Pyridoxamine (PAMDB000384)

IdentificationTaxonomyPhysical PropertiesBiological PropertiesSpectraConcentrationsLinksReferencesEnzymes Transporters
Proteins (3280)
Record Information
Version 1.0
Update Date 1/22/2018 12:54:54 PM
Metabolite IDPAMDB000384
Identification
Name: Pyridoxamine
Description:Pyridoxamine is the 4-aminomethyl form of vitamin B6. During transamination of amino acids, pyridoxal phosphate is transiently converted into pyridoxamine phosphate. -- Pubchem; Pyridoxamine is one of the compounds that can be called vitamin B6, along with Pyridoxal and Pyridoxine. -- Wikipedia
Structure
Thumb
🔍MOLSDFPDBSMILESInChIView Structure
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
Chemical Formula: C8H12N2O2
Average Molecular Weight: 168.1931
Monoisotopic Molecular Weight: 168.089877638
InChI Key: NHZMQXZHNVQTQA-UHFFFAOYSA-N
InChI:InChI=1S/C8H12N2O2/c1-5-8(12)7(2-9)6(4-11)3-10-5/h3,11-12H,2,4,9H2,1H3
CAS number: 85-87-0
IUPAC Name:4-(aminomethyl)-5-(hydroxymethyl)-2-methylpyridin-3-ol
Traditional IUPAC Name: pyridoxamine
SMILES:CC1=C(O)C(CN)=C(CO)C=N1
Chemical Taxonomy
Taxonomy DescriptionThis compound belongs to the class of organic compounds known as pyridoxamines. These are pyridoxal derivatives in which the pyridoxal moiety is substituted at position 2 by an amine.
Kingdom Organic compounds
Super ClassOrganoheterocyclic compounds
Class Pyridines and derivatives
Sub ClassPyridoxamines
Direct Parent Pyridoxamines
Alternative Parents
Substituents
  • Pyridoxamine
  • Methylpyridine
  • Hydroxypyridine
  • Aralkylamine
  • Heteroaromatic compound
  • Azacycle
  • Hydrocarbon derivative
  • Aromatic alcohol
  • Primary amine
  • Primary alcohol
  • Organooxygen compound
  • Organonitrogen compound
  • Primary aliphatic amine
  • Amine
  • Alcohol
  • Aromatic heteromonocyclic compound
Molecular Framework Aromatic heteromonocyclic compounds
External Descriptors
Physical Properties
State: Solid
Charge:1
Melting point: Not Available
Experimental Properties:
PropertyValueSource
Water Solubility:815 mg/mL [HMP experimental]PhysProp
Predicted Properties
PropertyValueSource
Water Solubility29.0 mg/mLALOGPS
logP-1.2ALOGPS
logP-1.6ChemAxon
logS-0.76ALOGPS
pKa (Strongest Acidic)7.82ChemAxon
pKa (Strongest Basic)9.82ChemAxon
Physiological Charge1ChemAxon
Hydrogen Acceptor Count4ChemAxon
Hydrogen Donor Count3ChemAxon
Polar Surface Area79.37 Å2ChemAxon
Rotatable Bond Count2ChemAxon
Refractivity45.76 m3·mol-1ChemAxon
Polarizability17.53 Å3ChemAxon
Number of Rings1ChemAxon
Bioavailability1ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations: Cytoplasm
Reactions:
Pyridoxamine + Water + Oxygen <> Pyridoxal + Ammonia + Hydrogen peroxide
Adenosine triphosphate + Pyridoxamine <> ADP + Pyridoxamine 5'-phosphate
Adenosine triphosphate + Pyridoxamine <> Hydrogen ion + ADP + Pyridoxamine 5'-phosphate
Pyridoxamine + Oxalacetic acid <> Pyridoxal + L-Aspartic acid
Pyridoxamine + Adenosine triphosphate > Pyridoxamine 5'-phosphate + Adenosine diphosphate + ADP
Pathways:
Spectra
Spectra:
Spectrum TypeDescriptionSplash Key
GC-MSGC-MS Spectrum - GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies)splash10-001j-0590000000-a4bf9fe291241c903e3dView in MoNA
GC-MSGC-MS Spectrum - GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies) (3 TMS)splash10-00di-9350000000-3b1415672e7ab22d5e64View in MoNA
GC-MSGC-MS Spectrum - GC-MS (3 TMS)splash10-001i-1490000000-7214a8743cbe260268ceView in MoNA
GC-MSGC-MS Spectrum - GC-MSNot Available
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 10V, Positive (Annotated)splash10-014i-0900000000-4ca97fcd886d80336a5cView in MoNA
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 25V, Positive (Annotated)splash10-001i-1900000000-499c48bce709456248bcView in MoNA
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 40V, Positive (Annotated)splash10-0059-9200000000-aee74b4498be7c8cea6fView in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 10V, Negativesplash10-014i-0900000000-f1da14360063a04c11b4View in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 20V, Negativesplash10-014r-0900000000-f5aea0fa928eb266a79dView in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 30V, Negativesplash10-00di-0900000000-bebad702dbdba57d61faView in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 40V, Negativesplash10-05fr-0900000000-7322846ca1b4d95b5b16View in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 50V, Negativesplash10-0ab9-2900000000-da43b1a049d349d91831View in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF (UPLC Q-Tof Premier, Waters) , Positivesplash10-014i-0900000000-6b5f1d606df91ae52eb4View in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF (UPLC Q-Tof Premier, Waters) 30V, Positivesplash10-0gb9-0900000000-d5a16a4cdc19453ae9c7View in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF (UPLC Q-Tof Premier, Waters) , Negativesplash10-01b9-0900000000-3a1f853ce36bb047e05fView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-0uxr-0900000000-a1db882596b08c2987a7View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-0ue9-0900000000-b0f20e8503b963c8a31fView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-001i-3900000000-b41efa32a572817ef0c9View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-014i-0900000000-cd842fcc776d552a0f07View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-052r-0900000000-ae76358c88e1a1cf17dcView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-0596-9600000000-eeec53c65ada2bc944b0View in MoNA
1D NMR1H NMR SpectrumNot Available
1D NMR1H NMR SpectrumNot Available
1D NMR13C NMR SpectrumNot Available
2D NMR[1H,1H] 2D NMR SpectrumNot Available
2D NMR[1H,13C] 2D NMR SpectrumNot Available
References
References:
  • Berzas Nevado JJ, Murillo Pulgarin JA, Gomez Laguna MA: Determination of pyridoxamine in urine by matrix isopotential synchronous fluorescence spectrometry. Analyst. 1995 Jan;120(1):171-4. Pubmed: 7710125
  • Esteve-Romero J, Capella-Peiro ME, Monferrer-Pons L, Gil-Agusti M: Micellar liquid chromatography in clinical chemistry: application to the monitorization of B6 vitamins. Clin Chim Acta. 2004 Oct;348(1-2):69-77. Pubmed: 15369738
  • Kanehisa, M., Goto, S., Sato, Y., Furumichi, M., Tanabe, M. (2012). "KEGG for integration and interpretation of large-scale molecular data sets." Nucleic Acids Res 40:D109-D114. Pubmed: 22080510
  • Keseler, I. M., Collado-Vides, J., Santos-Zavaleta, A., Peralta-Gil, M., Gama-Castro, S., Muniz-Rascado, L., Bonavides-Martinez, C., Paley, S., Krummenacker, M., Altman, T., Kaipa, P., Spaulding, A., Pacheco, J., Latendresse, M., Fulcher, C., Sarker, M., Shearer, A. G., Mackie, A., Paulsen, I., Gunsalus, R. P., Karp, P. D. (2011). "EcoCyc: a comprehensive database of Escherichia coli biology." Nucleic Acids Res 39:D583-D590. Pubmed: 21097882
  • Rokitzki L, Sagredos AN, Reuss F, Buchner M, Keul J: Acute changes in vitamin B6 status in endurance athletes before and after a marathon. Int J Sport Nutr. 1994 Jun;4(2):154-65. Pubmed: 8054960
  • Sharma SK, Dakshinamurti K: Determination of vitamin B6 vitamers and pyridoxic acid in biological samples. J Chromatogr. 1992 Jul 1;578(1):45-51. Pubmed: 1400785
  • Sreekumar A, Poisson LM, Rajendiran TM, Khan AP, Cao Q, Yu J, Laxman B, Mehra R, Lonigro RJ, Li Y, Nyati MK, Ahsan A, Kalyana-Sundaram S, Han B, Cao X, Byun J, Omenn GS, Ghosh D, Pennathur S, Alexander DC, Berger A, Shuster JR, Wei JT, Varambally S, Beecher C, Chinnaiyan AM: Metabolomic profiles delineate potential role for sarcosine in prostate cancer progression. Nature. 2009 Feb 12;457(7231):910-4. Pubmed: 19212411
  • van der Werf, M. J., Overkamp, K. M., Muilwijk, B., Coulier, L., Hankemeier, T. (2007). "Microbial metabolomics: toward a platform with full metabolome coverage." Anal Biochem 370:17-25. Pubmed: 17765195
  • Winder, C. L., Dunn, W. B., Schuler, S., Broadhurst, D., Jarvis, R., Stephens, G. M., Goodacre, R. (2008). "Global metabolic profiling of Escherichia coli cultures: an evaluation of methods for quenching and extraction of intracellular metabolites." Anal Chem 80:2939-2948. Pubmed: 18331064
Synthesis Reference: Not Available
Material Safety Data Sheet (MSDS) Not Available
External Links:
ResourceLink
CHEBI ID16410
HMDB IDHMDB01431
Pubchem Compound ID1052
Kegg IDC00534
ChemSpider ID1023
WikipediaPyridoxamine
BioCyc IDPYRIDOXAMINE
EcoCyc IDPYRIDOXAMINE
Ligand ExpoPXM

Enzymes

Protein Details
• Pyridoxamine kinase
General function:
Involved in pyridoxal kinase activity
Specific function:
Phosphorylates B6 vitamers; functions in a salvage pathway. Uses pyridoxamine, but has negligible activity toward pyridoxal and pyridoxine as substrates
Gene Name:
pdxY
Locus Tag:
PA5516
Molecular weight:
31.3 kDa
Reactions
ATP + pyridoxal = ADP + pyridoxal 5'-phosphate.
Protein Details
• Pyridoxine/pyridoxamine 5'-phosphate oxidase
General function:
Coenzyme transport and metabolism
Specific function:
Catalyzes the oxidation of either pyridoxine 5'- phosphate (PNP) or pyridoxamine 5'-phosphate (PMP) into pyridoxal 5'-phosphate (PLP)
Gene Name:
pdxH
Locus Tag:
PA1049
Molecular weight:
24.9 kDa
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).

Transporters