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Record Information

Version

5.0

Status

Expected but not Quantified

Creation Date

2017-03-23 05:38:57 UTC

Update Date

2022-03-07 03:17:58 UTC

HMDB ID

HMDB0062696

Secondary Accession Numbers

HMDB62696

Metabolite Identification

Common Name

Pyridoxaminium(1+)

Description

pyridoxaminium(1+), also known as pyridoxamine or pyridoxaminium cation, 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. pyridoxaminium(1+) is a very strong basic compound (based on its pKa). An ammonium ion that is the conjugate acid of pyridoxaminium(1+) arising from selective protonation of the primary amino group; major species at pH 7.3.

Structure

MOL 3D MOL SDF 3D SDF PDB 3D PDB SMILES InChI

HEADER    PROTEIN                                 23-MAR-17   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   23-MAR-17         0                                  
HETATM    1  C   UNK     0       1.334   3.850   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0       4.001   2.310   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0       2.667  -0.000   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       4.001  -0.770   0.000  0.00  0.00           C+0
HETATM    7  N   UNK     0       4.001  -2.310   0.000  0.00  0.00           N+1
HETATM    8  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       1.334  -2.310   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0       2.667  -3.080   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   12  N   UNK     0       0.000   1.540   0.000  0.00  0.00           N+0
CONECT    1    2                                                            
CONECT    2    1    3   12                                                  
CONECT    3    2    4    5                                                  
CONECT    4    3                                                            
CONECT    5    3    6    8                                                  
CONECT    6    5    7                                                       
CONECT    7    6                                                            
CONECT    8    5    9   11                                                  
CONECT    9    8   10                                                       
CONECT   10    9                                                            
CONECT   11    8   12                                                       
CONECT   12   11    2                                                       
MASTER        0    0    0    0    0    0    0    0   12    0   24    0
END

View in JSmol View NMR Assignments View Stereo Labels

Synonyms

Value	Source
Pyridoxamine	ChEBI
Pyridoxaminium cation	ChEBI

Chemical Formula

C₈H₁₃N₂O₂

Average Molecular Weight

169.203

Monoisotopic Molecular Weight

169.097154087

IUPAC Name

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

Traditional Name

pyridoxaminium(1+)

CAS Registry Number

Not Available

SMILES

CC1=C(O)C(C[NH3+])=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/p+1

InChI Key

NHZMQXZHNVQTQA-UHFFFAOYSA-O

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
Organic cation
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

ammonium ion (CHEBI:57761 )
organic cation (CHEBI:57761 )

Ontology

Not Available

Physical Properties

State

Not Available

Experimental Molecular Properties

Property	Value	Reference
Melting Point	Not Available	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	19.3 g/l	ALOGPS
LogP	-2.15	ALOGPS

Experimental Chromatographic Properties

Not Available

Predicted Molecular Properties

Property	Value	Source
logP	-2.2	ALOGPS
logP	-1.6	ChemAxon
logS	-1	ALOGPS
pKa (Strongest Acidic)	7.81	ChemAxon
pKa (Strongest Basic)	9.61	ChemAxon
Physiological Charge	1	ChemAxon
Hydrogen Acceptor Count	3	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	80.99 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	57.06 m³·mol⁻¹	ChemAxon
Polarizability	17.85 Å³	ChemAxon
Number of Rings	1	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Predicted Chromatographic Properties

Predicted Collision Cross Sections

Predictor	Adduct Type	CCS Value (Å²)	Reference
DeepCCS	[M+H]+	136.165	30932474
DeepCCS	[M-H]-	133.769	30932474
DeepCCS	[M-2H]-	168.802	30932474
DeepCCS	[M+Na]+	143.349	30932474
AllCCS	[M+H]+	134.9	32859911
AllCCS	[M+H-H2O]+	130.5	32859911
AllCCS	[M+NH4]+	138.9	32859911
AllCCS	[M+Na]+	140.1	32859911
AllCCS	[M-H]-	138.5	32859911
AllCCS	[M+Na-2H]-	139.8	32859911
AllCCS	[M+HCOO]-	141.2	32859911

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
Pyridoxaminium(1+)	CC1=C(O)C(C[NH3+])=C(CO)C=N1	2677.8	Standard polar	33892256
Pyridoxaminium(1+)	CC1=C(O)C(C[NH3+])=C(CO)C=N1	1630.4	Standard non polar	33892256
Pyridoxaminium(1+)	CC1=C(O)C(C[NH3+])=C(CO)C=N1	1711.4	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
Pyridoxaminium(1+),1TMS,isomer #1	CC1=NC=C(CO)C(C[NH3+])=C1O[Si](C)(C)C	1677.6	Semi standard non polar	33892256
Pyridoxaminium(1+),1TMS,isomer #2	CC1=NC=C(CO[Si](C)(C)C)C(C[NH3+])=C1O	1722.1	Semi standard non polar	33892256
Pyridoxaminium(1+),2TMS,isomer #1	CC1=NC=C(CO[Si](C)(C)C)C(C[NH3+])=C1O[Si](C)(C)C	1760.8	Semi standard non polar	33892256
Pyridoxaminium(1+),1TBDMS,isomer #1	CC1=NC=C(CO)C(C[NH3+])=C1O[Si](C)(C)C(C)(C)C	1962.1	Semi standard non polar	33892256
Pyridoxaminium(1+),1TBDMS,isomer #2	CC1=NC=C(CO[Si](C)(C)C(C)(C)C)C(C[NH3+])=C1O	1971.0	Semi standard non polar	33892256
Pyridoxaminium(1+),2TBDMS,isomer #1	CC1=NC=C(CO[Si](C)(C)C(C)(C)C)C(C[NH3+])=C1O[Si](C)(C)C(C)(C)C	2253.7	Semi standard non polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted GC-MS	Predicted GC-MS Spectrum - Pyridoxaminium(1+) GC-MS (Non-derivatized) - 70eV, Positive	splash10-0f79-2900000000-1ffcd3d1d1eddddb3ec4	2017-09-20	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Pyridoxaminium(1+) GC-MS (2 TMS) - 70eV, Positive	splash10-00dj-5090000000-e7585ca6901c1a1c9a09	2017-10-06	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Pyridoxaminium(1+) GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum

MS/MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Pyridoxaminium(1+) 10V, Positive-QTOF	splash10-0uxr-0900000000-bcbafab1837bbc1b7d31	2017-10-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Pyridoxaminium(1+) 20V, Positive-QTOF	splash10-0udi-0900000000-be087c27282781b1765a	2017-10-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Pyridoxaminium(1+) 40V, Positive-QTOF	splash10-0ued-9800000000-45c7d9e20d51c7fb1162	2017-10-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Pyridoxaminium(1+) 10V, Positive-QTOF	splash10-0udi-0900000000-48a01f9929a42387a6d0	2021-09-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Pyridoxaminium(1+) 20V, Positive-QTOF	splash10-0f89-0900000000-0425dcb71b44871ac515	2021-09-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Pyridoxaminium(1+) 40V, Positive-QTOF	splash10-00e9-5900000000-2cfb35312314c385171a	2021-09-24	Wishart Lab	View Spectrum

NMR Spectra

Spectrum Type	Description	Deposition Date	Source	View
Predicted 1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Not Available

Tissue Locations

Not Available

Pathways

Not Available

Name	SMPDB/PathBank	KEGG

Normal Concentrations

Not Available

Abnormal Concentrations

Not Available

Associated Disorders and Diseases

Disease References

None

Associated OMIM IDs

None

External Links

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

Not Available

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

Not Available

PDB ID

Not Available

ChEBI ID

57761

Food Biomarker Ontology

Not Available

VMH ID

Not Available

MarkerDB ID

Not Available

Good Scents ID

Not Available

References

Synthesis Reference

Not Available

Material Safety Data Sheet (MSDS)

Not Available

General References

Not Available

Showing metabocard for Pyridoxaminium(1+) (HMDB0062696)

MOL for HMDB0062696 (Pyridoxaminium(1+))

3D MOL for HMDB0062696 (Pyridoxaminium(1+))

3D SDF for HMDB0062696 (Pyridoxaminium(1+))

3D-SDF for HMDB0062696 (Pyridoxaminium(1+))

PDB for HMDB0062696 (Pyridoxaminium(1+))

3D PDB for HMDB0062696 (Pyridoxaminium(1+))

SMILES for HMDB0062696 (Pyridoxaminium(1+))

INCHI for HMDB0062696 (Pyridoxaminium(1+))

Structure for HMDB0062696 (Pyridoxaminium(1+))

3D Structure for HMDB0062696 (Pyridoxaminium(1+))

Predicted Collision Cross Sections

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra

NMR Spectra