Human Metabolome Database Version 3.5

Showing metabocard for Pyridoxine (HMDB00239)

Record Information
Version 3.5
Creation Date 2005-11-16 08:48:42 -0700
Update Date 2013-02-08 17:08:08 -0700
HMDB ID HMDB00239
Secondary Accession Numbers
  • HMDB02075
Metabolite Identification
Common Name Pyridoxine
Description The 4-methanol form of vitamin B6 which is converted to pyridoxal phosphate which is a coenzyme for synthesis of amino acids, neurotransmitters (serotonin, norepinephrine), sphingolipids, aminolevulinic acid. Although pyridoxine and Vitamin B6 are still frequently used as synonyms, especially by medical researchers, this practice is erroneous and sometimes misleading (EE Snell; Ann NY Acad Sci, vol 585 pg 1, 1990). Pyridoxine is one of the compounds that can be called vitamin B6. Pyridoxine assists in the balancing of sodium and potassium as well as promoting red blood cell production. It is linked to cancer immunity and helps fight the formation of homocysteine. It has been suggested that Pyridoxine might help children with learning difficulties, and may also prevent dandruff, eczema, and psoriasis. In addition, pyridoxine can help balance hormonal changes in women and aid in immune system. Lack of pyridoxine may cause anemia, nerve damage, seizures, skin problems, and sores in the mouth. -- Wikipedia Deficiency, though rare because of widespread distribution in foods, leads to the development of peripheral neuritis in adults and affects the central nervous system in children (DOSE - 3rd edition).
Structure Thumb
Download: MOL | SDF | PDB | SMILES | InChI
Display: 2D Structure | 3D Structure
Synonyms
  1. 2-Methyl-3-hydroxy-4,5-bis(hydroxymethyl)pyridine
  2. 2-Methyl-3-hydroxy-4,5-di(hydroxymethyl)pyridine
  3. 2-Methyl-4,5-bis(hydroxymethyl)-3-hydroxypyridine
  4. 3-Hydroxy-2-Picoline-4,5-dimethanol
  5. 3-Hydroxy-4,5-dimethylol-alpha-picoline
  6. 5-Hydroxy-6-methyl-3,4-pyridinedimethanol
  7. Adermine
  8. Gravidox
  9. Hydoxin
  10. Piridossina
  11. Piridoxina
  12. Pyridoxin
  13. Pyridoxine
  14. Pyridoxinum
  15. Pyridoxol
  16. Pyridoxolum
Chemical Formula C8H11NO3
Average Molecular Weight 169.1778
Monoisotopic Molecular Weight 169.073893223
IUPAC Name 4,5-bis(hydroxymethyl)-2-methylpyridin-3-ol
Traditional IUPAC Name pyridoxine
CAS Registry Number 65-23-6
SMILES CC1=NC=C(CO)C(CO)=C1O
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
Chemical Taxonomy
Kingdom Organic Compounds
Super Class Aromatic Heteromonocyclic Compounds
Class Pyridines and Derivatives
Sub Class Pyridoxines
Other Descriptors
  • Pyridines and Derivatives
  • Water-soluble vitamins(KEGG)
  • a vitamin B6(Cyc)
  • hydroxymethylpyridine(ChEBI)
  • methylpyridines(ChEBI)
  • monohydroxypyridine(ChEBI)
  • vitamin B6(ChEBI)
Substituents
  • Primary Alcohol
Direct Parent Pyridoxines
Ontology
Status Detected and Quantified
Origin
  • Endogenous
Biofunction Not Available
Application Not Available
Cellular locations
  • Extracellular
Physical Properties
State Solid
Experimental Properties
Property Value Reference
Melting Point 159 - 162 °C Not Available
Boiling Point Not Available Not Available
Water Solubility 79 mg/mL Not Available
LogP -0.77 SANGSTER (1993)
Predicted Properties
Property Value Source
Water Solubility 16.1 g/L ALOGPS
LogP -0.57 ALOGPS
LogP -0.95 ChemAxon
LogS -1.02 ALOGPS
pKa (strongest acidic) 9.4 ChemAxon
pKa (strongest basic) 5.58 ChemAxon
Hydrogen Acceptor Count 4 ChemAxon
Hydrogen Donor Count 3 ChemAxon
Polar Surface Area 73.58 A2 ChemAxon
Rotatable Bond Count 2 ChemAxon
Refractivity 44.11 ChemAxon
Polarizability 17.11 ChemAxon
Formal Charge 0 ChemAxon
Physiological Charge 0 ChemAxon
Spectra
Gas-MS Spectrum
1H NMR Spectrum
MS/MS Spectrum Quattro_QQQ 10
MS/MS Spectrum Quattro_QQQ 25
MS/MS Spectrum Quattro_QQQ 40
MS/MS Spectrum EI-B (HITACHI M-80)
MS/MS Spectrum LC-ESI-QQ (API3000, Applied Biosystems) 10
MS/MS Spectrum LC-ESI-QQ (API3000, Applied Biosystems) 20
MS/MS Spectrum LC-ESI-QQ (API3000, Applied Biosystems) 30
MS/MS Spectrum LC-ESI-QQ (API3000, Applied Biosystems) 40
MS/MS Spectrum LC-ESI-QQ (API3000, Applied Biosystems) 50
MS/MS Spectrum LC-ESI-QQ (API3000, Applied Biosystems) 10
MS/MS Spectrum LC-ESI-QQ (API3000, Applied Biosystems) 20
MS/MS Spectrum LC-ESI-QQ (API3000, Applied Biosystems) 30
MS/MS Spectrum LC-ESI-QQ (API3000, Applied Biosystems) 40
MS/MS Spectrum LC-ESI-QQ (API3000, Applied Biosystems) 50
MS/MS Spectrum GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies)
[1H,1H] 2D NMR Spectrum
[1H,13C] 2D NMR Spectrum
Biological Properties
Cellular Locations
  • Extracellular
Biofluid Locations
  • Blood
  • Urine
Tissue Location
  • Erythrocyte
  • Liver
Pathways
Name SMPDB Link KEGG Link
Vitamin B6 Metabolism SMP00017 map00750 Link_out
Normal Concentrations
Biofluid Status Value Age Sex Condition Reference
Blood Detected and Quantified
0.025 (0.007-0.060) uM Adult (>18 years old) Both Normal
Urine Detected but not Quantified
Not Applicable Adult (>18 years old) Male Normal
Urine Detected and Quantified
<1 nmol/mmol creatinine Adult (>18 years old) Both Normal
Urine Detected but not Quantified
Not Applicable Adult (>18 years old) Male Normal
Abnormal Concentrations
Biofluid Status Value Age Sex Condition Reference
Blood Detected and Quantified 0.119 +/- 0.038 uM Adult (>18 years old) Both Homozygous sickle cell disease
Associated Disorders and Diseases
Disease References
Homozygous sickle cell disease
  • van der Dijs FP, Schnog JJ, Brouwer DA, Velvis HJ, van den Berg GA, Bakker AJ, Duits AJ, Muskiet FD, Muskiet FA: Elevated homocysteine levels indicate suboptimal folate status in pediatric sickle cell patients. Am J Hematol. 1998 Nov;59(3):192-8. Pubmed: 9798656 Link_out
      Associated OMIM IDs None
      DrugBank ID Not Available
      DrugBank Metabolite ID Not Available
      Phenol Explorer Compound ID Not Available
      Phenol Explorer Metabolite ID Not Available
      FoodDB ID FDB000574
      KNApSAcK ID Not Available
      Chemspider ID 1025 Link_out
      KEGG Compound ID C00314 Link_out
      BioCyc ID CPD-455 Link_out
      BiGG ID 34590 Link_out
      Wikipedia Link Pyridoxine Link_out
      NuGOwiki Link HMDB00239 Link_out
      Metagene Link HMDB00239 Link_out
      METLIN ID 5245 Link_out
      PubChem Compound 1054 Link_out
      PDB ID Not Available
      ChEBI ID 16709 Link_out
      References
      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.
      Material Safety Data Sheet (MSDS) Not Available
      General References
      1. Henderson JM, Codner MA, Hollins B, Kutner MH, Merrill AH: The fasting B6 vitamer profile and response to a pyridoxine load in normal and cirrhotic subjects. Hepatology. 1986 May-Jun;6(3):464-71. Pubmed: 3710434 Link_out
      2. Chiang EP, Selhub J, Bagley PJ, Dallal G, Roubenoff R: Pyridoxine supplementation corrects vitamin B6 deficiency but does not improve inflammation in patients with rheumatoid arthritis. Arthritis Res Ther. 2005;7(6):R1404-11. Epub 2005 Oct 14. Pubmed: 16277693 Link_out
      3. Manyam BV, Ferraro TN, Hare TA: Isoniazid-induced alteration of CSF neurotransmitter amino acids in Huntington's disease. Brain Res. 1987 Apr 7;408(1-2):125-30. Pubmed: 2885064 Link_out
      4. Temesvari P, Szilagyi I, Eck E, Boda D: Effects of an antenatal load of pyridoxine (vitamin B6) on the blood oxygen affinity and prolactin levels in newborn infants and their mothers. Acta Paediatr Scand. 1983 Jul;72(4):525-9. Pubmed: 6624427 Link_out
      5. McCully KS: Homocysteine, vitamins, and prevention of vascular disease. Mil Med. 2004 Apr;169(4):325-9. Pubmed: 15132238 Link_out
      6. Chen S, Ito M, Saijo T, Naito E, Kuroda Y: Molecular genetic analysis of pyridoxine-nonresponsive homocystinuric siblings with different blood methionine levels during the neonatal period. J Med Invest. 1999 Aug;46(3-4):186-91. Pubmed: 10687314 Link_out
      7. Wasilewska A, Narkiewicz M, Rutkowski B, Lysiak-Szydlowska W: Is there any relationship between lipids and vitamin B levels in persons with elevated risk of atherosclerosis? Med Sci Monit. 2003 Mar;9(3):CR147-51. Pubmed: 12640345 Link_out
      8. Kidd GS, Dimond R, Kark JA, Whorton N, Vigersky RA: The effects of pyridoxine on pituitary hormone secretion in amenorrhea-galactorrhea syndromes. J Clin Endocrinol Metab. 1982 Apr;54(4):872-5. Pubmed: 6801073 Link_out
      9. Plecko B, Stockler-Ipsiroglu S, Paschke E, Erwa W, Struys EA, Jakobs C: Pipecolic acid elevation in plasma and cerebrospinal fluid of two patients with pyridoxine-dependent epilepsy. Ann Neurol. 2000 Jul;48(1):121-5. Pubmed: 10894227 Link_out
      10. Pirulli D, Marangella M, Amoroso A: Primary hyperoxaluria: genotype-phenotype correlation. J Nephrol. 2003 Mar-Apr;16(2):297-309. Pubmed: 12768081 Link_out
      11. Amoroso A, Pirulli D, Florian F, Puzzer D, Boniotto M, Crovella S, Zezlina S, Spano A, Mazzola G, Savoldi S, Ferrettini C, Berutti S, Petrarulo M, Marangella M: AGXT gene mutations and their influence on clinical heterogeneity of type 1 primary hyperoxaluria. J Am Soc Nephrol. 2001 Oct;12(10):2072-9. Pubmed: 11562405 Link_out
      12. Tolis G, Laliberte R, Guyda H, Naftolin F: Ineffectiveness of pyridoxine (B6) to alter secretion of growth hormone and prolactin and absence of therapeutic effects on galactorrhea-amenorrhea syndromes. J Clin Endocrinol Metab. 1977 Jun;44(6):1197-9. Pubmed: 559690 Link_out
      13. Esteve-Romero J, Capella-Peiro ME, Monferrer-Pons L, Gil-Agusti M: Micellar liquid chromatography in clinical chemistry: application to the monitorization of B6 vitamins. Clin Chim Acta. 2004 Oct;348(1-2):69-77. Pubmed: 15369738 Link_out

      Enzymes
      Name: Methylenetetrahydrofolate reductase
      Reactions: Not Available
      Gene Name: MTHFR
      Uniprot ID: P42898 Link_out
      Protein Sequence: FASTA
      Gene Sequence: FASTA
      Name: Alpha-aminoadipic semialdehyde dehydrogenase
      Reactions: Not Available
      Gene Name: ALDH7A1
      Uniprot ID: P49419 Link_out
      Protein Sequence: FASTA
      Gene Sequence: FASTA
      Name: Pyridoxine-5'-phosphate oxidase
      Reactions:
      Pyridoxine + Oxygen unknown Pyridoxal + Hydrogen peroxide details
      Gene Name: PNPO
      Uniprot ID: Q9NVS9 Link_out
      Protein Sequence: FASTA
      Gene Sequence: FASTA
      Name: Cystathionine beta-synthase
      Reactions: Not Available
      Gene Name: CBS
      Uniprot ID: P35520 Link_out
      Protein Sequence: FASTA
      Gene Sequence: FASTA
      Name: Phosphoserine aminotransferase
      Reactions: Not Available
      Gene Name: PSAT1
      Uniprot ID: Q9Y617 Link_out
      Protein Sequence: FASTA
      Gene Sequence: FASTA
      Name: Pyridoxal kinase
      Reactions:
      Adenosine triphosphate + Pyridoxine unknown ADP + Pyridoxine 5'-phosphate details
      Gene Name: PDXK
      Uniprot ID: O00764 Link_out
      Protein Sequence: FASTA
      Gene Sequence: FASTA
      Name: Serum albumin
      Reactions: Not Available
      Gene Name: ALB
      Uniprot ID: P02768 Link_out
      Protein Sequence: FASTA
      Gene Sequence: FASTA
      Name: Pyridoxal phosphate phosphatase
      Reactions:
      Pyridoxine + Phosphoric acid unknown Pyridoxine 5'-phosphate + Water details
      Gene Name: PDXP
      Uniprot ID: Q96GD0 Link_out
      Protein Sequence: FASTA
      Gene Sequence: FASTA
      Name: Pyridoxal phosphate phosphatase PHOSPHO2
      Reactions:
      Pyridoxine + Phosphoric acid unknown Pyridoxine 5'-phosphate + Water details
      Gene Name: PHOSPHO2
      Uniprot ID: Q8TCD6 Link_out
      Protein Sequence: FASTA
      Gene Sequence: FASTA