Pyridoxine (YMDB00037)

Identification

YMDB ID

YMDB00037

Name

Pyridoxine

Species

Saccharomyces cerevisiae

Strain

Baker's yeast

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. pyridoxine can be converted into pyridoxine 5'-phosphate through its interaction with the enzyme pyridoxal kinase. In yeast, pyridoxine is involved in the metabolic pathway called the vitamin B6 pathway. Pyridoxine is a potentially toxic compound.

Structure

MOL SDF PDB SMILES InChI

Synonyms

2-Methyl-3-hydroxy-4,5-bis(hydroxymethyl)pyridine
2-Methyl-3-hydroxy-4,5-di(hydroxymethyl)pyridine
2-Methyl-3-hydroxy-4,5-dihydroxymethylpyridine
2-Methyl-4,5-bis(hydroxymethyl)-3-hydroxypyridine
3-hydroxy-2-Picoline-4,5-dimethanol
3-Hydroxy-4,5-bis(hydroxymethyl)-2-methylpyridine
3-Hydroxy-4,5-dimethylol-a-picoline
3-Hydroxy-4,5-dimethylol-alpha-picoline
3-Hydroxy-4,5-dimethylol-α-picoline
5-Hydroxy-6-methyl-3,4-pyridinedimethanol
Adermine
Gravidox
Hydoxin
Piridossina
Piridoxina
Pyridoxin
Pyridoxine
Pyridoxine hydrochloride
Pyridoxinum
Pyridoxol
Pyridoxol hydrochloride
Pyridoxolum
Rodex
Vitamin b6

CAS number

65-23-6

Weight

Average: 169.1778
Monoisotopic: 169.073893223

InChI Key

LXNHXLLTXMVWPM-UHFFFAOYSA-N

InChI

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

IUPAC Name

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

Traditional IUPAC Name

pyridoxine

Chemical Formula

C₈H₁₁NO₃

SMILES

[H]OC1=C(C(=C([H])N=C1C([H])([H])[H])C([H])([H])O[H])C([H])([H])O[H]

Chemical Taxonomy

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 )

Physical Properties

State

Solid

Charge

Melting point

159-162°C

Experimental Properties

Property	Value	Reference
Water Solubility	79 mg/mL [HMP experimental]	PhysProp
LogP	-0.77 [SANGSTER (1993)]	PhysProp

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	1	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	Yes	ChemAxon
MDDR-like Rule	Yes	ChemAxon

Biological Properties

Cellular Locations

extracellular
cytoplasm

Organoleptic Properties

Not Available

SMPDB Pathways

Vitamin B6

PW002488

KEGG Pathways

Vitamin B6 metabolism

ec00750

SMPDB Reactions

Pyridoxine + Adenosine triphosphate → Pyridoxine 5'-phosphate + ADP + hydron

KEGG Reactions

Pyridoxine + Adenosine triphosphate → Pyridoxine 5'-phosphate + hydron + ADP

Pyridoxine + oxygen ↔ Hydrogen peroxide + Pyridoxal

Concentrations

Intracellular Concentrations

Not Available

Extracellular Concentrations

Intracellular Concentration	Substrate	Growth Conditions	Strain	Citation
3 ± 0 µM	hops, malted barley	anaerobic	Baker's yeast	Alcoholic beverage, beer, regular, all - U.S. Department of Agriculture, Agricultural Research Service. 2010. USDA National Nutrient Database for Standard Reference, Release 23. Nutrient Data Laboratory Home Page
3 ± 0 µM	grape juice	anaerobic	Baker's yeast	Alcoholic beverage, wine, table, red - U.S. Department of Agriculture, Agricultural Research Service. 2010. USDA National Nutrient Database for Standard Reference, Release 23. Nutrient Data Laboratory Home Page
Conversion Details Here

Spectra

Spectrum Type	Description	Splash Key	View
GC-MS	GC-MS Spectrum - GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies) (3 TMS)	splash10-000t-0940000000-30b4702623a6d8fcb4bb	JSpectraViewer \| MoNA
GC-MS	GC-MS Spectrum - GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies) (Non-derivatized)	splash10-001j-0690000000-0581e2b42fa48c1ea498	JSpectraViewer \| MoNA
GC-MS	GC-MS Spectrum - GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies) (3 TMS)	splash10-00di-9330000000-32929ff06762b9f5887f	JSpectraViewer \| MoNA
GC-MS	GC-MS Spectrum - GC-MS (3 TMS)	splash10-001i-0490000000-34a09ddbbb462aeb02a6	JSpectraViewer \| MoNA
GC-MS	GC-MS Spectrum - EI-B (Non-derivatized)	splash10-0f6x-9400000000-486db54a30b61c2eb9d4	JSpectraViewer \| MoNA
GC-MS	GC-MS Spectrum - GC-EI-TOF (Non-derivatized)	splash10-000t-0940000000-30b4702623a6d8fcb4bb	JSpectraViewer \| MoNA
GC-MS	GC-MS Spectrum - GC-EI-TOF (Non-derivatized)	splash10-001j-0690000000-0581e2b42fa48c1ea498	JSpectraViewer \| MoNA
GC-MS	GC-MS Spectrum - GC-EI-TOF (Non-derivatized)	splash10-00di-9330000000-32929ff06762b9f5887f	JSpectraViewer \| MoNA
GC-MS	GC-MS Spectrum - GC-MS (Non-derivatized)	splash10-001i-0490000000-34a09ddbbb462aeb02a6	JSpectraViewer \| MoNA
GC-MS	GC-MS Spectrum - GC-EI-TOF (Non-derivatized)	splash10-001j-0790000000-6f8f6e679e03f9119a65	JSpectraViewer \| MoNA
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	splash10-0f79-0900000000-0f727b3e23c2481951e8	JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (3 TMS) - 70eV, Positive	splash10-00di-7079000000-2f143e187cb8c078f936	JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	Not Available	JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	Not Available	JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_1) - 70eV, Positive	Not Available	JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_2) - 70eV, Positive	Not Available	JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_3) - 70eV, Positive	Not Available	JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_1) - 70eV, Positive	Not Available	JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_2) - 70eV, Positive	Not Available	JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_3) - 70eV, Positive	Not Available	JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_1_1) - 70eV, Positive	Not Available	JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_1_2) - 70eV, Positive	Not Available	JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_1_3) - 70eV, Positive	Not Available	JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_2_1) - 70eV, Positive	Not Available	JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_2_2) - 70eV, Positive	Not Available	JSpectraViewer
LC-MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 10V, Positive (Annotated)	splash10-0vi0-0900000000-bd0de86c072765a5caad	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 25V, Positive (Annotated)	splash10-001i-3900000000-2018b406a3c75213b733	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 40V, Positive (Annotated)	splash10-0059-9200000000-e69bb531deb2a103a476	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - EI-B (HITACHI M-80) , Positive	splash10-0f6x-9400000000-77c43a946c4ae1abf3b9	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 10V, Negative	splash10-014i-0900000000-479d4492cc8d634fa366	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 20V, Negative	splash10-0udi-0900000000-486d6a4e5e1a731b7c54	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 30V, Negative	splash10-05fr-0900000000-4ef09ce9c04561a1085e	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 40V, Negative	splash10-0ab9-1900000000-3298adf6db36689d5d43	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 50V, Negative	splash10-0a6r-7900000000-6711954ee96f08344434	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 10V, Positive	splash10-00di-0900000000-234e90d43a7febd7a098	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 20V, Positive	splash10-0udi-0900000000-137080765c0035b45258	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 30V, Positive	splash10-001i-0900000000-882ee900a8bba08e2c7c	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 40V, Positive	splash10-003r-8900000000-e0e11797b63cea991d81	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 50V, Positive	splash10-0059-9100000000-c25384179219411af02c	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QTOF (UPLC Q-Tof Premier, Waters) , Positive	splash10-0ue9-0900000000-c0e149ce890192397b7f	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QTOF (UPLC Q-Tof Premier, Waters) , Negative	splash10-0v4i-0900000000-f9f378af3d47ab006806	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ , negative	splash10-014i-0900000000-479d4492cc8d634fa366	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ , negative	splash10-0udi-0900000000-486d6a4e5e1a731b7c54	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ , negative	splash10-05fr-0900000000-4ef09ce9c04561a1085e	JSpectraViewer \| MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-0uk9-0900000000-eab5b3411261744df750	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0ue9-0900000000-cc4dc8719602182ef1eb	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-001i-5900000000-1c2637733578fcdd7c6a	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-014i-0900000000-e89cc69d8b21012ff982	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-059i-0900000000-0ad8d09e042015cb2e33	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0a4i-9500000000-577a3d87899ca47d539f	JSpectraViewer
MS	Mass Spectrum (Electron Ionization)	splash10-1003-6900000000-1237eaf82dfadfd54d4b	JSpectraViewer \| MoNA
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
2D NMR	[1H,1H] 2D NMR Spectrum	Not Available	JSpectraViewer
2D NMR	[1H,13C] 2D NMR Spectrum	Not Available	JSpectraViewer

References

References:

UniProt Consortium (2011). "Ongoing and future developments at the Universal Protein Resource." Nucleic Acids Res 39:D214-D219.21051339
Scheer, M., Grote, A., Chang, A., Schomburg, I., Munaretto, C., Rother, M., Sohngen, C., Stelzer, M., Thiele, J., Schomburg, D. (2011). "BRENDA, the enzyme information system in 2011." Nucleic Acids Res 39:D670-D676.21062828
Herrgard, M. J., Swainston, N., Dobson, P., Dunn, W. B., Arga, K. Y., Arvas, M., Bluthgen, N., Borger, S., Costenoble, R., Heinemann, M., Hucka, M., Le Novere, N., Li, P., Liebermeister, W., Mo, M. L., Oliveira, A. P., Petranovic, D., Pettifer, S., Simeonidis, E., Smallbone, K., Spasic, I., Weichart, D., Brent, R., Broomhead, D. S., Westerhoff, H. V., Kirdar, B., Penttila, M., Klipp, E., Palsson, B. O., Sauer, U., Oliver, S. G., Mendes, P., Nielsen, J., Kell, D. B. (2008). "A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology." Nat Biotechnol 26:1155-1160.18846089
Alcoholic beverage, beer, regular, all - U.S. Department of Agriculture, Agricultural Research Service. 2010. USDA National Nutrient Database for Standard Reference, Release 23. Nutrient Data Laboratory Home Page
Alcoholic beverage, wine, table, red - U.S. Department of Agriculture, Agricultural Research Service. 2010. USDA National Nutrient Database for Standard Reference, Release 23. Nutrient Data Laboratory Home Page
Stolz, J., Vielreicher, M. (2003). "Tpn1p, the plasma membrane vitamin B6 transporter of Saccharomyces cerevisiae." J Biol Chem 278:18990-18996.12649274

Synthesis Reference:

Itov, Z. I.; Stepanova, S. V.; El'yanov, B. S.; Gunar, V. I. Synthesis of pyridoxine under high pressure. Khimiko-Farmatsevticheskii Zhurnal (1987), 21(7), 858-62.

External Links:

Resource	Link
CHEBI ID	16709
HMDB ID	HMDB00239
Pubchem Compound ID	1054
Kegg ID	C00314
ChemSpider ID	1025
FOODB ID	FDB000574
Wikipedia	Pyridoxine
BioCyc ID	CPD-455

Enzymes

Protein Details

1. Putative pyridoxal reductase

General function:: Involved in oxidoreductase activity
Specific function:: Catalyzes the reduction of pyridoxal (PL) with NADPH and oxidation of pyridoxine (PN) with NADP(+)
Gene Name:: Not Available
Uniprot ID:: Q06494
Molecular weight:: 38600.39844

Reactions

Pyridoxine + NADP(+) → pyridoxal + NADPH.

Protein Details

2. Vitamin B6 transporter TPN1

General function:: Involved in nucleobase transmembrane transporter activity
Specific function:: Thiamine-regulated, high affinity import carrier of pyridoxine, pyridoxal and pyridoxamine
Gene Name:: TPN1
Uniprot ID:: P53099
Molecular weight:: 64545.80078

Protein Details

3. Pyridoxamine 5'-phosphate oxidase

General function:: Involved in pyridoxamine-phosphate oxidase activity
Specific function:: Catalyzes the oxidation of either pyridoxine 5'- phosphate (PNP) or pyridoxamine 5'-phosphate (PMP) into pyridoxal 5'-phosphate (PLP)
Gene Name:: PDX3
Uniprot ID:: P38075
Molecular weight:: 26908.0

Reactions

Pyridoxamine 5'-phosphate + H(2)O + O(2) → pyridoxal 5'-phosphate + NH(3) + H(2)O(2).
Pyridoxine 5'-phosphate + O(2) → pyridoxal 5'-phosphate + H(2)O(2).

Structure for #<Compound:0xaa870d48>

Enzymes

Reactions

Reactions