MiMeDB: Showing metabocard for Pyridoxamine (MMDBc0000195)

Plant

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2020-10-27 23:39:20 UTC

Update Date

2022-08-31 00:00:33 UTC

Metabolite ID

MMDBc0000195

Metabolite Identification

Common Name

Pyridoxamine

Description

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

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

HEADER    PROTEIN                                 04-SEP-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   04-SEP-20         0                                  
HETATM    1  C   UNK     0      -0.218   0.776   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       1.116   0.006   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -1.565   0.006   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -0.212   2.309   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       1.116  -1.546   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       2.437   0.776   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -1.565  -1.546   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0      -2.886   0.776   0.000  0.00  0.00           O+0
HETATM    9  N   UNK     0       1.116   3.072   0.000  0.00  0.00           N+0
HETATM   10  N   UNK     0      -0.218  -2.328   0.000  0.00  0.00           N+0
HETATM   11  O   UNK     0       3.771   0.006   0.000  0.00  0.00           O+0
HETATM   12  C   UNK     0      -2.892  -2.309   0.000  0.00  0.00           C+0
CONECT    1    2    3    4                                                  
CONECT    2    1    5    6                                                  
CONECT    3    1    7    8                                                  
CONECT    4    1    9                                                       
CONECT    5    2   10                                                       
CONECT    6    2   11                                                       
CONECT    7    3   12   10                                                  
CONECT    8    3                                                            
CONECT    9    4                                                            
CONECT   10    5    7                                                       
CONECT   11    6                                                            
CONECT   12    7                                                            
MASTER        0    0    0    0    0    0    0    0   12    0   24    0
END

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

Molecular Formula

C₈H₁₂N₂O₂

Average Mass

168.1931

Monoisotopic Mass

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 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	29 g/L	ALOGPS
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	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Spectra

Chromatographic Retention Times and Retention Indices

Retention Times

Not Available

Retention Indices

Not Available

Chromatographic Retention Times and Retention Indices

Retention Times

Not Available

Retention Indices

Not Available

Biological Properties

Cellular Locations

Extracellular

Biospecimen Locations

Blood
Cerebrospinal Fluid (CSF)
Feces
Placenta
Prostate
Urine

Tissue Locations

Placenta
Prostate

Associated OMIM IDs

114500 (Colorectal cancer)
610247 (Eosinophilic esophagitis)

Human Proteins and Enzymes

Protein ID	Protein Name	Protein Type	Uniprot ID	Species
MMDBp0192313	Pyridoxine-5'-phosphate oxidase	Unknown	Q9NVS9	Homo_sapiens
MMDBp0192664	Pyridoxal kinase	Unknown	O00764	Homo_sapiens
MMDBp0193940	Pyridoxal phosphate phosphatase	Unknown	Q96GD0	Homo_sapiens
MMDBp0195556	Pyridoxal phosphate phosphatase PHOSPHO2	Unknown	Q8TCD6	Homo_sapiens

Human Pathways

Pathways

Name	SMPDB/PathBank

Microbial Pathways

Pathways

Not Available

Metabolic Reactions

Reactions

This table shows at most 20 reactions. For the full list of associated reactions:

See All Associated Reactions

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference

Health Effects and Bioactivity

Health Outcome/Bioactivity	Metabolite Response/Effect	Evidence Type	Host and Biospecimen	Data Source	Reference

Microbial Sources

Superkingdom/Kingdom	Phylum	Total species	Hosts and Body Sites	Microbial Links
Bacteria	Firmicutes	590	Human ; Human feces; Goat feces; Sheep feces; Human pleural fluid plaque; Pig ; Cattle	Microbial culture; Indirect association between microbiota composition and metabolites measured in host biospecimen; Metabolic reconstruction
Bacteria	Proteobacteria	334	Human ; Human feces; Human feces; pleural fluid plaque; bal; Human sputum; Human unknown; Pig ; Human pleural fluid plaque; Human dental plaque; Human nasal swab; Turkey	Microbial culture; Indirect association between microbiota composition and metabolites measured in host biospecimen; Metabolic reconstruction
Eukaryota	Apicomplexa	1		Microbial culture
Bacteria	Spirochaetes	3	Human feces	Microbial culture; Metabolic reconstruction
Bacteria	Actinobacteria	244	Human ; Human feces; Human sputum; Human bronchial brush; Human nasopharyngeal swab; Human pleural fluid plaque; Human dental plaque	Microbial culture; Metabolic reconstruction
Bacteria	Bacteroidetes	164	Human feces; Human appendix biopsy; Human	Metabolic reconstruction
Archaea	Thaumarchaeota	2	Human feces	Metabolic reconstruction
Bacteria	Synergistetes	4	Human feces	Metabolic reconstruction
Bacteria	Fusobacteria	15	Human feces; Human	Metabolic reconstruction
Archaea	Euryarchaeota	6	Human feces; Cattle	Metabolic reconstruction
Archaea	Crenarchaeota	2	Human feces	Metabolic reconstruction
Eukaryota/Fungi	Ascomycota	1	Human feces	Unknown

Exposure Sources

Food Exposures

Other Exposures

Source Type	Data Source	Reference

Host Biospecimen and Location

Host and Biospecimen	Status	Mean	Std	Min	Max	Age	Sex	Health Condition	Data Source	Reference
Human Feces	Detected but not Quantified								HMDB
Human	Detected and Quantified			0.000100	0.000200	Children (1-13 years old)	Female	Epilepsy, early-onset, vitamin B6-dependent	HMDB	27912044
Human	Detected and Quantified			0.000300	0.000900	Children (1-13 years old)	Not Specified	Normal	HMDB	27912044
Human	Detected and Quantified	0.164	0.038			Adult (>18 years old)	Both	Normal	HMDB	Geigy Scientific Tables, 8th Rev edition, pp. 130. Edited by C. Lentner, West Cadwell, N.J.: Medical education Div., Ciba-Geigy Corp. Basel, Switzerland c1981-1992.
Human Placenta	Detected but not Quantified					Not Specified	Not Specified	Normal	HMDB	34986597
Human Prostate	Detected but not Quantified					Not Specified	Not Specified	Normal	HMDB	34986597
Human Feces	Detected but not Quantified					Adult (>18 years old)	Both	Normal	HMDB	27543620
Human Feces	Detected but not Quantified					Adult (>18 years old)	Both	Normal	HMDB	29808030
Human Urine	Detected but not Quantified					Adult (>18 years old)	Both	Normal	HMDB	32966057
Human Blood	Detected but not Quantified					Adult (>18 years old)	Both	Normal	HMDB	32966057

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

Food Biomarker Ontology

Not Available

CMMC Knowledgebase

Not Available

General References

Sharma SK, Dakshinamurti K: Determination of vitamin B6 vitamers and pyridoxic acid in biological samples. J Chromatogr. 1992 Jul 1;578(1):45-51. doi: 10.1016/0378-4347(92)80223-d. [PubMed:1400785 ]
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. doi: 10.1039/an9952000171. [PubMed:7710125 ]
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. doi: 10.1123/ijsn.4.2.154. [PubMed:8054960 ]
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. doi: 10.1016/j.cccn.2004.05.009. [PubMed:15369738 ]
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 ]
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 ]

Showing metabocard for Pyridoxamine (MMDBc0000195)

MOL for #<Metabolite:0x0000560be1a7c9f0>

3D MOL for #<Metabolite:0x0000560be1a7c9f0>

3D SDF for #<Metabolite:0x0000560be1a7c9f0>

3D-SDF for #<Metabolite:0x0000560be1a7c9f0>

PDB for #<Metabolite:0x0000560be1a7c9f0>

3D PDB for #<Metabolite:0x0000560be1a7c9f0>

SMILES for #<Metabolite:0x0000560be1a7c9f0>

INCHI for #<Metabolite:0x0000560be1a7c9f0>

Structure for #<Metabolite:0x0000560be1a7c9f0>

3D Structure for #<Metabolite:0x0000560be1a7c9f0>