You are using an unsupported browser. Please upgrade your browser to a newer version to get the best experience on Yeast Metabolome Database.
Identification
YMDB IDYMDB00037
NamePyridoxine
SpeciesSaccharomyces cerevisiae
StrainBaker's yeast
DescriptionPyridoxine, 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 the action of 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
Thumb
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 number65-23-6
WeightAverage: 169.1778
Monoisotopic: 169.073893223
InChI KeyLXNHXLLTXMVWPM-UHFFFAOYSA-N
InChIInChI=1S/C8H11NO3/c1-5-8(12)7(4-11)6(3-10)2-9-5/h2,10-12H,3-4H2,1H3
IUPAC Name4,5-bis(hydroxymethyl)-2-methylpyridin-3-ol
Traditional IUPAC Namepyridoxine
Chemical FormulaC8H11NO3
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.
KingdomOrganic compounds
Super ClassOrganoheterocyclic compounds
ClassPyridines and derivatives
Sub ClassPyridoxines
Direct ParentPyridoxines
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 FrameworkAromatic heteromonocyclic compounds
External Descriptors
Physical Properties
StateSolid
Charge0
Melting point159-162°C
Experimental Properties
PropertyValueReference
Water Solubility79 mg/mL [HMP experimental]PhysProp
LogP-0.77 [SANGSTER (1993)]PhysProp
Predicted Properties
PropertyValueSource
Water Solubility16.1 g/LALOGPS
logP-0.57ALOGPS
logP-0.95ChemAxon
logS-1ALOGPS
pKa (Strongest Acidic)9.4ChemAxon
pKa (Strongest Basic)5.58ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count4ChemAxon
Hydrogen Donor Count3ChemAxon
Polar Surface Area73.58 ŲChemAxon
Rotatable Bond Count2ChemAxon
Refractivity44.11 m³·mol⁻¹ChemAxon
Polarizability17.11 ųChemAxon
Number of Rings1ChemAxon
Bioavailability1ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations
  • extracellular
  • cytoplasm
Organoleptic PropertiesNot Available
SMPDB Pathways
Vitamin B6PW002488 ThumbThumb?image type=greyscaleThumb?image type=simple
KEGG Pathways
Vitamin B6 metabolismec00750 Map00750
SMPDB Reactions
Pyridoxine + Adenosine triphosphatePyridoxine 5'-phosphate + ADP + hydron
KEGG Reactions
Pyridoxine + Adenosine triphosphatePyridoxine 5'-phosphate + hydron + ADP
Pyridoxine + oxygenHydrogen peroxide + Pyridoxal
Concentrations
Intracellular ConcentrationsNot Available
Extracellular Concentrations
Intracellular ConcentrationSubstrateGrowth ConditionsStrainCitation
3 ± 0 µM hops, malted barleyanaerobicBaker's yeastAlcoholic 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 juiceanaerobicBaker's yeastAlcoholic 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
Spectra
Spectrum TypeDescriptionSplash KeyView
GC-MSGC-MS Spectrum - GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies) (3 TMS)splash10-000t-0940000000-30b4702623a6d8fcb4bbJSpectraViewer | MoNA
GC-MSGC-MS Spectrum - GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies) (Non-derivatized)splash10-001j-0690000000-0581e2b42fa48c1ea498JSpectraViewer | MoNA
GC-MSGC-MS Spectrum - GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies) (3 TMS)splash10-00di-9330000000-32929ff06762b9f5887fJSpectraViewer | MoNA
GC-MSGC-MS Spectrum - GC-MS (3 TMS)splash10-001i-0490000000-34a09ddbbb462aeb02a6JSpectraViewer | MoNA
GC-MSGC-MS Spectrum - EI-B (Non-derivatized)splash10-0f6x-9400000000-486db54a30b61c2eb9d4JSpectraViewer | MoNA
GC-MSGC-MS Spectrum - GC-EI-TOF (Non-derivatized)splash10-000t-0940000000-30b4702623a6d8fcb4bbJSpectraViewer | MoNA
GC-MSGC-MS Spectrum - GC-EI-TOF (Non-derivatized)splash10-001j-0690000000-0581e2b42fa48c1ea498JSpectraViewer | MoNA
GC-MSGC-MS Spectrum - GC-EI-TOF (Non-derivatized)splash10-00di-9330000000-32929ff06762b9f5887fJSpectraViewer | MoNA
GC-MSGC-MS Spectrum - GC-MS (Non-derivatized)splash10-001i-0490000000-34a09ddbbb462aeb02a6JSpectraViewer | MoNA
GC-MSGC-MS Spectrum - GC-EI-TOF (Non-derivatized)splash10-001j-0790000000-6f8f6e679e03f9119a65JSpectraViewer | MoNA
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-0f79-0900000000-0f727b3e23c2481951e8JSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (3 TMS) - 70eV, Positivesplash10-00di-7079000000-2f143e187cb8c078f936JSpectraViewer
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 10V, Positive (Annotated)splash10-0vi0-0900000000-bd0de86c072765a5caadJSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 25V, Positive (Annotated)splash10-001i-3900000000-2018b406a3c75213b733JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 40V, Positive (Annotated)splash10-0059-9200000000-e69bb531deb2a103a476JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - EI-B (HITACHI M-80) , Positivesplash10-0f6x-9400000000-77c43a946c4ae1abf3b9JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 10V, Negativesplash10-014i-0900000000-479d4492cc8d634fa366JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 20V, Negativesplash10-0udi-0900000000-486d6a4e5e1a731b7c54JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 30V, Negativesplash10-05fr-0900000000-4ef09ce9c04561a1085eJSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 40V, Negativesplash10-0ab9-1900000000-3298adf6db36689d5d43JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 50V, Negativesplash10-0a6r-7900000000-6711954ee96f08344434JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 10V, Positivesplash10-00di-0900000000-234e90d43a7febd7a098JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 20V, Positivesplash10-0udi-0900000000-137080765c0035b45258JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 30V, Positivesplash10-001i-0900000000-882ee900a8bba08e2c7cJSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 40V, Positivesplash10-003r-8900000000-e0e11797b63cea991d81JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 50V, Positivesplash10-0059-9100000000-c25384179219411af02cJSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF (UPLC Q-Tof Premier, Waters) , Positivesplash10-0ue9-0900000000-c0e149ce890192397b7fJSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF (UPLC Q-Tof Premier, Waters) , Negativesplash10-0v4i-0900000000-f9f378af3d47ab006806JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , negativesplash10-014i-0900000000-479d4492cc8d634fa366JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , negativesplash10-0udi-0900000000-486d6a4e5e1a731b7c54JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , negativesplash10-05fr-0900000000-4ef09ce9c04561a1085eJSpectraViewer | MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-0uk9-0900000000-eab5b3411261744df750JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-0ue9-0900000000-cc4dc8719602182ef1ebJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-001i-5900000000-1c2637733578fcdd7c6aJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-014i-0900000000-e89cc69d8b21012ff982JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-059i-0900000000-0ad8d09e042015cb2e33JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-0a4i-9500000000-577a3d87899ca47d539fJSpectraViewer
MSMass Spectrum (Electron Ionization)splash10-1003-6900000000-1237eaf82dfadfd54d4bJSpectraViewer | MoNA
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
2D NMR[1H,1H] 2D NMR SpectrumNot AvailableJSpectraViewer
2D NMR[1H,13C] 2D NMR SpectrumNot AvailableJSpectraViewer
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:
ResourceLink
CHEBI ID16709
HMDB IDHMDB00239
Pubchem Compound ID1054
Kegg IDC00314
ChemSpider ID1025
FOODB IDFDB000574
WikipediaPyridoxine
BioCyc IDCPD-455

Enzymes

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.
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
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).