P. aeruginosa Metabolome Database: pyridoxamine (PAMDB110781)

Identification Taxonomy Physical Properties Biological Properties Spectra Concentrations Links References Enzymes Transporters

Proteins (3280)

Record Information

Version

1.0

Update Date

1/22/2018 12:54:54 PM

Metabolite ID

PAMDB110781

Identification

Name:

pyridoxamine

Description:

An ammonium ion that is the conjugate acid of pyridoxamine arising from selective protonation of the primary amino group; major species at pH 7.3.

Structure

🔍MOL SDF PDB SMILES InChI View Structure

Synonyms:

Chemical Formula:

C₈H₁₃N₂O₂

Average Molecular Weight:

169.2

Monoisotopic Molecular Weight:

169.0977026719

InChI Key:

NHZMQXZHNVQTQA-UHFFFAOYSA-O

InChI:

InChI=1S/C8H12N2O2/c1-5-8(12)7(2-9)6(4-11)3-10-5/h3,11-12H,2,4,9H2,1H3/p+1

CAS number:

85-87-0

IUPAC Name:

[3-hydroxy-5-(hydroxymethyl)-2-methylpyridin-4-yl]methanaminium

Traditional IUPAC Name:

pyridoxamine

SMILES:

CC1(=NC=C(CO)C(C[N+])=C(O)1)

Chemical Taxonomy

Taxonomy Description

This compound 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 )

Physical Properties

State:

Solid

Charge:

Melting point:

Not Available

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
Water Solubility	29.0 mg/mL	ALOGPS
logP	-1.2	ALOGPS
logP	-1.6	ChemAxon
logS	-0.76	ALOGPS
pKa (Strongest Acidic)	7.82	ChemAxon
pKa (Strongest Basic)	9.82	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	17.53 Å³	ChemAxon
Number of Rings	1	ChemAxon
Bioavailability	1	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	Yes	ChemAxon
MDDR-like Rule	Yes	ChemAxon

Biological Properties

Cellular Locations:

Not Available

Reactions:

Pathways:

Vitamin B6 Metabolism pae00750

Spectra

Spectra:

Spectrum Type	Description	Splash Key
GC-MS	GC-MS Spectrum - GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies)	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
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS	Not Available
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
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	Not Available
1D NMR	1H NMR Spectrum	Not Available
1D NMR	13C NMR Spectrum	Not Available
2D NMR	[1H,1H] 2D NMR Spectrum	Not Available
2D NMR	[1H,13C] 2D NMR Spectrum	Not Available

References

References:

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. [19212411 ]
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. [15369738 ]
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. [7710125 ]
Sharma SK, Dakshinamurti K: Determination of vitamin B6 vitamers and pyridoxic acid in biological samples. J Chromatogr. 1992 Jul 1;578(1):45-51. [1400785 ]
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. [8054960 ]

Synthesis Reference:

Not Available

Material Safety Data Sheet (MSDS)

Not Available

Links

External Links:

Resource	Link
CAS	85-87-0
ChEBI	57761
HMDB	HMDB01431
IAF1260	35277
KEGG	C00534
MetaboLights	MTBLC57761
PubChem	25245492

pyridoxamine (PAMDB110781)

Structure for pyridoxamine (PAMDB110781)