Showing Compound Card for Pyridoxamine (CDB004915)

Jump To Section:
IdentificationTaxonomyOntologyPhysical propertiesSpectraProtein targetPathwaysConcentrationsLinksReferencesenzymes (4) Show 6 proteinsXML
Record Information
Version1.0
Created at2020-04-17 18:50:04 UTC
Updated at2020-11-18 16:38:59 UTC
CannabisDB IDCDB004915
Secondary Accession NumbersNot Available
Cannabis Compound Identification
Common NamePyridoxamine
DescriptionPyridoxamine, also known as PM, 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 is a very strong basic compound (based on its pKa). Pyridoxamine exists in all living species, ranging from bacteria to humans. Within humans, pyridoxamine participates in a number of enzymatic reactions. In particular, pyridoxamine can be converted into pyridoxal through its interaction with the enzyme pyridoxine-5'-phosphate oxidase. In addition, pyridoxamine can be converted into pyridoxamine 5'-phosphate; which is catalyzed by the enzyme pyridoxal kinase. In humans, pyridoxamine is involved in vitamin B6 metabolism. Outside of the human body, Pyridoxamine is found, on average, in the highest concentration within milk (cow). Pyridoxamine has also been detected, but not quantified in, several different foods, such as rocket salad, rose hips, globe artichokes, groundcherries, and wild leeks. This could make pyridoxamine a potential biomarker for the consumption of these foods. A monohydroxypyridine that is pyridine substituted by a hydroxy group at position 3, an aminomethyl group at position 4, a hydroxymethyl group at position 5 and a methyl group at position 2. Pyridoxamine is expected to be in Cannabis as all living plants are known to produce and metabolize it.
Structure
Thumb
MOLSDFPDBSMILESInChI
Synonyms
ValueSource
4-(AMINOMETHYL)-5-(hydroxymethyl)-2-methylpyridin-3-olChEBI
PMChEBI
2-Methyl-4-aminomethyl-5-hydroxymethyl-3-pyridinolHMDB
4-(Aminomethyl)-5-(hydroxymethyl)-2-methyl-3-pyridinolHMDB
4-(Aminomethyl)-5-hydroxy-6-methyl-3-pyridinemethanolHMDB
PyridoxylamineHMDB
Chemical FormulaC8H12N2O2
Average Molecular Weight168.19
Monoisotopic Molecular Weight168.0899
IUPAC Name4-(aminomethyl)-5-(hydroxymethyl)-2-methylpyridin-3-ol
Traditional Namepyridoxamine
CAS Registry Number85-87-0
SMILES
CC1=C(O)C(CN)=C(CO)C=N1
InChI Identifier
InChI=1S/C8H12N2O2/c1-5-8(12)7(2-9)6(4-11)3-10-5/h3,11-12H,2,4,9H2,1H3
InChI KeyNHZMQXZHNVQTQA-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
  • Aralkylamine
  • Hydroxypyridine
  • Methylpyridine
  • Heteroaromatic compound
  • Azacycle
  • Amine
  • Hydrocarbon derivative
  • Alcohol
  • Aromatic alcohol
  • Primary amine
  • Primary alcohol
  • Organooxygen compound
  • Organonitrogen compound
  • Primary aliphatic amine
  • Organic nitrogen compound
  • 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 Solubility815 mg/mLNot Available
logPNot AvailableNot Available
Predicted Properties
PropertyValueSource
logP-1.2ALOGPS
logP-1.6ChemAxon
logS-0.76ALOGPS
pKa (Strongest Acidic)7.81ChemAxon
pKa (Strongest Basic)9.61ChemAxon
Physiological Charge1ChemAxon
Hydrogen Acceptor Count4ChemAxon
Hydrogen Donor Count3ChemAxon
Polar Surface Area79.37 ŲChemAxon
Rotatable Bond Count2ChemAxon
Refractivity45.76 m³·mol⁻¹ChemAxon
Polarizability17.52 ųChemAxon
Number of Rings1ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Spectra
EI-MS/GC-MS
TypeDescriptionSplash KeyView
GC-MSPyridoxamine, non-derivatized, GC-MS Spectrumsplash10-001j-0590000000-a4bf9fe291241c903e3dSpectrum
GC-MSPyridoxamine, 3 TMS, GC-MS Spectrumsplash10-00di-9350000000-3b1415672e7ab22d5e64Spectrum
GC-MSPyridoxamine, 3 TMS, GC-MS Spectrumsplash10-001i-1490000000-7214a8743cbe260268ceSpectrum
GC-MSPyridoxamine, non-derivatized, GC-MS Spectrumsplash10-001j-0590000000-a4bf9fe291241c903e3dSpectrum
GC-MSPyridoxamine, non-derivatized, GC-MS Spectrumsplash10-00di-9350000000-3b1415672e7ab22d5e64Spectrum
GC-MSPyridoxamine, non-derivatized, GC-MS Spectrumsplash10-001i-1490000000-7214a8743cbe260268ceSpectrum
Predicted GC-MSPyridoxamine, non-derivatized, Predicted GC-MS Spectrum - 70eV, Positivesplash10-0f79-2900000000-1dfbec04a6ae497e3229Spectrum
Predicted GC-MSPyridoxamine, 2 TMS, Predicted GC-MS Spectrum - 70eV, Positivesplash10-00dj-6090000000-1aab191c7ca62559a838Spectrum
Predicted GC-MSPyridoxamine, non-derivatized, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSPyridoxamine, non-derivatized, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
MS/MS
TypeDescriptionSplash KeyView
MS/MSLC-MS/MS Spectrum - Quattro_QQQ 10V, Positive (Annotated)splash10-014i-0900000000-4ca97fcd886d80336a5c2012-07-24View Spectrum
MS/MSLC-MS/MS Spectrum - Quattro_QQQ 25V, Positive (Annotated)splash10-001i-1900000000-499c48bce709456248bc2012-07-24View Spectrum
MS/MSLC-MS/MS Spectrum - Quattro_QQQ 40V, Positive (Annotated)splash10-0059-9200000000-aee74b4498be7c8cea6f2012-07-24View Spectrum
MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 10V, Negativesplash10-014i-0900000000-f1da14360063a04c11b42012-08-31View Spectrum
MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 20V, Negativesplash10-014r-0900000000-f5aea0fa928eb266a79d2012-08-31View Spectrum
MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 30V, Negativesplash10-00di-0900000000-bebad702dbdba57d61fa2012-08-31View Spectrum
MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 40V, Negativesplash10-05fr-0900000000-7322846ca1b4d95b5b162012-08-31View Spectrum
MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 50V, Negativesplash10-0ab9-2900000000-da43b1a049d349d918312012-08-31View Spectrum
MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF (UPLC Q-Tof Premier, Waters) , Positivesplash10-014i-0900000000-6b5f1d606df91ae52eb42012-08-31View Spectrum
MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF (UPLC Q-Tof Premier, Waters) 30V, Positivesplash10-0gb9-0900000000-d5a16a4cdc19453ae9c72012-08-31View Spectrum
MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF (UPLC Q-Tof Premier, Waters) , Negativesplash10-01b9-0900000000-3a1f853ce36bb047e05f2012-08-31View Spectrum
MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , negativesplash10-014i-0900000000-f1da14360063a04c11b42017-09-14View Spectrum
MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , negativesplash10-014r-0900000000-f5aea0fa928eb266a79d2017-09-14View Spectrum
MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , negativesplash10-00di-0900000000-c7a2dec0f7555dcc5ef72017-09-14View Spectrum
MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , negativesplash10-05fr-0900000000-fe3f1f78fad714162a1c2017-09-14View Spectrum
MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , negativesplash10-0ab9-2900000000-da43b1a049d349d918312017-09-14View Spectrum
MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF , negativesplash10-01b9-0900000000-f0cc74a9651686c1610c2017-09-14View Spectrum
MS/MSLC-MS/MS Spectrum - , negativesplash10-014i-0900000000-9303a95b8f51c5ce6c222017-09-14View Spectrum
MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF , positivesplash10-014i-0900000000-6b5f1d606df91ae52eb42017-09-14View Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-0uxr-0900000000-a1db882596b08c2987a72015-05-26View Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-0ue9-0900000000-b0f20e8503b963c8a31f2015-05-26View Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-001i-3900000000-b41efa32a572817ef0c92015-05-26View Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-014i-0900000000-cd842fcc776d552a0f072015-05-27View Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-052r-0900000000-ae76358c88e1a1cf17dc2015-05-27View Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-0596-9600000000-eeec53c65ada2bc944b02015-05-27View Spectrum
NMR
TypeDescriptionView
1D NMR1H NMR Spectrum (1D, 500 MHz, H2O, experimental)Spectrum
1D NMR1H NMR Spectrum (1D, D2O, experimental)Spectrum
1D NMR13C NMR Spectrum (1D, D2O, experimental)Spectrum
1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)Spectrum
1D NMR13C NMR Spectrum (1D, 100 MHz, D2O, predicted)Spectrum
1D NMR1H NMR Spectrum (1D, 1000 MHz, D2O, predicted)Spectrum
1D NMR13C NMR Spectrum (1D, 1000 MHz, D2O, predicted)Spectrum
1D NMR1H NMR Spectrum (1D, 200 MHz, D2O, predicted)Spectrum
1D NMR13C NMR Spectrum (1D, 200 MHz, D2O, predicted)Spectrum
1D NMR1H NMR Spectrum (1D, 300 MHz, D2O, predicted)Spectrum
1D NMR13C NMR Spectrum (1D, 300 MHz, D2O, predicted)Spectrum
1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, predicted)Spectrum
1D NMR13C NMR Spectrum (1D, 400 MHz, D2O, predicted)Spectrum
1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, predicted)Spectrum
1D NMR13C NMR Spectrum (1D, 500 MHz, D2O, predicted)Spectrum
1D NMR1H NMR Spectrum (1D, 600 MHz, D2O, predicted)Spectrum
1D NMR13C NMR Spectrum (1D, 600 MHz, D2O, predicted)Spectrum
1D NMR1H NMR Spectrum (1D, 700 MHz, D2O, predicted)Spectrum
1D NMR13C NMR Spectrum (1D, 700 MHz, D2O, predicted)Spectrum
1D NMR1H NMR Spectrum (1D, 800 MHz, D2O, predicted)Spectrum
1D NMR13C NMR Spectrum (1D, 800 MHz, D2O, predicted)Spectrum
1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)Spectrum
1D NMR13C NMR Spectrum (1D, 900 MHz, D2O, predicted)Spectrum
2D NMR[1H, 1H]-TOCSY. Unexported temporarily by An Chi on Oct 15, 2021 until json or nmrML file is generated. 2D NMR Spectrum (experimental)Spectrum
2D NMR[1H, 13C]-HSQC NMR Spectrum (2D, 600 MHz, H2O, experimental)Spectrum
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 IDHMDB0001431
DrugBank IDDB11673
Phenol Explorer Compound IDNot Available
FoodDB IDFDB021819
KNApSAcK IDC00007504
Chemspider ID1023
KEGG Compound IDC00534
BioCyc IDPYRIDOXAMINE
BiGG ID35277
Wikipedia LinkPyridoxamine
METLIN ID238
PubChem Compound1052
PDB IDNot Available
ChEBI ID16410
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