Showing Compound Card for Pyridoxamine 5'-phosphate (CDB005282)

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IdentificationTaxonomyOntologyPhysical propertiesSpectraProtein targetPathwaysConcentrationsLinksReferencesenzymes (4) Show 6 proteinsXML
Record Information
Version1.0
Created at2020-04-17 19:27:34 UTC
Updated at2020-11-18 16:39:40 UTC
CannabisDB IDCDB005282
Secondary Accession NumbersNot Available
Cannabis Compound Identification
Common NamePyridoxamine 5'-phosphate
DescriptionPyridoxamine 5'-phosphate, also known as pyridoxamine phosphoric acid or pyridoxamine-p, belongs to the class of organic compounds known as pyridoxamine 5'-phosphates. These are heterocyclic aromatic compounds containing a pyridoxamine that carries a phosphate group at the 5'-position. Pyridoxamine 5'-phosphate is a very strong basic compound (based on its pKa). Pyridoxamine 5'-phosphate exists in all living species, ranging from bacteria to humans. Within humans, pyridoxamine 5'-phosphate participates in a number of enzymatic reactions. In particular, pyridoxamine 5'-phosphate can be biosynthesized from pyridoxamine through the action of the enzyme pyridoxal kinase. In addition, pyridoxamine 5'-phosphate can be converted into pyridoxal 5'-phosphate through its interaction with the enzyme pyridoxine-5'-phosphate oxidase. In humans, pyridoxamine 5'-phosphate is involved in vitamin B6 metabolism. Outside of the human body, Pyridoxamine 5'-phosphate is found, on average, in the highest concentration within milk (cow). Pyridoxamine 5'-phosphate has also been detected, but not quantified in, several different foods, such as lovages, small-leaf lindens, cocoa beans, american cranberries, and mango. This could make pyridoxamine 5'-phosphate a potential biomarker for the consumption of these foods. A vitamin B6 phosphate that is the phosphoric ester derivative of pyridoxamine. Pyridoxamine 5'-phosphate is expected to be in Cannabis as all living plants are known to produce and metabolize it.
Structure
Thumb
MOLSDFPDBSMILESInChI
Synonyms
ValueSource
4'-Deoxy-4'-aminopyridoxal-5'-phosphateChEBI
Pyridoxamine 5'-(dihydrogen phosphate)ChEBI
Pyridoxamine 5'-phosphoric acidChEBI
Pyridoxamine 5-phosphateChEBI
Pyridoxamine 5-phosphoric acidChEBI
Pyridoxamine phosphateChEBI
4'-Deoxy-4'-aminopyridoxal-5'-phosphoric acidGenerator
Pyridoxamine 5'-(dihydrogen phosphoric acid)Generator
Pyridoxamine phosphoric acidGenerator
Pyridoxamine-PMeSH, HMDB
PMPHMDB
Pyridoxamine 5'-phosphateHMDB
Pyridoxamine 5’-phosphateHMDB
4’-Deoxy-4’-aminopyridoxal-5’-phosphateHMDB
4’-Deoxy-4’-aminopyridoxal-5’-phosphoric acidHMDB
Chemical FormulaC8H13N2O5P
Average Molecular Weight248.17
Monoisotopic Molecular Weight248.0562
IUPAC Name{[4-(aminomethyl)-5-hydroxy-6-methylpyridin-3-yl]methoxy}phosphonic acid
Traditional Namepyridoxamine-5'-phosphate
CAS Registry Number529-96-4
SMILES
CC1=NC=C(COP(O)(O)=O)C(CN)=C1O
InChI Identifier
InChI=1S/C8H13N2O5P/c1-5-8(11)7(2-9)6(3-10-5)4-15-16(12,13)14/h3,11H,2,4,9H2,1H3,(H2,12,13,14)
InChI KeyZMJGSOSNSPKHNH-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as pyridoxamine 5'-phosphates. These are heterocyclic aromatic compounds containing a pyridoxamine that carries a phosphate group at the 5'-position.
KingdomOrganic compounds
Super ClassOrganoheterocyclic compounds
ClassPyridines and derivatives
Sub ClassPyridoxamines
Direct ParentPyridoxamine 5'-phosphates
Alternative Parents
Substituents
  • Pyridoxamine 5'-phosphate
  • Monoalkyl phosphate
  • Aralkylamine
  • Hydroxypyridine
  • Methylpyridine
  • Organic phosphoric acid derivative
  • Alkyl phosphate
  • Phosphoric acid ester
  • Heteroaromatic compound
  • Azacycle
  • Primary aliphatic amine
  • Hydrocarbon derivative
  • Amine
  • Primary amine
  • Organooxygen compound
  • Organonitrogen compound
  • Organic nitrogen compound
  • Organic oxide
  • Organopnictogen compound
  • Organic oxygen compound
  • Aromatic heteromonocyclic compound
Molecular FrameworkAromatic heteromonocyclic compounds
External Descriptors
Ontology
Disposition

Route of exposure:

Source:

Biological location:

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
logP-0.99ALOGPS
logP-2.2ChemAxon
logS-1.6ALOGPS
pKa (Strongest Acidic)1.74ChemAxon
pKa (Strongest Basic)9.91ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count6ChemAxon
Hydrogen Donor Count4ChemAxon
Polar Surface Area125.9 ŲChemAxon
Rotatable Bond Count4ChemAxon
Refractivity56.64 m³·mol⁻¹ChemAxon
Polarizability22.15 ųChemAxon
Number of Rings1ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Spectra
EI-MS/GC-MS
TypeDescriptionSplash KeyView
Predicted GC-MSPyridoxamine 5'-phosphate, non-derivatized, Predicted GC-MS Spectrum - 70eV, Positivesplash10-0002-9540000000-0747e0335474ec0d9563Spectrum
Predicted GC-MSPyridoxamine 5'-phosphate, 1 TMS, Predicted GC-MS Spectrum - 70eV, Positivesplash10-006t-9163000000-e2b4a252a1b0d401376fSpectrum
Predicted GC-MSPyridoxamine 5'-phosphate, non-derivatized, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
MS/MS
TypeDescriptionSplash KeyView
MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , negativesplash10-0002-0090000000-475764d1b4ff6c463f912017-09-14View Spectrum
MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , negativesplash10-001i-5390000000-825fef9f04e27485e8682017-09-14View Spectrum
MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , negativesplash10-004i-9300000000-695db8e4ce16577ae4412017-09-14View Spectrum
MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , negativesplash10-004i-9100000000-b6ae171abe36c54c40312017-09-14View Spectrum
MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , negativesplash10-004i-9000000000-a5aaa4d9b60dc24fd8182017-09-14View Spectrum
MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , positivesplash10-0002-0190000000-0eb0fd727d4bb1b2816f2017-09-14View Spectrum
MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , positivesplash10-001i-0590000000-2003e26a12279fef54dd2017-09-14View Spectrum
MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , positivesplash10-001i-1910000000-acfc81bd682a779ef9e52017-09-14View Spectrum
MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , positivesplash10-053r-3900000000-262c33692f3c3bc194a22017-09-14View Spectrum
MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , positivesplash10-004i-9500000000-7d847cf14edccf6f52942017-09-14View Spectrum
MS/MSLC-MS/MS Spectrum - LC-ESI-IT , positivesplash10-001i-0190000000-d1a5e6c1c22d70906b6c2017-09-14View Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-001j-0590000000-f2e78df6839a1a6c3c532015-09-15View Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-0f89-0900000000-45ff9c035fa30cea77bf2015-09-15View Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-001i-2900000000-96d22fb2e9dd035fa2e52015-09-15View Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0002-9080000000-908c35d20c168506f92c2015-09-15View Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-004i-9010000000-97480b70e97796d591012015-09-15View Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-004i-9000000000-c77bbc411daf4c046f202015-09-15View Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-001j-0290000000-8ef287b4599ae8a2912d2021-09-24View Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-001i-0920000000-b0020ec751a9b36bcc172021-09-24View Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-001i-0900000000-7721d9affd7d73f7020f2021-09-24View Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-002b-9010000000-569274c47ce9c516ff5e2021-09-24View Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-004i-9000000000-ef724d5177083af378f02021-09-24View Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-004i-9000000000-a5e502a2627af2048a1f2021-09-24View Spectrum
NMRNot Available
Pathways
Pathways
Protein Targets
Enzymes
Protein NameGene NameLocusUniprot IDDetails
Pyridoxine-5'-phosphate oxidasePNPO17q21.32Q9NVS9 details
Pyridoxal kinasePDXK21q22.3O00764 details
Pyridoxal phosphate phosphatasePDXP22q12.3Q96GD0 details
Pyridoxal phosphate phosphatase PHOSPHO2PHOSPHO22q31.1Q8TCD6 details
TransportersNot Available
Metal Bindings
Protein NameGene NameLocusUniprot IDDetails
Pyridoxal phosphate phosphatasePDXP22q12.3Q96GD0 details
Pyridoxal phosphate phosphatase PHOSPHO2PHOSPHO22q31.1Q8TCD6 details
ReceptorsNot Available
Transcriptional FactorsNot Available
Concentrations Data
Not Available
HMDB IDHMDB0001555
DrugBank IDDB02142
Phenol Explorer Compound IDNot Available
FoodDB IDFDB021821
KNApSAcK IDC00007506
Chemspider ID1024
KEGG Compound IDC00647
BioCyc IDPYRIDOXAMINE-5P
BiGG ID35609
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound1053
PDB IDNot Available
ChEBI ID18335
References
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
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
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
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