Bovine Metabolome Database: Showing metabocard for Pyridoxamine (BMDB0001431)

Identification Taxonomy Physical properties Pathways Spectra Concentrations Links References enzymes (2) Show 2 proteins XML

Record Information

Version

1.0

Creation Date

2016-09-30 22:45:52 UTC

Update Date

2020-06-04 19:13:37 UTC

BMDB ID

BMDB0001431

Secondary Accession Numbers

BMDB01431

Metabolite Identification

Common Name

Pyridoxamine

Description

Pyridoxamine, 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 possibly soluble (in water) and a very strong basic compound (based on its pKa). Pyridoxamine exists in all living species, ranging from bacteria to humans. Pyridoxamine participates in a number of enzymatic reactions, within cattle. In particular, Pyridoxamine can be converted into pyridoxal; which is catalyzed by the enzyme pyridoxine-5'-phosphate oxidase. In addition, Pyridoxamine can be converted into pyridoxamine 5'-phosphate through its interaction with the enzyme pyridoxal kinase. In cattle, pyridoxamine is involved in the metabolic pathway called the vitamin B6 metabolism pathway.

Structure

MOL SDF PDB SMILES InChI

Synonyms

Value	Source
4-(AMINOMETHYL)-5-(hydroxymethyl)-2-methylpyridin-3-ol	ChEBI
PM	ChEBI
2-Methyl-4-aminomethyl-5-hydroxymethyl-3-pyridinol	HMDB
4-(Aminomethyl)-5-(hydroxymethyl)-2-methyl-3-pyridinol	HMDB
4-(Aminomethyl)-5-hydroxy-6-methyl-3-pyridinemethanol	HMDB
Pyridoxylamine	HMDB

Chemical Formula

C₈H₁₂N₂O₂

Average Molecular Weight

168.1931

Monoisotopic Molecular Weight

168.089877638

IUPAC Name

4-(aminomethyl)-5-(hydroxymethyl)-2-methylpyridin-3-ol

Traditional Name

pyridoxamine

CAS Registry Number

85-87-0

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 Key

NHZMQXZHNVQTQA-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.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Pyridines and derivatives

Sub Class

Pyridoxamines

Direct Parent

Pyridoxamine 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 Framework

Aromatic heteromonocyclic compounds

External Descriptors

monohydroxypyridine (CHEBI:16410 )
aminoalkylpyridine (CHEBI:16410 )
vitamin B6 (CHEBI:16410 )
hydroxymethylpyridine (CHEBI:16410 )
Water-soluble vitamins (C00534 )

Ontology

Status

Detected and Quantified

Origin

Endogenous

Biofunction

Not Available

Application

Not Available

Cellular locations

Not Available

Physical Properties

State

Solid

Experimental Properties

Property	Value	Reference
Melting Point	Not Available	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	815 mg/mL	Not Available
LogP	Not Available	Not Available

Predicted Properties

Property	Value	Source
logP	-1.2	ALOGPS
logP	-1.6	ChemAxon
logS	-0.76	ALOGPS
pKa (Strongest Acidic)	7.81	ChemAxon
pKa (Strongest Basic)	9.61	ChemAxon
Physiological Charge	1	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	79.37 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	45.76 m³·mol⁻¹	ChemAxon
Polarizability	17.52 Å³	ChemAxon
Number of Rings	1	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	Yes	ChemAxon
MDDR-like Rule	Yes	ChemAxon

Spectra

Spectrum Type	Description	Splash Key
GC-MS	GC-MS Spectrum - GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies) (Non-derivatized)	splash10-001j-0590000000-a4bf9fe291241c903e3d	View in MoNA
GC-MS	GC-MS Spectrum - GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies) (3 TMS)	splash10-00di-9350000000-3b1415672e7ab22d5e64	View in MoNA
GC-MS	GC-MS Spectrum - GC-MS (3 TMS)	splash10-001i-1490000000-7214a8743cbe260268ce	View in MoNA
GC-MS	GC-MS Spectrum - GC-EI-TOF (Non-derivatized)	splash10-001j-0590000000-a4bf9fe291241c903e3d	View in MoNA
GC-MS	GC-MS Spectrum - GC-EI-TOF (Non-derivatized)	splash10-00di-9350000000-3b1415672e7ab22d5e64	View in MoNA
GC-MS	GC-MS Spectrum - GC-MS (Non-derivatized)	splash10-001i-1490000000-7214a8743cbe260268ce	View in MoNA
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	splash10-0f79-2900000000-1dfbec04a6ae497e3229	View in MoNA
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (2 TMS) - 70eV, Positive	splash10-00dj-6090000000-1aab191c7ca62559a838	View in MoNA
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	Not Available	View in JSpectraViewer
LC-MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 10V, Positive (Annotated)	splash10-014i-0900000000-4ca97fcd886d80336a5c	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 25V, Positive (Annotated)	splash10-001i-1900000000-499c48bce709456248bc	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 40V, Positive (Annotated)	splash10-0059-9200000000-aee74b4498be7c8cea6f	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 10V, Negative	splash10-014i-0900000000-f1da14360063a04c11b4	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 20V, Negative	splash10-014r-0900000000-f5aea0fa928eb266a79d	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 30V, Negative	splash10-00di-0900000000-bebad702dbdba57d61fa	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 40V, Negative	splash10-05fr-0900000000-7322846ca1b4d95b5b16	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 50V, Negative	splash10-0ab9-2900000000-da43b1a049d349d91831	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QTOF (UPLC Q-Tof Premier, Waters) , Positive	splash10-014i-0900000000-6b5f1d606df91ae52eb4	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QTOF (UPLC Q-Tof Premier, Waters) 30V, Positive	splash10-0gb9-0900000000-d5a16a4cdc19453ae9c7	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QTOF (UPLC Q-Tof Premier, Waters) , Negative	splash10-01b9-0900000000-3a1f853ce36bb047e05f	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ , negative	splash10-014i-0900000000-f1da14360063a04c11b4	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ , negative	splash10-014r-0900000000-f5aea0fa928eb266a79d	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ , negative	splash10-00di-0900000000-c7a2dec0f7555dcc5ef7	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ , negative	splash10-05fr-0900000000-fe3f1f78fad714162a1c	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ , negative	splash10-0ab9-2900000000-da43b1a049d349d91831	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QTOF , negative	splash10-01b9-0900000000-f0cc74a9651686c1610c	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - , negative	splash10-014i-0900000000-9303a95b8f51c5ce6c22	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QTOF , positive	splash10-014i-0900000000-6b5f1d606df91ae52eb4	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-0uxr-0900000000-a1db882596b08c2987a7	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0ue9-0900000000-b0f20e8503b963c8a31f	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-001i-3900000000-b41efa32a572817ef0c9	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-014i-0900000000-cd842fcc776d552a0f07	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-052r-0900000000-ae76358c88e1a1cf17dc	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0596-9600000000-eeec53c65ada2bc944b0	View in MoNA
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, experimental)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, D₂O, experimental)	Not Available	View in JSpectraViewer
1D NMR	¹³C NMR Spectrum (1D, D₂O, experimental)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
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)	Not Available	View in JSpectraViewer
2D NMR	[¹H, ¹³C]-HSQC NMR Spectrum (2D, 600 MHz, H₂O, experimental)	Not Available	View in JSpectraViewer

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Milk
Placenta
Prostate Tissue

Pathways

Name	SMPDB/Pathwhiz	KEGG
Vitamin B6 Metabolism		Not Available

Normal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Milk	Detected and Quantified	0.099 +/- 0.038 uM	Not Specified	Not Specified	Normal	PMID: 1453218	details
Milk	Detected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	PMID: 23438684	details
Placenta	Expected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	Not Applicable	details
Prostate Tissue	Expected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	Not Applicable	details

Abnormal Concentrations

Not Available

External Links

HMDB ID

HMDB0001431

DrugBank ID

DB11673

Phenol Explorer Compound ID

Not Available

FooDB ID

KNApSAcK ID

Chemspider ID

KEGG Compound ID

BioCyc ID

BiGG ID

Wikipedia Link

METLIN ID

PubChem Compound

PDB ID

Not Available

ChEBI ID

16410

References

Synthesis Reference

Not Available

Material Safety Data Sheet (MSDS)

Not Available

General References

Coburn SP, Mahuren JD, Pauly TA, Ericson KL, Townsend DW: Alkaline phosphatase activity and pyridoxal phosphate concentrations in the milk of various species. J Nutr. 1992 Dec;122(12):2348-53. doi: 10.1093/jn/122.12.2348. [PubMed:1453218 ]
Melzer N, Wittenburg D, Hartwig S, Jakubowski S, Kesting U, Willmitzer L, Lisec J, Reinsch N, Repsilber D: Investigating associations between milk metabolite profiles and milk traits of Holstein cows. J Dairy Sci. 2013 Mar;96(3):1521-34. doi: 10.3168/jds.2012-5743. [PubMed:23438684 ]
Mung D, Li L: Development of Chemical Isotope Labeling LC-MS for Milk Metabolomics: Comprehensive and Quantitative Profiling of the Amine/Phenol Submetabolome. Anal Chem. 2017 Apr 18;89(8):4435-4443. doi: 10.1021/acs.analchem.6b03737. Epub 2017 Mar 28. [PubMed:28306241 ]
Mung D, Li L: Applying quantitative metabolomics based on chemical isotope labeling LC-MS for detecting potential milk adulterant in human milk. Anal Chim Acta. 2018 Feb 25;1001:78-85. doi: 10.1016/j.aca.2017.11.019. Epub 2017 Nov 14. [PubMed:29291809 ]

Enzymes

Enzyme Details

1. Pyridoxine-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:: PNPO
Uniprot ID:: Q5E9K3
Molecular weight:: 30366.0

Reactions

Pyridoxamine + Water + Oxygen → Pyridoxal + Ammonia + Hydrogen peroxide	details

Enzyme Details

2. Pyridoxal kinase

General function:: Coenzyme transport and metabolism
Specific function:: Required for synthesis of pyridoxal-5-phosphate from vitamin B6.
Gene Name:: PDXK
Uniprot ID:: Q0II59
Molecular weight:: 34817.0

Reactions

Pyridoxamine + Hydrogen phosphate → Pyridoxamine 5'-phosphate + Water	details

Showing metabocard for Pyridoxamine (BMDB0001431)

Structure for BMDB0001431 (Pyridoxamine)

Enzymes

Reactions

Reactions