Showing metabocard for Pyridoxal (BMDB0001545)

IdentificationTaxonomyPhysical propertiesPathwaysSpectraConcentrationsLinksReferencesenzymes (3) Show 3 proteinsXML
Record Information
Version1.0
Creation Date2016-09-30 22:47:28 UTC
Update Date2020-06-04 20:45:40 UTC
BMDB IDBMDB0001545
Secondary Accession Numbers
  • BMDB01545
Metabolite Identification
Common NamePyridoxal
DescriptionPyridoxal, also known as pyridoxaldehyde, 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. Pyridoxal exists as a solid, possibly soluble (in water), and a strong basic compound (based on its pKa) molecule. Pyridoxal exists in all living species, ranging from bacteria to humans. In cattle, pyridoxal is involved in the metabolic pathway called the glycine and serine metabolism pathway. Pyridoxal is a potentially toxic compound.
Structure
Thumb
MOLSDFPDBSMILESInChI
Synonyms
ValueSource
3-HYDROXY-5-(hydroxymethyl)-2-methylisonicotinaldehydeChEBI
PyridoxaldehydeChEBI
3-Hydroxy-5-(hydroxymethyl)-2-methylpyridine-4-carboxaldehydeHMDB
Chemical FormulaC8H9NO3
Average Molecular Weight167.162
Monoisotopic Molecular Weight167.058243159
IUPAC Name3-hydroxy-5-(hydroxymethyl)-2-methylpyridine-4-carbaldehyde
Traditional Namepyridoxal
CAS Registry Number66-72-8
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 KeyRADKZDMFGJYCBB-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.
KingdomOrganic compounds
Super ClassOrganoheterocyclic compounds
ClassPyridines and derivatives
Sub ClassPyridine carboxaldehydes
Direct ParentPyridoxals 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 FrameworkAromatic heteromonocyclic compounds
External Descriptors
Ontology
StatusDetected and Quantified
Origin
  • Endogenous
BiofunctionNot Available
ApplicationNot Available
Cellular locations
  • Cytoplasm
Physical Properties
StateSolid
Experimental Properties
PropertyValueReference
Melting Point165 °CNot Available
Boiling PointNot AvailableNot Available
Water Solubility500.0 mg/mLNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
logP0.02ALOGPS
logP0.18ChemAxon
logS-1.2ALOGPS
pKa (Strongest Acidic)7.97ChemAxon
pKa (Strongest Basic)4.11ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count4ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area70.42 ŲChemAxon
Rotatable Bond Count2ChemAxon
Refractivity43.87 m³·mol⁻¹ChemAxon
Polarizability16.28 ųChemAxon
Number of Rings1ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Spectra
Spectra
Biological Properties
Cellular Locations
  • Cytoplasm
Biospecimen Locations
  • Erythrocyte
  • Fibroblasts
  • Kidney
  • Milk
  • Placenta
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
ErythrocyteExpected but not QuantifiedNot QuantifiedNot SpecifiedNot SpecifiedNormal
  • Not Applicable
 details
FibroblastsExpected but not QuantifiedNot QuantifiedNot SpecifiedNot SpecifiedNormal
  • Not Applicable
 details
KidneyExpected but not QuantifiedNot QuantifiedNot SpecifiedNot SpecifiedNormal
  • Not Applicable
 details
MilkDetected and Quantified0.763 +/- 0.19 uMNot SpecifiedNot Specified
Normal		 details
MilkDetected and Quantified16.185 - 52.601 uMNot SpecifiedNot SpecifiedNormal details
MilkDetected and Quantified0.541 - 0.763 uMNot SpecifiedNot SpecifiedNormal details
MilkDetected and Quantified1.619 - 1.740 uMNot SpecifiedNot SpecifiedNormal details
MilkDetected but not QuantifiedNot QuantifiedNot SpecifiedNot Specified
Normal
    • Kurt J. Boudonck,...
 details
MilkDetected but not QuantifiedNot QuantifiedNot SpecifiedNot Specified
Normal
    • Kurt J. Boudonck,...
 details
MilkDetected and Quantified1.699 uMNot SpecifiedNot SpecifiedNormal
    • Park, Y. W; Juáre...
 details
PlacentaExpected but not QuantifiedNot QuantifiedNot SpecifiedNot SpecifiedNormal
  • Not Applicable
 details
Abnormal Concentrations
Not Available
HMDB IDHMDB0001545
DrugBank IDDB00147
Phenol Explorer Compound IDNot Available
FooDB IDFDB011169
KNApSAcK IDC00007509
Chemspider ID1021
KEGG Compound IDC00250
BioCyc IDPYRIDOXAL
BiGG ID34393
Wikipedia LinkPyridoxal
METLIN ID6312
PubChem Compound1050
PDB IDNot Available
ChEBI ID17310
References
Synthesis ReferenceFujimoto, Yasuo. Pyridoxal. Jpn. Tokkyo Koho (1971), 2 pp.
Material Safety Data Sheet (MSDS)Not Available
General References
  1. 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 ]
  2. Agostini TS, Scherer R, Godoy HT: Simultaneous determination of B-group vitamins in enriched Brazilian dairy products. Crit Rev Food Sci Nutr. 2007;47(5):435-9. doi: 10.1080/10408390600846309. [PubMed:17558655 ]
  3. 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 ]
  4. 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 ]
  5. Gaucheron F: Milk and dairy products: a unique micronutrient combination. J Am Coll Nutr. 2011 Oct;30(5 Suppl 1):400S-9S. [PubMed:22081685 ]
  6. 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 ]
  7. Kurt J. Boudonck, Matthew W. Mitchell, Jacob Wulff and John A. Ryals (2009). Kurt J. Boudonck, Matthew W. Mitchell, Jacob Wulff and John A. Ryals. Characterization of the biochemical variability of bovine milk using metabolomics. Metabolomics (2009) 5:375?386. Metabolomics.
  8. Park, Y. W; Juárez, Manuela ; Ramos, M.; Haenlein, G. F. W. (2007). Park, Y. W; Juárez, Manuela ; Ramos, M.; Haenlein, G. F. W. Physico-chemical characteristics of goat and sheep milk. Small Ruminant Res.(2007) 68:88-113 doi: 10.1016/j.smallrumres.2006.09.013. Small Ruminant Research.

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 peroxidedetails
Pyridoxine + Oxygen → Pyridoxal + Hydrogen peroxidedetails
Enzyme Details
2. Pyridoxal phosphate phosphatase
General function:
Carbohydrate transport and metabolism
Specific function:
Protein serine phosphatase that dephosphorylates 'Ser-3' in cofilin and probably also dephosphorylates phospho-serine residues in DSTN. Regulates cofilin-dependent actin cytoskeleton reorganization. Required for normal progress through mitosis and normal cytokinesis. Does not dephosphorylate phospho-threonines in LIMK1. Does not dephosphorylate peptides containing phospho-tyrosine (PubMed:15580268). Pyridoxal phosphate (PLP) phosphatase, which also catalyzes the dephosphorylation of pyridoxine 5'-phosphate (PNP) and pyridoxamine 5'-phosphate (PMP), with order of substrate preference PLP > PNP > PMP (By similarity).
Gene Name:
PDXP
Uniprot ID:
Q3ZBF9
Molecular weight:
31749.0
Reactions
Pyridoxal 5'-phosphate + Water → Pyridoxal + Hydrogen phosphatedetails
Enzyme Details
3. Aldehyde oxidase 1
General function:
Nucleotide transport and metabolism
Specific function:
Oxidase with broad substrate specificity, oxidizing aromatic azaheterocycles, such as N1-methylnicotinamide, N-methylphthalazinium and phthalazine, as well as aldehydes, such as benzaldehyde, retinal, pyridoxal, and vanillin. Plays a key role in the metabolism of xenobiotics and drugs containing aromatic azaheterocyclic substituents. Is probably involved in the regulation of reactive oxygen species homeostasis. May be a prominent source of superoxide generation via the one-electron reduction of molecular oxygen. Also may catalyze nitric oxide (NO) production via the reduction of nitrite to NO with NADH or aldehyde as electron donor. May play a role in adipogenesis.
Gene Name:
AOX1
Uniprot ID:
P48034
Molecular weight:
147611.0
Reactions
Pyridoxal + Oxygen + Water → 4-Pyridoxic acid + Hydrogen peroxidedetails