Pyridoxal (YMDB00392)

Identification

YMDB ID

YMDB00392

Name

Pyridoxal

Species

Saccharomyces cerevisiae

Strain

Baker's yeast

Description

Pyridoxal, 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 is a strong basic compound (based on its pKa). Pyridoxal exists in all living species, ranging from bacteria to humans. Pyridoxal is a potentially toxic compound.

Structure

MOL SDF PDB SMILES InChI

Synonyms

3-Hydroxy-5-(hydroxymethyl)-2-methylpyridine-4-carboxaldehyde
Pyridoxal
Pyridoxaldehyde
3-HYDROXY-5-(hydroxymethyl)-2-methylisonicotinaldehyde

CAS number

66-72-8

Weight

Average: 167.162
Monoisotopic: 167.058243159

InChI Key

RADKZDMFGJYCBB-UHFFFAOYSA-N

InChI

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

IUPAC Name

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

Traditional IUPAC Name

pyridoxal

Chemical Formula

C₈H₉NO₃

SMILES

[H]OC1=C(N=C([H])C(=C1C([H])=O)C([H])([H])O[H])C([H])([H])[H]

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 )

Physical Properties

State

Solid

Charge

Melting point

165 °C

Experimental Properties

Property	Value	Reference
Water Solubility	500 mg/mL [COFFEN,DL (1978)]	PhysProp
LogP	Not Available	PhysProp

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	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

cytoplasm

Organoleptic Properties

Not Available

SMPDB Pathways

Vitamin B6

PW002488

KEGG Pathways

Vitamin B6 metabolism

ec00750

SMPDB Reactions

Pyridoxal + Adenosine triphosphate → Pyridoxal 5'-phosphate + ADP

KEGG Reactions

Adenosine triphosphate + Pyridoxal → Pyridoxal 5'-phosphate + hydron + ADP

water + oxygen + Ammonium + Pyridoxal ↔ Hydrogen peroxide + Pyridoxamine

Pyridoxine + oxygen ↔ Hydrogen peroxide + Pyridoxal

Concentrations

Intracellular Concentrations

Not Available

Extracellular Concentrations

Not Available

Spectra

Spectrum Type	Description	Splash Key	View
GC-MS	GC-MS Spectrum - GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies) (Non-derivatized)	splash10-00di-2690000000-5d018202be238b10582a	JSpectraViewer \| MoNA
GC-MS	GC-MS Spectrum - GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies) (Non-derivatized)	splash10-0aou-3974000000-8c963fdc714896ad343a	JSpectraViewer \| MoNA
GC-MS	GC-MS Spectrum - GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies) (Non-derivatized)	splash10-001j-0590000000-ed8a55680a0c9fa9cbaf	JSpectraViewer \| MoNA
GC-MS	GC-MS Spectrum - GC-MS (1 MEOX; 2 TMS)	splash10-0a4i-5695000000-bd3bb22a5dd4a600cb6c	JSpectraViewer \| MoNA
GC-MS	GC-MS Spectrum - GC-MS (1 MEOX; 2 TMS)	splash10-0aor-5895000000-e55e01ca30d17d2a8a72	JSpectraViewer \| MoNA
GC-MS	GC-MS Spectrum - GC-MS (Non-derivatized)	splash10-0a4i-5695000000-bd3bb22a5dd4a600cb6c	JSpectraViewer \| MoNA
GC-MS	GC-MS Spectrum - GC-MS (Non-derivatized)	splash10-0aor-5895000000-e55e01ca30d17d2a8a72	JSpectraViewer \| MoNA
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	splash10-000i-1900000000-56d1f96c5ac868ce42a6	JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (2 TMS) - 70eV, Positive	splash10-00fs-6190000000-78d7f54ce0c5338f815f	JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	Not Available	JSpectraViewer
LC-MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 10V, Positive (Annotated)	splash10-0002-0900000000-4ce3f52baa36006ef4b2	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 25V, Positive (Annotated)	splash10-00kg-9500000000-658a96f6cda4a96de045	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 40V, Positive (Annotated)	splash10-0gbc-9000000000-233fc8ab067b0dcd1f14	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 10V, Negative	splash10-014i-0900000000-c49b207cafcf1c21302d	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 20V, Negative	splash10-000i-0900000000-cad83f5f123a879fa0bb	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 30V, Negative	splash10-0a4i-0900000000-4f12feae0e11a6d9016b	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 40V, Negative	splash10-0a4i-2900000000-56fcdbb9b4363c84d2d0	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 50V, Negative	splash10-056r-9400000000-9700c9585f6c540bf007	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 10V, Positive	splash10-0gb9-0900000000-e646a99b0c1521d1c8dd	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 20V, Positive	splash10-0udi-0900000000-8fce1a7d8ceb3fced3ed	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 30V, Positive	splash10-0udl-6900000000-e2fc0eaa17e57d0a2556	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 40V, Positive	splash10-00kf-9200000000-0bda29931f8b6f2fcc77	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 50V, Positive	splash10-014l-9000000000-469c127d1aef4f8a51d7	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QTOF (UPLC Q-Tof Premier, Waters) , Positive	splash10-0udi-2900000000-63ebef5a0818d6a1ccb8	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QTOF (UPLC Q-Tof Premier, Waters) , Negative	splash10-05n0-0900000000-f468a00d88bedc116485	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ , negative	splash10-014i-0900000000-c49b207cafcf1c21302d	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ , negative	splash10-000i-0900000000-bf0686eb8e3c28c30e85	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ , negative	splash10-0a4i-0900000000-686848e0f222273e5089	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ , negative	splash10-0a4i-2900000000-99577e7f4a39e47c5c42	JSpectraViewer \| MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-0uxr-0900000000-7f4ef736d1a810b2e8ab	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0udi-0900000000-9c4ead9423b52a47b2fe	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0udi-9500000000-aa6a11948622748c8469	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-014i-0900000000-dd6386614990770eaae5	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-000i-0900000000-e9de9bab2598f0316525	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0abc-9300000000-f4bc767c42577b6a1d5f	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
2D NMR	[1H,13C] 2D NMR Spectrum	Not Available	JSpectraViewer

References

References:

UniProt Consortium (2011). "Ongoing and future developments at the Universal Protein Resource." Nucleic Acids Res 39:D214-D219.21051339
Scheer, M., Grote, A., Chang, A., Schomburg, I., Munaretto, C., Rother, M., Sohngen, C., Stelzer, M., Thiele, J., Schomburg, D. (2011). "BRENDA, the enzyme information system in 2011." Nucleic Acids Res 39:D670-D676.21062828
Herrgard, M. J., Swainston, N., Dobson, P., Dunn, W. B., Arga, K. Y., Arvas, M., Bluthgen, N., Borger, S., Costenoble, R., Heinemann, M., Hucka, M., Le Novere, N., Li, P., Liebermeister, W., Mo, M. L., Oliveira, A. P., Petranovic, D., Pettifer, S., Simeonidis, E., Smallbone, K., Spasic, I., Weichart, D., Brent, R., Broomhead, D. S., Westerhoff, H. V., Kirdar, B., Penttila, M., Klipp, E., Palsson, B. O., Sauer, U., Oliver, S. G., Mendes, P., Nielsen, J., Kell, D. B. (2008). "A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology." Nat Biotechnol 26:1155-1160.18846089

Synthesis Reference:

Fujimoto, Yasuo. Pyridoxal. Jpn. Tokkyo Koho (1971), 2 pp.

External Links:

Resource	Link
CHEBI ID	17310
HMDB ID	HMDB01545
Pubchem Compound ID	1050
Kegg ID	C00250
ChemSpider ID	1021
FOODB ID	FDB011169
Wikipedia	Pyridoxal
BioCyc ID	PYRIDOXAL

Enzymes

Protein Details

1. Putative pyridoxal reductase

General function:: Involved in oxidoreductase activity
Specific function:: Catalyzes the reduction of pyridoxal (PL) with NADPH and oxidation of pyridoxine (PN) with NADP(+)
Gene Name:: Not Available
Uniprot ID:: Q06494
Molecular weight:: 38600.39844

Reactions

Pyridoxine + NADP(+) → pyridoxal + NADPH.

Protein Details

2. Pyridoxamine 5'-phosphate oxidase

General function:: Involved in pyridoxamine-phosphate oxidase activity
Specific function:: Catalyzes the oxidation of either pyridoxine 5'- phosphate (PNP) or pyridoxamine 5'-phosphate (PMP) into pyridoxal 5'-phosphate (PLP)
Gene Name:: PDX3
Uniprot ID:: P38075
Molecular weight:: 26908.0

Reactions

Pyridoxamine 5'-phosphate + H(2)O + O(2) → pyridoxal 5'-phosphate + NH(3) + H(2)O(2).
Pyridoxine 5'-phosphate + O(2) → pyridoxal 5'-phosphate + H(2)O(2).

Protein Details

3. Putative pyridoxal kinase BUD16

General function:: Involved in pyridoxal kinase activity
Specific function:: Required for synthesis of pyridoxal-5-phosphate from vitamin B6. Important for bud site selection
Gene Name:: BUD16
Uniprot ID:: P39988
Molecular weight:: 35558.89844

Reactions

ATP + pyridoxal → ADP + pyridoxal 5'-phosphate.

Protein Details

4. Putative pyridoxal kinase BUD17

General function:: Involved in pyridoxal kinase activity
Specific function:: Required for synthesis of pyridoxal-5-phosphate from vitamin B6. Important for bud site selection
Gene Name:: BUD17
Uniprot ID:: P53727
Molecular weight:: 35366.5

Reactions

ATP + pyridoxal → ADP + pyridoxal 5'-phosphate.

Structure for #<Compound:0xa7f3b8b0>

Enzymes

Reactions

Reactions

Reactions

Reactions