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Pyridoxamine 5'-phosphate (YMDB00397)

Identification
YMDB IDYMDB00397
NamePyridoxamine 5'-phosphate
SpeciesSaccharomyces cerevisiae
StrainBaker's yeast
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 yeast, pyridoxamine 5'-phosphate participates in a number of enzymatic reactions. In particular, pyridoxamine 5'-phosphate can be converted into pyridoxal 5'-phosphate and ammonium through its interaction with the enzyme pyridoxine 5'-phosphate oxidase. In addition, pyridoxamine 5'-phosphate can be biosynthesized from pyridoxamine; which is catalyzed by the enzyme pyridoxal kinase. In yeast, pyridoxamine 5'-phosphate is involved in the metabolic pathway called the vitamin B6 pathway.
Structure
Thumb
MOLSDFPDBSMILESInChI
Synonyms
  • Pyridoxamine 5'-phosphate
  • Pyridoxamine 5'-phosphic acid
  • 4'-Deoxy-4'-aminopyridoxal-5'-phosphate
  • Pyridoxamine 5'-(dihydrogen phosphate)
  • Pyridoxamine 5'-phosphoric acid
  • Pyridoxamine 5-phosphate
  • Pyridoxamine 5-phosphoric acid
  • Pyridoxamine phosphate
  • 4'-Deoxy-4'-aminopyridoxal-5'-phosphoric acid
  • Pyridoxamine 5'-(dihydrogen phosphoric acid)
  • Pyridoxamine phosphoric acid
  • Pyridoxamine-P
  • PMP
  • Pyridoxamine 5’-phosphate
  • 4’-Deoxy-4’-aminopyridoxal-5’-phosphate
  • 4’-Deoxy-4’-aminopyridoxal-5’-phosphoric acid
CAS number529-96-4
WeightAverage: 248.173
Monoisotopic: 248.056208048
InChI KeyZMJGSOSNSPKHNH-UHFFFAOYSA-N
InChIInChI=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)
IUPAC Name{[4-(aminomethyl)-5-hydroxy-6-methylpyridin-3-yl]methoxy}phosphonic acid
Traditional IUPAC Namepyridoxamine-5'-phosphate
Chemical FormulaC8H13N2O5P
SMILES[H]OC1=C(C(=C([H])N=C1C([H])([H])[H])C([H])([H])OP(=O)(O[H])O[H])C([H])([H])N([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
  • 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
Physical Properties
StateSolid
Charge0
Melting pointNot Available
Experimental Properties
PropertyValueReference
Water SolubilityNot AvailablePhysProp
LogPNot AvailablePhysProp
Predicted Properties
PropertyValueSource
Water Solubility6.61 g/LALOGPS
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
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
Pyridoxamine 5'-phosphate + oxygen + water → Pyridoxal 5'-phosphate + Hydrogen peroxide + Ammonium
KEGG Reactions
water + Pyridoxamine 5'-phosphate → phosphate + Pyridoxamine
water + Pyridoxamine 5'-phosphate + oxygen → Pyridoxal 5'-phosphate + Hydrogen peroxide + Ammonium
Adenosine triphosphate + Pyridoxamine → hydron + Pyridoxamine 5'-phosphate + ADP
Concentrations
Intracellular ConcentrationsNot Available
Extracellular ConcentrationsNot Available
Spectra
Spectra
Spectrum TypeDescriptionSplash KeyView
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-0002-9540000000-0747e0335474ec0d9563JSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (1 TMS) - 70eV, Positivesplash10-006t-9163000000-e2b4a252a1b0d401376fJSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, PositiveNot AvailableJSpectraViewer
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , negativesplash10-0002-0090000000-475764d1b4ff6c463f91JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , negativesplash10-001i-5390000000-825fef9f04e27485e868JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , negativesplash10-004i-9300000000-695db8e4ce16577ae441JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , negativesplash10-004i-9100000000-b6ae171abe36c54c4031JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , negativesplash10-004i-9000000000-a5aaa4d9b60dc24fd818JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , positivesplash10-0002-0190000000-0eb0fd727d4bb1b2816fJSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , positivesplash10-001i-0590000000-2003e26a12279fef54ddJSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , positivesplash10-001i-1910000000-acfc81bd682a779ef9e5JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , positivesplash10-053r-3900000000-262c33692f3c3bc194a2JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , positivesplash10-004i-9500000000-7d847cf14edccf6f5294JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-IT , positivesplash10-001i-0190000000-d1a5e6c1c22d70906b6cJSpectraViewer | MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-001j-0590000000-f2e78df6839a1a6c3c53JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-0f89-0900000000-45ff9c035fa30cea77bfJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-001i-2900000000-96d22fb2e9dd035fa2e5JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0002-9080000000-908c35d20c168506f92cJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-004i-9010000000-97480b70e97796d59101JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-004i-9000000000-c77bbc411daf4c046f20JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-001j-0290000000-8ef287b4599ae8a2912dJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-001i-0920000000-b0020ec751a9b36bcc17JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-001i-0900000000-7721d9affd7d73f7020fJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-002b-9010000000-569274c47ce9c516ff5eJSpectraViewer
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
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:Katsunishi, Masatoshi; Kondo, Osamu. Pyridoxamine-5'-phosphate. Jpn. Tokkyo Koho (1972), 2 pp.
External Links:
ResourceLink
CHEBI ID18335
HMDB IDHMDB01555
Pubchem Compound ID1053
Kegg IDC00647
ChemSpider ID1024
FOODB IDFDB021821
Wikipedia IDNot Available
BioCyc IDPYRIDOXAMINE-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).