Pyridoxamine (YMDB00889)

Identification
YMDB IDYMDB00889
NamePyridoxamine
SpeciesSaccharomyces cerevisiae
StrainBaker's yeast
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. pyridoxamine can be converted into pyridoxamine 5'-phosphate; which is catalyzed by the enzyme pyridoxal kinase. In yeast, pyridoxamine is involved in the metabolic pathway called the vitamin B6 pathway.
Structure
Thumb
MOLSDFPDBSMILESInChI
Synonyms
  • 2-methyl-4-aminomethyl-5-hydroxymethyl-3-Pyridinol
  • 4-(Aminomethyl)-5-(hydroxymethyl)-2-methyl-3-pyridinol
  • 4-(aminomethyl)-5-hydroxy-6-methyl-3-Pyridinemethanol
  • PM
  • Pyridoxylamine
  • 4-(AMINOMETHYL)-5-(hydroxymethyl)-2-methylpyridin-3-ol
CAS number85-87-0
WeightAverage: 168.1931
Monoisotopic: 168.089877638
InChI KeyNHZMQXZHNVQTQA-UHFFFAOYSA-N
InChIInChI=1S/C8H12N2O2/c1-5-8(12)7(2-9)6(4-11)3-10-5/h3,11-12H,2,4,9H2,1H3
IUPAC Name4-(aminomethyl)-5-(hydroxymethyl)-2-methylpyridin-3-ol
Traditional IUPAC Namepyridoxamine
Chemical FormulaC8H12N2O2
SMILES[H]OC1=C(N=C([H])C(=C1C([H])([H])N([H])[H])C([H])([H])O[H])C([H])([H])[H]
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
Physical Properties
StateSolid
Charge0
Melting pointNot Available
Experimental Properties
PropertyValueReference
Water Solubility815 mg/mL [HMP experimental]PhysProp
LogPNot AvailablePhysProp
Predicted Properties
PropertyValueSource
Water Solubility29 g/LALOGPS
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
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
Pyridoxamine + Adenosine triphosphate → Pyridoxamine 5'-phosphate + ADP
KEGG Reactions
water + Pyridoxamine 5'-phosphate → phosphate + Pyridoxamine
water + oxygen + Ammonium + Pyridoxal ↔ Hydrogen peroxide + Pyridoxamine
Adenosine triphosphate + Pyridoxamine → hydron + Pyridoxamine 5'-phosphate + ADP
Concentrations
Intracellular ConcentrationsNot Available
Extracellular ConcentrationsNot Available
Spectra
Spectra
Spectrum TypeDescriptionSplash KeyView
GC-MSGC-MS Spectrum - GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies) (Non-derivatized)splash10-001j-0590000000-a4bf9fe291241c903e3dJSpectraViewer | MoNA
GC-MSGC-MS Spectrum - GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies) (3 TMS)splash10-00di-9350000000-3b1415672e7ab22d5e64JSpectraViewer | MoNA
GC-MSGC-MS Spectrum - GC-MS (3 TMS)splash10-001i-1490000000-7214a8743cbe260268ceJSpectraViewer | MoNA
GC-MSGC-MS Spectrum - GC-EI-TOF (Non-derivatized)splash10-001j-0590000000-a4bf9fe291241c903e3dJSpectraViewer | MoNA
GC-MSGC-MS Spectrum - GC-EI-TOF (Non-derivatized)splash10-00di-9350000000-3b1415672e7ab22d5e64JSpectraViewer | MoNA
GC-MSGC-MS Spectrum - GC-MS (Non-derivatized)splash10-001i-1490000000-7214a8743cbe260268ceJSpectraViewer | MoNA
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-0f79-2900000000-1dfbec04a6ae497e3229JSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (2 TMS) - 70eV, Positivesplash10-00dj-6090000000-1aab191c7ca62559a838JSpectraViewer
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
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 10V, Positive (Annotated)splash10-014i-0900000000-4ca97fcd886d80336a5cJSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 25V, Positive (Annotated)splash10-001i-1900000000-499c48bce709456248bcJSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 40V, Positive (Annotated)splash10-0059-9200000000-aee74b4498be7c8cea6fJSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 10V, Negativesplash10-014i-0900000000-f1da14360063a04c11b4JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 20V, Negativesplash10-014r-0900000000-f5aea0fa928eb266a79dJSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 30V, Negativesplash10-00di-0900000000-bebad702dbdba57d61faJSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 40V, Negativesplash10-05fr-0900000000-7322846ca1b4d95b5b16JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 50V, Negativesplash10-0ab9-2900000000-da43b1a049d349d91831JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF (UPLC Q-Tof Premier, Waters) , Positivesplash10-014i-0900000000-6b5f1d606df91ae52eb4JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF (UPLC Q-Tof Premier, Waters) 30V, Positivesplash10-0gb9-0900000000-d5a16a4cdc19453ae9c7JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF (UPLC Q-Tof Premier, Waters) , Negativesplash10-01b9-0900000000-3a1f853ce36bb047e05fJSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , negativesplash10-014i-0900000000-f1da14360063a04c11b4JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , negativesplash10-014r-0900000000-f5aea0fa928eb266a79dJSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , negativesplash10-00di-0900000000-c7a2dec0f7555dcc5ef7JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , negativesplash10-05fr-0900000000-fe3f1f78fad714162a1cJSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , negativesplash10-0ab9-2900000000-da43b1a049d349d91831JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF , negativesplash10-01b9-0900000000-f0cc74a9651686c1610cJSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - , negativesplash10-014i-0900000000-9303a95b8f51c5ce6c22JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF , positivesplash10-014i-0900000000-6b5f1d606df91ae52eb4JSpectraViewer | MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-0uxr-0900000000-a1db882596b08c2987a7JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-0ue9-0900000000-b0f20e8503b963c8a31fJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-001i-3900000000-b41efa32a572817ef0c9JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-014i-0900000000-cd842fcc776d552a0f07JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-052r-0900000000-ae76358c88e1a1cf17dcJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-0596-9600000000-eeec53c65ada2bc944b0JSpectraViewer
1D NMR1H 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
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
2D NMR[1H,1H] 2D NMR SpectrumNot AvailableJSpectraViewer
2D NMR[1H,13C] 2D NMR SpectrumNot AvailableJSpectraViewer
References
References:
  • 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
  • Zeidler, J., Gupta, R. N., Sayer, B. G., Spenser, I. D. (2003). "Biosynthesis of Vitamin B(6) in yeast. Incorporation pattern of trioses." J Org Chem 68:3486-3493.12713350
Synthesis Reference:Not Available
External Links:
ResourceLink
CHEBI ID16410
HMDB IDHMDB01431
Pubchem Compound ID1052
Kegg IDC00534
ChemSpider ID1023
FOODB IDFDB021819
WikipediaPiridoxamine
BioCyc IDPYRIDOXAMINE

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).