Pyridoxine 5'-phosphate (YMDB00407)

Identification
YMDB IDYMDB00407
NamePyridoxine 5'-phosphate
SpeciesSaccharomyces cerevisiae
StrainBaker's yeast
DescriptionPyridoxine 5'-phosphate, also known as pyridoxine-5P or pyridoxine phosphoric acid, belongs to the class of organic compounds known as pyridoxine-5'-phosphates. These are pyridoxines that carry a phosphate group at the 5-position. Pyridoxine 5'-phosphate is a very strong basic compound (based on its pKa). Pyridoxine 5'-phosphate exists in all living species, ranging from bacteria to humans. Within yeast, pyridoxine 5'-phosphate participates in a number of enzymatic reactions. In particular, pyridoxine 5'-phosphate can be biosynthesized from 1-deoxy-D-xylulose 5-phosphate and 2-amino-3-phosphonopropionic acid; which is catalyzed by the enzyme pyridoxine 5'-phosphate synthase. In addition, pyridoxine 5'-phosphate can be biosynthesized from pyridoxine; which is mediated by the enzyme pyridoxal kinase. In yeast, pyridoxine 5'-phosphate is involved in the metabolic pathway called the vitamin B6 pathway.
Structure
Thumb
MOLSDFPDBSMILESInChI
Synonyms
  • 5-Hydroxy-4-(hydroxymethyl)-6-methyl-3-pyridylmethyl dihydrogen phosphate
  • 5-hydroxy-6-methyl-3,4-Pyridinedimethanol alpha( 3)-(dihydrogen phosphate)
  • Pyridoxine 5-phosphate
  • Pyridoxine 5'-phosphate
  • Pyridoxine 5'-phosphic acid
  • Pyridoxine-5'-phosphate
  • pyridoxine-5P
  • pyridoxine-P
  • pyridoxine-phosphate
  • Pyridoxol 5-phosphate
  • Pyridoxyl-5-phosphate
  • Pyridoxine 5'-(dihydrogen phosphate)
  • Pyridoxine phosphate
  • Pyridoxol 5'-phosphate
  • Pyridoxine 5'-(dihydrogen phosphoric acid)
  • Pyridoxine 5-phosphoric acid
  • Pyridoxine phosphoric acid
  • PYRIDOXINE-5'-phosphoric acid
  • Pyridoxol 5'-phosphoric acid
  • Pyridoxol 5-phosphoric acid
  • Pyridoxyl-5-phosphoric acid
  • Pyridoxine 5'-phosphoric acid
  • Pyridoxine 5-phosphate hydrochloride
  • 5-Phosphopyridoxine
CAS number447-05-2
WeightAverage: 249.1577
Monoisotopic: 249.040223633
InChI KeyWHOMFKWHIQZTHY-UHFFFAOYSA-N
InChIInChI=1S/C8H12NO6P/c1-5-8(11)7(3-10)6(2-9-5)4-15-16(12,13)14/h2,10-11H,3-4H2,1H3,(H2,12,13,14)
IUPAC Name{[5-hydroxy-4-(hydroxymethyl)-6-methylpyridin-3-yl]methoxy}phosphonic acid
Traditional IUPAC Namepyridoxine-5'-phosphate
Chemical FormulaC8H12NO6P
SMILES[H]OC1=C(C(=C([H])N=C1C([H])([H])[H])C([H])([H])OP(=O)(O[H])O[H])C([H])([H])O[H]
Chemical Taxonomy
Description belongs to the class of organic compounds known as pyridoxine-5'-phosphates. These are pyridoxines that carry a phosphate group at the 5-position.
KingdomOrganic compounds
Super ClassOrganoheterocyclic compounds
ClassPyridines and derivatives
Sub ClassPyridoxines
Direct ParentPyridoxine-5'-phosphates
Alternative Parents
Substituents
  • Pyridoxine-5'-phosphate
  • Monoalkyl phosphate
  • Hydroxypyridine
  • Methylpyridine
  • Organic phosphoric acid derivative
  • Alkyl phosphate
  • Phosphoric acid ester
  • Heteroaromatic compound
  • Azacycle
  • Hydrocarbon derivative
  • Alcohol
  • Aromatic alcohol
  • Organic nitrogen compound
  • Primary alcohol
  • Organooxygen compound
  • Organonitrogen compound
  • Organic oxide
  • Organopnictogen compound
  • Organic oxygen compound
  • Aromatic heteromonocyclic compound
Molecular FrameworkAromatic heteromonocyclic compounds
External Descriptors
Physical Properties
StateSolid
Charge0
Melting pointNot Available
Experimental Properties
PropertyValueReference
Water SolubilityNot AvailablePhysProp
LogPNot AvailablePhysProp
Predicted Properties
PropertyValueSource
Water Solubility9.41 g/LALOGPS
logP-0.8ALOGPS
logP-3.6ChemAxon
logS-1.4ALOGPS
pKa (Strongest Acidic)1.74ChemAxon
pKa (Strongest Basic)5.55ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count6ChemAxon
Hydrogen Donor Count4ChemAxon
Polar Surface Area120.11 ŲChemAxon
Rotatable Bond Count4ChemAxon
Refractivity54.98 m³·mol⁻¹ChemAxon
Polarizability21.73 ųChemAxon
Number of Rings1ChemAxon
Bioavailability1ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations
  • cytoplasm
Organoleptic PropertiesNot Available
SMPDB Pathways
Vitamin B6PW002488 ThumbThumb?image type=greyscaleThumb?image type=simple
KEGG Pathways
Vitamin B6 metabolismec00750 Map00750
SMPDB Reactions
1-Deoxy-D-xylulose 5-phosphate + 2-Amino-3-phosphonopropionic acid → Pyridoxine 5'-phosphate + phosphate + hydron + water
Pyridoxine + Adenosine triphosphate → Pyridoxine 5'-phosphate + ADP + hydron
Pyridoxine 5'-phosphate + oxygen → Pyridoxal 5'-phosphate + Hydrogen peroxide
KEGG Reactions
Pyridoxine 5'-phosphate + oxygen ↔ Pyridoxal 5'-phosphate + Hydrogen peroxide
Pyridoxine + Adenosine triphosphate → Pyridoxine 5'-phosphate + hydron + ADP
Concentrations
Intracellular ConcentrationsNot Available
Extracellular ConcentrationsNot Available
Spectra
Spectra
Spectrum TypeDescriptionSplash KeyView
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-0002-9530000000-1e967afad92165e82beeJSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (2 TMS) - 70eV, Positivesplash10-00di-9226000000-49f5293644ca681d401bJSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, PositiveNot AvailableJSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, PositiveNot AvailableJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-0ue9-0590000000-68640055ed308d852fd0JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-0f89-0900000000-1450b9f084acf6421d59JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-001i-4900000000-8fd6492e6f2a6bea9879JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0002-8090000000-65f73f2c7a460a3fca23JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-004i-9010000000-5b0859a6a40a458fcc9fJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-004i-9000000000-a6fead236e12d88986b8JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-0udi-0290000000-da88c1789911b79c0362JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-0ff0-0910000000-366dc9237952c888f4b8JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-001i-2900000000-cd37cb30cd544c5f866aJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-002b-9010000000-64a9d47104102ec4486fJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-004i-9000000000-ef724d5177083af378f0JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-004i-9000000000-a5e502a2627af2048a1fJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C 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
Synthesis Reference:Argoudelis, Chris J. Preparation of crystalline pyridoxine 5'-phosphate and some of its properties. Journal of Agricultural and Food Chemistry (1986), 34(6), 995-8.
External Links:
ResourceLink
CHEBI ID28803
HMDB IDHMDB01319
Pubchem Compound ID1055
Kegg IDC00627
ChemSpider ID1026
FOODB IDFDB031140
Wikipedia IDNot Available
BioCyc IDPYRIDOXINE-5P

Enzymes

Protein Details
1. 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).