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Showing metabocard for Pyridoxine 5'-phosphate (HMDB0001319)

IdentificationTaxonomyOntologyPhysical propertiesSpectraBiological propertiesConcentrationsLinksReferencesenzymes (4) Show 4 proteinsXML
enzymes (4) Show 4 proteins
Record Information
Version4.0
StatusDetected and Quantified
Creation Date2005-11-16 15:48:42 UTC
Update Date2019-01-11 19:15:50 UTC
HMDB IDHMDB0001319
Secondary Accession Numbers
  • HMDB01319
Metabolite Identification
Common NamePyridoxine 5'-phosphate
DescriptionPyridoxine 5'-phosphate is a substrate for Pyridoxine-5'-phosphate oxidase and Pyridoxal kinase.
Structure
Data?1547234150
MOLSDF3D-SDFPDBSMILESInChI View 3D Structure
Synonyms
ValueSource
Pyridoxine 5'-(dihydrogen phosphate)ChEBI
Pyridoxine 5-phosphateChEBI
Pyridoxine phosphateChEBI
PYRIDOXINE-5'-phosphATEChEBI
Pyridoxol 5'-phosphateChEBI
Pyridoxol 5-phosphateChEBI
Pyridoxyl-5-phosphateChEBI
Pyridoxine 5'-(dihydrogen phosphoric acid)Generator
Pyridoxine 5-phosphoric acidGenerator
Pyridoxine phosphoric acidGenerator
PYRIDOXINE-5'-phosphoric acidGenerator
Pyridoxol 5'-phosphoric acidGenerator
Pyridoxol 5-phosphoric acidGenerator
Pyridoxyl-5-phosphoric acidGenerator
Pyridoxine 5'-phosphoric acidGenerator
5-Hydroxy-4-(hydroxymethyl)-6-methyl-3-pyridylmethyl dihydrogen phosphateHMDB
5-Hydroxy-6-methyl-3,4-pyridinedimethanol alpha( 3)-(dihydrogen phosphate)HMDB
Pyridoxine-5PHMDB
Pyridoxine-pHMDB
Pyridoxine-phosphateHMDB
Pyridoxine 5-phosphate hydrochlorideHMDB
5-PhosphopyridoxineHMDB
Chemical FormulaC8H12NO6P
Average Molecular Weight249.1577
Monoisotopic Molecular Weight249.040223633
IUPAC Name{[5-hydroxy-4-(hydroxymethyl)-6-methylpyridin-3-yl]methoxy}phosphonic acid
Traditional Namepyridoxine-5'-phosphate
CAS Registry Number447-05-2
SMILES
CC1=NC=C(COP(O)(O)=O)C(CO)=C1O
InChI Identifier
InChI=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)
InChI KeyWHOMFKWHIQZTHY-UHFFFAOYSA-N
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
Ontology
Physiological effect

Health effect:

Disposition

Source:

Biological location:

Process

Naturally occurring process:

Role

Industrial application:

Physical Properties
StateSolid
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
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
Polarizability21.72 ųChemAxon
Number of Rings1ChemAxon
Bioavailability1ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Spectra
Spectrum TypeDescriptionSplash KeyView
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-0002-9530000000-1e967afad92165e82beeJSpectraViewer | MoNA
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (2 TMS) - 70eV, Positivesplash10-00di-9226000000-49f5293644ca681d401bJSpectraViewer | MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-0ue9-0590000000-68640055ed308d852fd0JSpectraViewer | MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-0f89-0900000000-1450b9f084acf6421d59JSpectraViewer | MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-001i-4900000000-8fd6492e6f2a6bea9879JSpectraViewer | MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0002-8090000000-65f73f2c7a460a3fca23JSpectraViewer | MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-004i-9010000000-5b0859a6a40a458fcc9fJSpectraViewer | MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-004i-9000000000-a6fead236e12d88986b8JSpectraViewer | MoNA
Biological Properties
Cellular Locations
  • Cytoplasm (predicted from logP)
Biospecimen Locations
  • Blood
Tissue LocationsNot Available
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodDetected and Quantified0.003 (0.0-0.01) uMAdult (>18 years old)FemaleObesity details
Associated Disorders and Diseases
Disease References
Obesity
  1. Driskell JA, Chrisley BM, Reynolds LK, Moak SW: Plasma B6 vitamer and plasma and urinary 4-pyridoxic acid concentrations of middle-aged obese black women. J Chromatogr. 1991 Aug 23;568(2):333-40. [PubMed:1783639 ]
Associated OMIM IDs
DrugBank IDDB02209
Phenol Explorer Compound IDNot Available
FoodDB IDFDB022552
KNApSAcK IDC00007505
Chemspider ID1026
KEGG Compound IDC00627
BioCyc IDNot Available
BiGG ID35527
Wikipedia LinkNot Available
METLIN ID6156
PubChem Compound1055
PDB IDNot Available
ChEBI ID28803
References
Synthesis ReferenceArgoudelis, Chris J. Preparation of crystalline pyridoxine 5'-phosphate and some of its properties. Journal of Agricultural and Food Chemistry (1986), 34(6), 995-8.
Material Safety Data Sheet (MSDS)Not Available
General ReferencesNot Available

Enzymes

Enzyme Details
1. Pyridoxine-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:
PNPO
Uniprot ID:
Q9NVS9
Molecular weight:
29987.79
Reactions
Pyridoxine 5'-phosphate + Oxygen → Pyridoxal 5'-phosphate + Hydrogen peroxidedetails
Enzyme Details
2. Pyridoxal kinase
General function:
Involved in pyridoxal kinase activity
Specific function:
Required for synthesis of pyridoxal-5-phosphate from vitamin B6.
Gene Name:
PDXK
Uniprot ID:
O00764
Molecular weight:
35102.105
Reactions
Adenosine triphosphate + Pyridoxine → ADP + Pyridoxine 5'-phosphatedetails
Enzyme Details
3. Pyridoxal phosphate phosphatase
General function:
Involved in catalytic activity
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. Pyridoxal phosphate phosphatase. Has some activity towards pyridoxal 5'-phosphate (PLP), pyridoxine 5'-phosphate (PMP) and pyridoxine 5'-phosphate (PNP), with a highest activity with PLP followed by PNP.
Gene Name:
PDXP
Uniprot ID:
Q96GD0
Molecular weight:
31697.735
Reactions
Pyridoxine + Phosphoric acid → Pyridoxine 5'-phosphate + Waterdetails
Enzyme Details
4. Pyridoxal phosphate phosphatase PHOSPHO2
General function:
Involved in phosphatase activity
Specific function:
Phosphatase that has high activity toward pyridoxal 5'-phosphate (PLP). Also active at much lower level toward pyrophosphate, phosphoethanolamine (PEA), phosphocholine (PCho), phospho-l-tyrosine, fructose-6-phosphate, p-nitrophenyl phosphate, and h-glycerophosphate.
Gene Name:
PHOSPHO2
Uniprot ID:
Q8TCD6
Molecular weight:
27768.72
Reactions
Pyridoxine + Phosphoric acid → Pyridoxine 5'-phosphate + Waterdetails