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Record Information
Version4.0
StatusDetected and Quantified
Creation Date2005-11-16 15:48:42 UTC
Update Date2020-02-26 21:23:20 UTC
HMDB IDHMDB0001431
Secondary Accession Numbers
  • HMDB01431
Metabolite 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. However, in the United States, the FDA ruled in January 2009 that pyridoxamine must be regulated as a pharmaceutical drug because it is the active ingredient in Pyridorin, a drug designed by Biostratum, Inc., to prevent the progression of diabetic nephropathy. Pyridoxamine is a drug. Pyridoxamine is a very strong basic compound (based on its pKa). Pyridoxamine exists in all living species, ranging from bacteria to humans. It differs from pyridoxine by the substituent at the 4-position. Within humans, pyridoxamine participates in a number of enzymatic reactions. In particular, pyridoxamine can be converted into pyridoxal; which is mediated by the enzyme pyridoxine-5'-phosphate oxidase. In addition, pyridoxamine can be converted into pyridoxamine 5'-phosphate; which is catalyzed by the enzyme pyridoxal kinase. Pyridoxamine also inhibits the formation of advanced lipoxidation endproducts during lipid peroxidation reactions by reaction with dicarbonyl intermediates. In humans, pyridoxamine is involved in vitamin B6 metabolism. Outside of the human body, pyridoxamine has been detected, but not quantified in, several different foods, such as nutmegs, sparkleberries, fennels, turmerics, and swiss chards. This could make pyridoxamine a potential biomarker for the consumption of these foods. The 3'-hydroxyl group of pyridoxamine allows for efficient hydroxyl radical scavenging. Pyridoxamine is one form of vitamin B6. In other preclinical research, pyridoxamine may be efficacious in treating diabetic neuropathy and retinopathy associated with diabetes and kidney stone disease. One research study found that pyridoxamine specifically reacts with the carbonyl group in Amadori products, but inhibition of post-Amadori reactions (that can lead to advanced glycation endproducts) is due in much greater part to the metal chelation effects of pyridoxamine.
Structure
Data?1582752200
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 Weight168.1931
Monoisotopic Molecular Weight168.089877638
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:

Process

Naturally occurring process:

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
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
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
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-a4bf9fe291241c903e3dSpectrum
GC-MSGC-MS Spectrum - GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies) (3 TMS)splash10-00di-9350000000-3b1415672e7ab22d5e64Spectrum
GC-MSGC-MS Spectrum - GC-MS (3 TMS)splash10-001i-1490000000-7214a8743cbe260268ceSpectrum
GC-MSGC-MS Spectrum - GC-EI-TOF (Non-derivatized)splash10-001j-0590000000-a4bf9fe291241c903e3dSpectrum
GC-MSGC-MS Spectrum - GC-EI-TOF (Non-derivatized)splash10-00di-9350000000-3b1415672e7ab22d5e64Spectrum
GC-MSGC-MS Spectrum - GC-MS (Non-derivatized)splash10-001i-1490000000-7214a8743cbe260268ceSpectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-0f79-2900000000-1dfbec04a6ae497e3229Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (2 TMS) - 70eV, Positivesplash10-00dj-6090000000-1aab191c7ca62559a838Spectrum
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 10V, Positive (Annotated)splash10-014i-0900000000-4ca97fcd886d80336a5cSpectrum
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 25V, Positive (Annotated)splash10-001i-1900000000-499c48bce709456248bcSpectrum
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 40V, Positive (Annotated)splash10-0059-9200000000-aee74b4498be7c8cea6fSpectrum
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 10V, Negativesplash10-014i-0900000000-f1da14360063a04c11b4Spectrum
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 20V, Negativesplash10-014r-0900000000-f5aea0fa928eb266a79dSpectrum
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 30V, Negativesplash10-00di-0900000000-bebad702dbdba57d61faSpectrum
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 40V, Negativesplash10-05fr-0900000000-7322846ca1b4d95b5b16Spectrum
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 50V, Negativesplash10-0ab9-2900000000-da43b1a049d349d91831Spectrum
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF (UPLC Q-Tof Premier, Waters) , Positivesplash10-014i-0900000000-6b5f1d606df91ae52eb4Spectrum
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF (UPLC Q-Tof Premier, Waters) 30V, Positivesplash10-0gb9-0900000000-d5a16a4cdc19453ae9c7Spectrum
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF (UPLC Q-Tof Premier, Waters) , Negativesplash10-01b9-0900000000-3a1f853ce36bb047e05fSpectrum
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , negativesplash10-014i-0900000000-f1da14360063a04c11b4Spectrum
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , negativesplash10-014r-0900000000-f5aea0fa928eb266a79dSpectrum
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , negativesplash10-00di-0900000000-c7a2dec0f7555dcc5ef7Spectrum
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , negativesplash10-05fr-0900000000-fe3f1f78fad714162a1cSpectrum
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , negativesplash10-0ab9-2900000000-da43b1a049d349d91831Spectrum
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF , negativesplash10-01b9-0900000000-f0cc74a9651686c1610cSpectrum
LC-MS/MSLC-MS/MS Spectrum - , negativesplash10-014i-0900000000-9303a95b8f51c5ce6c22Spectrum
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF , positivesplash10-014i-0900000000-6b5f1d606df91ae52eb4Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-0uxr-0900000000-a1db882596b08c2987a7Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-0ue9-0900000000-b0f20e8503b963c8a31fSpectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-001i-3900000000-b41efa32a572817ef0c9Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-014i-0900000000-cd842fcc776d552a0f07Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-052r-0900000000-ae76358c88e1a1cf17dcSpectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-0596-9600000000-eeec53c65ada2bc944b0Spectrum
1D NMR1H NMR SpectrumNot AvailableSpectrum
1D NMR1H NMR SpectrumNot AvailableSpectrum
1D NMR13C NMR SpectrumNot AvailableSpectrum
2D NMR[1H,1H] 2D NMR SpectrumNot AvailableSpectrum
2D NMR[1H,13C] 2D NMR SpectrumNot AvailableSpectrum
Biological Properties
Cellular Locations
  • Extracellular
Biospecimen Locations
  • Blood
  • Cerebrospinal Fluid (CSF)
  • Feces
Tissue Locations
  • Placenta
  • Prostate
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodDetected and Quantified0.164 +/- 0.038 uMAdult (>18 years old)BothNormal
    • Geigy Scientific ...
details
Cerebrospinal Fluid (CSF)Detected and Quantified0.000300-0.000900 uMChildren (1-13 years old)Not SpecifiedNormal details
FecesDetected but not Quantified Adult (>18 years old)Both
Normal
details
FecesDetected but not Quantified Adult (>18 years old)Both
Normal
details
Abnormal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
Cerebrospinal Fluid (CSF)Detected and Quantified0.000100-0.000200 uMChildren (1-13 years old)FemaleEpilepsy, early-onset, vitamin B6-dependent details
Associated Disorders and Diseases
Disease References
Epilepsy, early-onset, vitamin B6-dependent
  1. Darin N, Reid E, Prunetti L, Samuelsson L, Husain RA, Wilson M, El Yacoubi B, Footitt E, Chong WK, Wilson LC, Prunty H, Pope S, Heales S, Lascelles K, Champion M, Wassmer E, Veggiotti P, de Crecy-Lagard V, Mills PB, Clayton PT: Mutations in PROSC Disrupt Cellular Pyridoxal Phosphate Homeostasis and Cause Vitamin-B6-Dependent Epilepsy. Am J Hum Genet. 2016 Dec 1;99(6):1325-1337. doi: 10.1016/j.ajhg.2016.10.011. [PubMed:27912044 ]
Associated OMIM IDs
  • 617290 (Epilepsy, early-onset, vitamin B6-dependent)
DrugBank IDDB11673
Phenol Explorer Compound IDNot Available
FooDB IDFDB021819
KNApSAcK IDC00007504
Chemspider ID1023
KEGG Compound IDC00534
BioCyc IDPYRIDOXAMINE
BiGG ID35277
Wikipedia LinkPyridoxamine
METLIN ID238
PubChem Compound1052
PDB IDNot Available
ChEBI ID16410
Food Biomarker OntologyNot Available
VMH IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General References
  1. 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 ]
  2. 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 ]
  3. 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 ]
  4. 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 ]
  5. 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. doi: 10.1038/nature07762. [PubMed:19212411 ]
  6. Elshenawy S, Pinney SE, Stuart T, Doulias PT, Zura G, Parry S, Elovitz MA, Bennett MJ, Bansal A, Strauss JF 3rd, Ischiropoulos H, Simmons RA: The Metabolomic Signature of the Placenta in Spontaneous Preterm Birth. Int J Mol Sci. 2020 Feb 4;21(3). pii: ijms21031043. doi: 10.3390/ijms21031043. [PubMed:32033212 ]

Enzymes

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
Reactions
Pyridoxamine + Water + Oxygen → Pyridoxal + Ammonia + Hydrogen peroxidedetails
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
Reactions
Adenosine triphosphate + Pyridoxamine → ADP + Pyridoxamine 5'-phosphatedetails
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
Reactions
Pyridoxamine + Phosphate → Pyridoxamine 5'-phosphate + Waterdetails
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
Reactions
Pyridoxamine + Phosphate → Pyridoxamine 5'-phosphate + Waterdetails