Showing metabocard for Pyridoxine (BMDB0000239)

IdentificationTaxonomyPhysical propertiesPathwaysSpectraConcentrationsLinksReferencesenzymes (4) Show 4 proteinsXML
Record Information
Version1.0
Creation Date2016-09-30 22:27:13 UTC
Update Date2020-06-04 20:48:26 UTC
BMDB IDBMDB0000239
Secondary Accession Numbers
  • BMDB00239
Metabolite Identification
Common NamePyridoxine
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 exists as a solid, possibly soluble (in water), and a very strong basic compound (based on its pKa) molecule. Pyridoxine exists in all living species, ranging from bacteria to humans. Pyridoxine participates in a number of enzymatic reactions, within cattle. 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; which is catalyzed by the enzyme pyridoxal kinase. In cattle, pyridoxine is involved in the metabolic pathway called the vitamin B6 metabolism pathway. Pyridoxine is a potentially toxic compound.
Structure
Thumb
MOLSDFPDBSMILESInChI
Synonyms
ValueSource
2-Methyl-3-hydroxy-4,5-dihydroxymethylpyridineChEBI
3-Hydroxy-4,5-bis(hydroxymethyl)-2-methylpyridineChEBI
3-Hydroxy-4,5-dimethylol-alpha-picolineChEBI
5-Hydroxy-6-methyl-3,4-pyridinedimethanolChEBI
PyridoxolChEBI
Vitamin b6ChEBI
3-Hydroxy-4,5-dimethylol-a-picolineGenerator
3-Hydroxy-4,5-dimethylol-α-picolineGenerator
2-Methyl-3-hydroxy-4,5-bis(hydroxymethyl)pyridineHMDB
2-Methyl-3-hydroxy-4,5-di(hydroxymethyl)pyridineHMDB
2-Methyl-4,5-bis(hydroxymethyl)-3-hydroxypyridineHMDB
3-Hydroxy-2-picoline-4,5-dimethanolHMDB
AdermineHMDB
GravidoxHMDB
HydoxinHMDB
PiridossinaHMDB
PiridoxinaHMDB
PyridoxinHMDB
PyridoxinumHMDB
PyridoxolumHMDB
Pyridoxol hydrochlorideHMDB
RodexHMDB
Pyridoxine hydrochlorideHMDB
Chemical FormulaC8H11NO3
Average Molecular Weight169.1778
Monoisotopic Molecular Weight169.073893223
IUPAC Name4,5-bis(hydroxymethyl)-2-methylpyridin-3-ol
Traditional Namepyridoxine
CAS Registry Number65-23-6
SMILES
CC1=C(O)C(CO)=C(CO)C=N1
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 KeyLXNHXLLTXMVWPM-UHFFFAOYSA-N
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
Ontology
StatusDetected and Quantified
Origin
  • Endogenous
BiofunctionNot Available
ApplicationNot Available
Cellular locations
  • Extracellular
Physical Properties
StateSolid
Experimental Properties
PropertyValueReference
Melting Point159 - 162 °CNot Available
Boiling PointNot AvailableNot Available
Water Solubility79 mg/mLNot Available
LogP-0.77SANGSTER (1993)
Predicted Properties
PropertyValueSource
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
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Spectra
Spectra
Biological Properties
Cellular Locations
  • Extracellular
Biospecimen Locations
  • Blood
  • Erythrocyte
  • Liver
  • Milk
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodDetected but not QuantifiedNot QuantifiedNot SpecifiedNot Specified
Normal		 details
ErythrocyteExpected but not QuantifiedNot QuantifiedNot SpecifiedNot SpecifiedNormal
  • Not Applicable
 details
LiverExpected but not QuantifiedNot QuantifiedNot SpecifiedNot SpecifiedNormal
  • Not Applicable
 details
MilkDetected and Quantified2.483 uMNot SpecifiedNot SpecifiedNormal
    • Park, Y. W; Juáre...
 details
MilkDetected and Quantified1.8 +/- 0.1 uMNot SpecifiedNot Specified
Normal		 details
MilkDetected and Quantified1.8 +/- 0.1 uMNot SpecifiedNot Specified
Normal		 details
MilkDetected and Quantified1.8 +/- 0.1 uMNot SpecifiedNot Specified
Normal		 details
MilkDetected and Quantified2.0 +/- 0.1 uMNot SpecifiedNot Specified
Normal		 details
MilkDetected and Quantified2.364 uMNot SpecifiedNot Specified
Normal		 details
MilkDetected and Quantified2.364 uMNot SpecifiedNot Specified
Normal		 details
MilkDetected and Quantified2.187 uMNot SpecifiedNot Specified
Normal		 details
MilkDetected and Quantified2.364 uMNot SpecifiedNot Specified
Normal		 details
MilkDetected and Quantified2.00972 uMNot SpecifiedNot Specified
Normal		 details
MilkDetected and Quantified2.955 uMNot SpecifiedNot Specified
Normal		 details
MilkDetected and Quantified2.66 uMNot SpecifiedNot Specified
Normal		 details
MilkDetected and Quantified2.187 uMNot SpecifiedNot Specified
Normal		 details
MilkDetected and Quantified2.955 uMNot SpecifiedNot Specified
Normal		 details
MilkDetected and Quantified2.719 uMNot SpecifiedNot Specified
Normal		 details
MilkDetected and Quantified2.187 uMNot SpecifiedNot Specified
Normal		 details
MilkDetected and Quantified2.187 uMNot SpecifiedNot Specified
Normal		 details
MilkDetected and Quantified2.896 uMNot SpecifiedNot Specified
Normal		 details
MilkDetected and Quantified2.955 uMNot SpecifiedNot Specified
Normal		 details
MilkDetected and Quantified2.483 uMNot SpecifiedNot Specified
Normal		 details
MilkDetected and Quantified3.0146 uMNot SpecifiedNot Specified
Normal		 details
MilkDetected and Quantified2.66 uMNot SpecifiedNot Specified
Normal		 details
MilkDetected and Quantified2.719 uMNot SpecifiedNot Specified
Normal		 details
MilkDetected and Quantified2.246 uMNot SpecifiedNot Specified
Normal		 details
MilkDetected and Quantified2.246 uMNot SpecifiedNot Specified
Normal		 details
MilkDetected and Quantified2.955 uMNot SpecifiedNot Specified
Normal		 details
MilkDetected and Quantified2.896 uMNot SpecifiedNot Specified
Normal		 details
MilkDetected and Quantified2.955 uMNot SpecifiedNot Specified
Normal		 details
MilkDetected and Quantified2.128 uMNot SpecifiedNot Specified
Normal		 details
MilkDetected and Quantified2.128 uMNot SpecifiedNot Specified
Normal		 details
MilkDetected and Quantified2.778 uMNot SpecifiedNot Specified
Normal		 details
MilkDetected and Quantified2.719 uMNot SpecifiedNot Specified
Normal		 details
MilkDetected and Quantified2.955 uMNot SpecifiedNot Specified
Normal		 details
MilkDetected and Quantified41.377 uMNot SpecifiedNot Specified
Normal		 details
Abnormal Concentrations
Not Available
HMDB IDHMDB0000239
DrugBank IDDB00165
Phenol Explorer Compound IDNot Available
FooDB IDFDB000574
KNApSAcK IDC00001551
Chemspider ID1025
KEGG Compound IDC00314
BioCyc IDPYRIDOXINE
BiGG IDNot Available
Wikipedia LinkPyridoxine
METLIN IDNot Available
PubChem Compound1054
PDB IDNot Available
ChEBI ID16709
References
Synthesis ReferenceItov, 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.
Material Safety Data Sheet (MSDS)Not Available
General References
  1. Agostini TS, Scherer R, Godoy HT: Simultaneous determination of B-group vitamins in enriched Brazilian dairy products. Crit Rev Food Sci Nutr. 2007;47(5):435-9. doi: 10.1080/10408390600846309. [PubMed:17558655 ]
  2. Park, Y. W; Juárez, Manuela ; Ramos, M.; Haenlein, G. F. W. (2007). Park, Y. W; Juárez, Manuela ; Ramos, M.; Haenlein, G. F. W.. Physico-chemical characteristics of goat and sheep milk. Small Ruminant Res.(2007) 68:88-113 doi: 10.1016/j.smallrumres.2006.09.013. Small Ruminant Research.
  3. A. Foroutan et al. (2019). A. Foroutan et al. The Chemical Composition of Commercial Cow's Milk (in preparation). Journal of Agricultural and Food Chemistry.
  4. USDA Food Composition Databases [Link]
  5. Fooddata+, The Technical University of Denmark (DTU) [Link]

Enzymes

Enzyme Details
1. Pyridoxine-5'-phosphate oxidase
General function:
Coenzyme transport and metabolism
Specific function:
Catalyzes the oxidation of either pyridoxine 5'-phosphate (PNP) or pyridoxamine 5'-phosphate (PMP) into pyridoxal 5'-phosphate (PLP).
Gene Name:
PNPO
Uniprot ID:
Q5E9K3
Molecular weight:
30366.0
Reactions
Pyridoxine + Oxygen → Pyridoxal + Hydrogen peroxidedetails
Enzyme Details
2. Pyridoxal phosphate phosphatase
General function:
Carbohydrate transport and metabolism
Specific function:
Protein serine phosphatase that dephosphorylates 'Ser-3' in cofilin and probably also dephosphorylates phospho-serine residues in DSTN. Regulates cofilin-dependent actin cytoskeleton reorganization. Required for normal progress through mitosis and normal cytokinesis. Does not dephosphorylate phospho-threonines in LIMK1. Does not dephosphorylate peptides containing phospho-tyrosine (PubMed:15580268). Pyridoxal phosphate (PLP) phosphatase, which also catalyzes the dephosphorylation of pyridoxine 5'-phosphate (PNP) and pyridoxamine 5'-phosphate (PMP), with order of substrate preference PLP > PNP > PMP (By similarity).
Gene Name:
PDXP
Uniprot ID:
Q3ZBF9
Molecular weight:
31749.0
Reactions
Pyridoxine 5'-phosphate + Water → Pyridoxine + Hydrogen phosphatedetails
Enzyme Details
3. Alkaline phosphatase, tissue-nonspecific isozyme
General function:
Inorganic ion transport and metabolism
Specific function:
This isozyme plays a key role in skeletal mineralization by regulating levels of diphosphate (PPi).
Gene Name:
ALPL
Uniprot ID:
P09487
Molecular weight:
57193.0
Reactions
Pyridoxine 5'-phosphate + Water → Pyridoxine + Hydrogen phosphatedetails
Enzyme Details
4. Pyridoxal kinase
General function:
Coenzyme transport and metabolism
Specific function:
Required for synthesis of pyridoxal-5-phosphate from vitamin B6.
Gene Name:
PDXK
Uniprot ID:
Q0II59
Molecular weight:
34817.0
Reactions
Pyridoxine + Hydrogen phosphate → Pyridoxine 5'-phosphate + Waterdetails