MiMeDB: Showing metabocard for Pyridoxal (MMDBc0000200)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2020-10-27 23:39:31 UTC

Update Date

2024-10-06 18:37:20 UTC

Metabolite ID

MMDBc0000200

Metabolite Identification

Common Name

Pyridoxal

Description

The 4-carboxyaldehyde form of vitamin B6 which is converted to pyridoxal phosphate which is a coenzyme for synthesis of amino acids, neurotransmitters (serotonin, norepinephrine), sphingolipids, aminolevulinic acid. Pyridoxal has been identified in the human placenta (PMID: 32033212 ).

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       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  N   UNK     0       2.667   1.540   0.000  0.00  0.00           N+0
HETATM    4  C   UNK     0       2.667   0.000   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0      -1.334   2.310   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0      -1.334  -0.770   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0      -2.667   0.000   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0       1.334  -2.310   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0       2.667  -3.080   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    7                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6   11                                                  
CONECT    6    5    7    9                                                  
CONECT    7    6    2    8                                                  
CONECT    8    7                                                            
CONECT    9    6   10                                                       
CONECT   10    9                                                            
CONECT   11    5   12                                                       
CONECT   12   11                                                            
MASTER        0    0    0    0    0    0    0    0   12    0   24    0
END

Synonyms

Value	Source
3-HYDROXY-5-(hydroxymethyl)-2-methylisonicotinaldehyde	ChEBI
Pyridoxaldehyde	ChEBI
3-Hydroxy-5-(hydroxymethyl)-2-methylpyridine-4-carboxaldehyde	HMDB

Molecular Formula

C₈H₉NO₃

Average Mass

167.162

Monoisotopic Mass

167.058243159

IUPAC Name

3-hydroxy-5-(hydroxymethyl)-2-methylpyridine-4-carbaldehyde

Traditional Name

pyridoxal

CAS Registry Number

66-72-8

SMILES

CC1=NC=C(CO)C(C=O)=C1O

InChI Identifier

InChI=1S/C8H9NO3/c1-5-8(12)7(4-11)6(3-10)2-9-5/h2,4,10,12H,3H2,1H3

InChI Key

RADKZDMFGJYCBB-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as pyridoxals and derivatives. Pyridoxals and derivatives are compounds containing a pyridoxal moiety, which consists of a pyridine ring substituted at positions 2,3,4, and 5 by a methyl group, a hydroxyl group, a carbaldehyde group, and a hydroxymethyl group, respectively.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Pyridines and derivatives

Sub Class

Pyridine carboxaldehydes

Direct Parent

Pyridoxals and derivatives

Alternative Parents

Substituents

Pyridoxal
Aryl-aldehyde
Hydroxypyridine
Methylpyridine
Vinylogous acid
Heteroaromatic compound
Azacycle
Hydrocarbon derivative
Aldehyde
Alcohol
Organic oxygen compound
Aromatic alcohol
Organic nitrogen compound
Primary alcohol
Organooxygen compound
Organonitrogen compound
Organopnictogen compound
Organic oxide
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

monohydroxypyridine (CHEBI:17310 )
pyridinecarbaldehyde (CHEBI:17310 )
methylpyridines (CHEBI:17310 )
vitamin B6 (CHEBI:17310 )
hydroxymethylpyridine (CHEBI:17310 )
Water-soluble vitamins (C00250 )
a vitamin B6 (PYRIDOXAL )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	11.7 g/L	ALOGPS
logP	0.02	ALOGPS
logP	0.18	ChemAxon
logS	-1.2	ALOGPS
pKa (Strongest Acidic)	7.97	ChemAxon
pKa (Strongest Basic)	4.11	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	70.42 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	43.87 m³·mol⁻¹	ChemAxon
Polarizability	16.28 Å³	ChemAxon
Number of Rings	1	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Spectra

Not Available

Biological Properties

Cellular Locations

Cytoplasm
Extracellular

Biospecimen Locations

Blood
Cerebrospinal Fluid (CSF)
Erythrocyte
Feces
Fibroblasts
Kidney
Placenta
Urine

Tissue Locations

Erythrocyte
Fibroblasts
Kidney
Placenta

Associated OMIM IDs

114500 (Colorectal cancer)
610247 (Eosinophilic esophagitis)

Human Proteins and Enzymes

Protein ID	Protein Name	Protein Type	Uniprot ID	Species
MMDBp0191797	Aldehyde oxidase	Unknown	Q06278	Homo sapiens
MMDBp0192313	Pyridoxine-5'-phosphate oxidase	Unknown	Q9NVS9	Homo sapiens
MMDBp0192415	Glycine dehydrogenase [decarboxylating], mitochondrial	Enzyme	P23378	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

Metabolic Reactions

Reactions

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference
MMDBr0018456	Pyridoxal	Pyridoxal 5'-phosphate	Pyridoxine/pyridoxal/pyridoxamine kinase	Phosphorylation	PathBank	31602464
MMDBr0019957	Pyridoxal	Pyridoxal 5'-phosphate	Unknown Protein		PathBank	31602464

Health Effects and Bioactivity

Health Outcome/Bioactivity	Metabolite Response/Effect	Evidence Type	Host and Biospecimen	Data Source	Reference
Sickle cell anemia	Decreased	Association	Human Blood	HMDB	12218594

Microbial Sources

Superkingdom/Kingdom	Phylum	Total species	Hosts and Body Sites	Microbial Links
Bacteria/Eubacteria	Firmicutes	655	Human ; Human feces; Goat feces; Sheep feces; Human mucosa; Human supragingival plaque; Human saliva; Human subgingival plaque; Human urine; Human pleural fluid plaque; Pig ; Human sputum; Cattle ; Human stool	Microbial culture; Indirect association between microbiota composition and metabolites measured in host biospecimen; Metabolic reconstruction
Bacteria/Eubacteria	Proteobacteria	396	Human ; Human feces; Human feces; pleural fluid plaque; bal; Human stool; Human sputum; Human unknown; Pig ; Human pleural fluid plaque; Human dental plaque; Human nasal swab; Turkey ; Cattle ; Chicken	Microbial culture; Metabolic reconstruction
Eukaryota	Apicomplexa	1		Microbial culture
Bacteria/Eubacteria	Spirochaetes	4	Human feces; Human	Microbial culture; Metabolic reconstruction
Bacteria/Eubacteria	Actinobacteria	222	Human ; Human feces; Human saliva; Human mucosa; Human supragingival plaque; Human stool; Human sputum; Human bronchial brush; Human nasopharyngeal swab; Human pleural fluid plaque; Human dental plaque; Human subgingival plaque	Microbial culture; Metabolic reconstruction
Bacteria	Actinobacteria	29	Human ; Human feces; Human saliva; Human mucosa; Human supragingival plaque; Human stool; Human sputum; Human bronchial brush; Human nasopharyngeal swab; Human pleural fluid plaque; Human dental plaque; Human subgingival plaque	Microbial culture; Metabolic reconstruction
Bacteria/Eubacteria	Bacteroidetes	169	Human feces; Human appendix biopsy; Human ; Human stool; Human saliva; Human gastric fluid; Human urine	Metabolic reconstruction
Bacteria	Firmicutes	52	Human ; Human feces; Goat feces; Sheep feces; Human mucosa; Human supragingival plaque; Human saliva; Human subgingival plaque; Human urine; Human pleural fluid plaque; Pig ; Human sputum; Cattle ; Human stool	Microbial culture; Indirect association between microbiota composition and metabolites measured in host biospecimen; Metabolic reconstruction
Bacteria	Proteobacteria	18	Human ; Human feces; Human feces; pleural fluid plaque; bal; Human stool; Human sputum; Human unknown; Pig ; Human pleural fluid plaque; Human dental plaque; Human nasal swab; Turkey ; Cattle ; Chicken	Microbial culture; Metabolic reconstruction
Archaea	Thaumarchaeota	2		Metabolic reconstruction
Bacteria/Eubacteria	Synergistetes	4	Human feces	Metabolic reconstruction
Bacteria/Eubacteria	Fusobacteria	15	Human feces; Human	Metabolic reconstruction
Archaea	Euryarchaeota	6		Metabolic reconstruction
Bacteria/Eubacteria	Tenericutes	2	Human feces	Metabolic reconstruction
Archaea	Crenarchaeota	2		Metabolic reconstruction
Eukaryota/Fungi	Ascomycota	3	Human feces; Human saliva	Unknown
Bacteria/Eubacteria	Deinococcus-thermus	2

Exposure Sources

Food Exposures

Other Exposures

Source Type	Data Source	Reference
Drugs - Antimicrobial	U.S. Environmental Protection Agency	CompTox
Cosmetics	U.S. Environmental Protection Agency	CompTox
Domestics	U.S. Environmental Protection Agency	CompTox

Host Biospecimen and Location

Host and Biospecimen	Status	Mean	Std	Min	Max	Units	Age	Sex	Health Condition	Data Source	Reference
Human Feces	Detected but not Quantified									HMDB
Human Cerebrospinal fluid (csf)	Detected and Quantified	0.015				uM	Children (1-13 years old)	Female	Epilepsy, early-onset, vitamin B6-dependent	HMDB	27912044
Human Blood	Detected and Quantified	0.036	0.031			uM	Adult (>18 years old)	Both	Sickle cell disease-SS (SCD-SS)	HMDB	12218594
Human Cerebrospinal fluid (csf)	Detected and Quantified			0.0160	0.0560	uM	Children (1-13 years old)	Not Specified	Normal	HMDB	27912044
Human Blood	Detected and Quantified	0.251	0.051			uM	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 Erythrocyte	Detected but not Quantified						Not Specified	Not Specified	Normal	HMDB	34986597
Human Fibroblasts	Detected but not Quantified						Not Specified	Not Specified	Normal	HMDB	34986597
Human Kidney	Detected but not Quantified						Not Specified	Not Specified	Normal	HMDB	34986597
Human Placenta	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	25037050
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

HMDB0001545

DrugBank ID

DB00147

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

17310

Food Biomarker Ontology

Not Available

References

Synthesis Reference

Not Available

General References

Brenner A, Wapnir RA: A pyridoxine-dependent behavioral disorder unmasked by isoniazid. Am J Dis Child. 1978 Aug;132(8):773-6. doi: 10.1001/archpedi.1978.02120330045011. [PubMed:150790 ]
Bosse TR, Donald EA: The vitamin B6 requirement in oral contraceptive users. I. Assessment by pyridoxal level and transferase activity in erythrocytes. Am J Clin Nutr. 1979 May;32(5):1015-23. doi: 10.1093/ajcn/32.5.1015. [PubMed:433818 ]
Schenker S, Johnson RF, Mahuren JD, Henderson GI, Coburn SP: Human placental vitamin B6 (pyridoxal) transport: normal characteristics and effects of ethanol. Am J Physiol. 1992 Jun;262(6 Pt 2):R966-74. doi: 10.1152/ajpregu.1992.262.6.R966. [PubMed:1621875 ]
el-Habet AE, el-Sewedy SM, el-Sharaky A, Gaafar NK, Abdel-Rafee A, Hamoud F: Biochemical studies on bilharzial and nonbilharzial hyperoxaluria: effect of pyridoxine and allopurinol treatment. Biochem Med Metab Biol. 1987 Aug;38(1):1-8. doi: 10.1016/0885-4505(87)90055-7. [PubMed:3663392 ]
Linares P, Luque de Castro MD, Valcarcel M: Simultaneous determination of pyridoxal and pyridoxal 5-phosphate in human serum by flow injection analysis. Anal Chem. 1985 Sep;57(11):2101-6. doi: 10.1021/ac00288a022. [PubMed:4051187 ]
Kark JA, Tarassoff PG, Bongiovanni R: Pyridoxal phosphate as an antisickling agent in vitro. J Clin Invest. 1983 May;71(5):1224-9. doi: 10.1172/jci110871. [PubMed:6853710 ]
Kark JA, Bongiovanni R, Hicks CU, Tarassoff PG, Hannah JS, Yoshida GY: Modification of intracellular hemoglobin with pyridoxal and pyridoxal 5'-phosphate. Blood Cells. 1982;8(2):299-314. [PubMed:7159754 ]
Mehansho H, Henderson LM: Transport and accumulation of pyridoxine and pyridoxal by erythrocytes. J Biol Chem. 1980 Dec 25;255(24):11901-7. [PubMed:7440576 ]
Fonda ML: Vitamin B6 metabolism and binding to proteins in the blood of alcoholic and nonalcoholic men. Alcohol Clin Exp Res. 1993 Dec;17(6):1171-8. doi: 10.1111/j.1530-0277.1993.tb05223.x. [PubMed:8116826 ]
Huang YC, Lan PH, Cheng CH, Lee BJ, Kan MN: Vitamin B6 intakes and status of mechanically ventilated critically ill patients in Taiwan. Eur J Clin Nutr. 2002 May;56(5):387-92. doi: 10.1038/sj.ejcn.1601321. [PubMed:12001008 ]
Rajamohan F, Nelms L, Joslin DL, Lu B, Reagan WJ, Lawton M: cDNA cloning, expression, purification, distribution, and characterization of biologically active canine alanine aminotransferase-1. Protein Expr Purif. 2006 Jul;48(1):81-9. doi: 10.1016/j.pep.2005.12.009. Epub 2006 Jan 30. [PubMed:16495081 ]
Yiakouvaki A, Savovic J, Al-Qenaei A, Dowden J, Pourzand C: Caged-iron chelators a novel approach towards protecting skin cells against UVA-induced necrotic cell death. J Invest Dermatol. 2006 Oct;126(10):2287-95. doi: 10.1038/sj.jid.5700373. Epub 2006 May 18. [PubMed:16710308 ]
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 Pyridoxal (MMDBc0000200)

MOL for #<Metabolite:0x00007f925081d938>

3D MOL for #<Metabolite:0x00007f925081d938>

3D SDF for #<Metabolite:0x00007f925081d938>

3D-SDF for #<Metabolite:0x00007f925081d938>

PDB for #<Metabolite:0x00007f925081d938>

3D PDB for #<Metabolite:0x00007f925081d938>

SMILES for #<Metabolite:0x00007f925081d938>

INCHI for #<Metabolite:0x00007f925081d938>

Structure for #<Metabolite:0x00007f925081d938>

3D Structure for #<Metabolite:0x00007f925081d938>