ddbbb462aeb02a6	Spectrum
GC-MS	Pyridoxine, non-derivatized, GC-MS Spectrum	splash10-001j-0790000000-6f8f6e679e03f9119a65	Spectrum
Predicted GC-MS	Pyridoxine, non-derivatized, Predicted GC-MS Spectrum - 70eV, Positive	splash10-0f79-0900000000-0f727b3e23c2481951e8	Spectrum
Predicted GC-MS	Pyridoxine, 3 TMS, Predicted GC-MS Spectrum - 70eV, Positive	splash10-00di-7079000000-2f143e187cb8c078f936	Spectrum
Predicted GC-MS	Pyridoxine, non-derivatized, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Pyridoxine, non-derivatized, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Pyridoxine, TMS_1_1, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Pyridoxine, TMS_1_2, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Pyridoxine, TMS_1_3, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Pyridoxine, TMS_2_1, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Pyridoxine, TMS_2_2, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Pyridoxine, TMS_2_3, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Pyridoxine, TBDMS_1_1, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Pyridoxine, TBDMS_1_2, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Pyridoxine, TBDMS_1_3, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Pyridoxine, TBDMS_2_1, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Pyridoxine, TBDMS_2_2, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum

MS/MS

Type	Description	Splash Key	View
MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 10V, Positive (Annotated)	splash10-0vi0-0900000000-bd0de86c072765a5caad	2012-07-24	View Spectrum
MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 25V, Positive (Annotated)	splash10-001i-3900000000-2018b406a3c75213b733	2012-07-24	View Spectrum
MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 40V, Positive (Annotated)	splash10-0059-9200000000-e69bb531deb2a103a476	2012-07-24	View Spectrum
MS/MS	LC-MS/MS Spectrum - EI-B (HITACHI M-80) , Positive	splash10-0f6x-9400000000-77c43a946c4ae1abf3b9	2012-08-31	View Spectrum
MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 10V, Negative	splash10-014i-0900000000-479d4492cc8d634fa366	2012-08-31	View Spectrum
MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 20V, Negative	splash10-0udi-0900000000-486d6a4e5e1a731b7c54	2012-08-31	View Spectrum
MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 30V, Negative	splash10-05fr-0900000000-4ef09ce9c04561a1085e	2012-08-31	View Spectrum
MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 40V, Negative	splash10-0ab9-1900000000-3298adf6db36689d5d43	2012-08-31	View Spectrum
MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 50V, Negative	splash10-0a6r-7900000000-6711954ee96f08344434	2012-08-31	View Spectrum
MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 10V, Positive	splash10-00di-0900000000-234e90d43a7febd7a098	2012-08-31	View Spectrum
MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 20V, Positive	splash10-0udi-0900000000-137080765c0035b45258	2012-08-31	View Spectrum
MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 30V, Positive	splash10-001i-0900000000-882ee900a8bba08e2c7c	2012-08-31	View Spectrum
MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 40V, Positive	splash10-003r-8900000000-e0e11797b63cea991d81	2012-08-31	View Spectrum
MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 50V, Positive	splash10-0059-9100000000-c25384179219411af02c	2012-08-31	View Spectrum
MS/MS	LC-MS/MS Spectrum - LC-ESI-QTOF (UPLC Q-Tof Premier, Waters) , Positive	splash10-0ue9-0900000000-c0e149ce890192397b7f	2012-08-31	View Spectrum
MS/MS	LC-MS/MS Spectrum - LC-ESI-QTOF (UPLC Q-Tof Premier, Waters) , Negative	splash10-0v4i-0900000000-f9f378af3d47ab006806	2012-08-31	View Spectrum
MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ , negative	splash10-014i-0900000000-479d4492cc8d634fa366	2017-09-14	View Spectrum
MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ , negative	splash10-0udi-0900000000-486d6a4e5e1a731b7c54	2017-09-14	View Spectrum
MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ , negative	splash10-05fr-0900000000-4ef09ce9c04561a1085e	2017-09-14	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-0uk9-0900000000-eab5b3411261744df750	2015-05-26	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0ue9-0900000000-cc4dc8719602182ef1eb	2015-05-26	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-001i-5900000000-1c2637733578fcdd7c6a	2015-05-26	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-014i-0900000000-e89cc69d8b21012ff982	2015-05-27	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-059i-0900000000-0ad8d09e042015cb2e33	2015-05-27	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0a4i-9500000000-577a3d87899ca47d539f	2015-05-27	View Spectrum

NMR

Type	Description	View
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, experimental)	Spectrum
1D NMR	¹H NMR Spectrum (1D, D₂O, experimental)	Spectrum
1D NMR	¹³C NMR Spectrum (1D, D₂O, experimental)	Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	Spectrum
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, D₂O, predicted)	Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, D₂O, predicted)	Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	Spectrum
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, D₂O, predicted)	Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, D₂O, predicted)	Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	Spectrum
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, predicted)	Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	Spectrum
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, D₂O, predicted)	Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	Spectrum
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, D₂O, predicted)	Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	Spectrum
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, D₂O, predicted)	Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, predicted)	Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	Spectrum
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	Spectrum
2D NMR	[¹H, ¹H]-TOCSY. Unexported temporarily by An Chi on Oct 15, 2021 until json or nmrML file is generated. 2D NMR Spectrum (experimental)	Spectrum
2D NMR	[¹H, ¹³C]-HSQC NMR Spectrum (2D, 600 MHz, H₂O, experimental)	Spectrum

External Links

ChemSpider ID

ChEMBL ID

KEGG Compound ID

Pubchem Compound ID

Pubchem Substance ID

Not Available

ChEBI ID

16709

Phenol-Explorer ID

Not Available

DrugBank ID

DB00165

HMDB ID

HMDB00239

CRC / DFC (Dictionary of Food Compounds) ID

BDV40-Q:BDV40-Q

EAFUS ID

3262

Dr. Duke ID

VITAMIN-B-6|VIT-B-6|PYRIDOXINE

BIGG ID

34590

KNApSAcK ID

Not Available

HET ID

Not Available

Food Biomarker Ontology

Not Available

VMH ID

Not Available

Flavornet ID

Not Available

GoodScent ID

Not Available

SuperScent ID

Not Available

Wikipedia ID

Pyridoxine

Phenol-Explorer Metabolite ID

Not Available

Duplicate IDS

Not Available

Old DFC IDS

Not Available

Associated Foods

Food	Content Range	Average	Reference
Food			Reference

Biological Effects and Interactions

Health Effects / Bioactivities

Descriptor	ID	Definition	Reference
analgesic	35480	An agent capable of relieving pain without the loss of consciousness or without producing anaesthesia. In addition, analgesic is a role played by a compound which is exhibited by a capability to cause a reduction of pain symptoms.	DUKE
anti acne	50177	A drug used to treat or prevent skin disorders or for the routine care of skin.	DUKE
anti aggregant			DUKE
anti anemic	52217	Any substance introduced into a living organism with therapeutic or diagnostic purpose.	DUKE
anti asthmatic	49167	A drug used to treat asthma.	DUKE
anti atherosclerotic	38070	A drug used for the treatment or prevention of cardiac arrhythmias. Anti-arrhythmia drugs may affect the polarisation-repolarisation phase of the action potential, its excitability or refractoriness, or impulse conduction or membrane responsiveness within cardiac fibres.	DUKE
anti autistic	52217	Any substance introduced into a living organism with therapeutic or diagnostic purpose.	DUKE
anti carpal-tunnel			DUKE
anti cheilitic			DUKE
anti depressant	52217	Any substance introduced into a living organism with therapeutic or diagnostic purpose.	DUKE
anti dermatitic	50177	A drug used to treat or prevent skin disorders or for the routine care of skin.	DUKE
anti diabetic	52217	Any substance introduced into a living organism with therapeutic or diagnostic purpose.	DUKE
antidote	50247	Any protective agent counteracting or neutralizing the action of poisons.	DUKE
anti dyskinetic			DUKE
anti emetic	50919	A drug used to prevent nausea or vomiting. An antiemetic may act by a wide range of mechanisms: it might affect the medullary control centres (the vomiting centre and the chemoreceptive trigger zone) or affect the peripheral receptors.	DUKE
anti epileptic	52217	Any substance introduced into a living organism with therapeutic or diagnostic purpose.	DUKE
anti glossitic			DUKE
anti homocystinuric			DUKE
anti hyperkinetic			DUKE
anti hyperventilation	52217	Any substance introduced into a living organism with therapeutic or diagnostic purpose.	DUKE
anti infertility	52217	Any substance introduced into a living organism with therapeutic or diagnostic purpose.	DUKE
anti lithic			DUKE
anti morning sickness	52217	Any substance introduced into a living organism with therapeutic or diagnostic purpose.	DUKE
anti monosodium-glutamate-sensitivity			DUKE
anti nephritic	52217	Any substance introduced into a living organism with therapeutic or diagnostic purpose.	DUKE
anti neuritic	52217	Any substance introduced into a living organism with therapeutic or diagnostic purpose.	DUKE
anti neuropathic			DUKE
anti oxaluric			DUKE
anti Parkinsonian	48407	A drug used in the treatment of Parkinson's disease.	DUKE
anti premenstrual syndrome	52217	Any substance introduced into a living organism with therapeutic or diagnostic purpose.	DUKE
anti prolactin			DUKE
anti radiation			DUKE
anti schizophrenic	52217	Any substance introduced into a living organism with therapeutic or diagnostic purpose.	DUKE
anti seborrheic	52217	Any substance introduced into a living organism with therapeutic or diagnostic purpose.	DUKE
anti sickling			DUKE
anti spasmodic	52217	Any substance introduced into a living organism with therapeutic or diagnostic purpose.	DUKE
anti TMJ			DUKE
anti ulcer	49201	One of various classes of drugs with different action mechanisms used to treat or ameliorate peptic ulcer or irritation of the gastrointestinal tract.	DUKE
anti vertigo	52217	Any substance introduced into a living organism with therapeutic or diagnostic purpose.	DUKE
dopaminergic	48560	A drug used for its effects on dopamine receptors, on the life cycle of dopamine, or on the survival of dopaminergic neurons.	DUKE
neurotoxic	50910	A poison that interferes with the functions of the nervous system.	DUKE
progesteronigenic			DUKE

Enzymes

Name	Gene Name	UniProt ID
Phosphoserine aminotransferase	PSAT1	Q9Y617

Pathways

Name	SMPDB Link	KEGG Link
Vitamin B6 Metabolism	SMP00017	map00750

Metabolism

Not Available

Biosynthesis

Not Available

Organoleptic Properties

Flavours

Not Available

Files

MSDS

Not Available

References

Synthesis Reference

Not Available

General Reference

Not Available

Content Reference

— Saxholt, E., et al. 'Danish food composition databank, revision 7.' Department of Nutrition, National Food Institute, Technical University of Denmark (2008).
— U.S. Department of Agriculture, Agricultural Research Service. 2008. USDA National Nutrient Database for Standard Reference, Release 21. Nutrient Data Laboratory Home Page.
— Duke, James. 'Dr. Duke's Phytochemical and Ethnobotanical Databases. United States Department of Agriculture.' Agricultural Research Service, Accessed April 27 (2004).

Pyridoxine (FDB000574)

Structure for FDB000574 (Pyridoxine)