Pyridoxal 5'-phosphate (YMDB00363)

Identification

YMDB ID

YMDB00363

Name

Pyridoxal 5'-phosphate

Species

Saccharomyces cerevisiae

Strain

Baker's yeast

Description

Pyridoxal 5'-phosphate, also known as phosphopyridoxal or PLP, 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 5'-phosphate is a strong basic compound (based on its pKa). Pyridoxal 5'-phosphate exists in all living species, ranging from bacteria to humans. Pyridoxal 5'-phosphate is a potentially toxic compound.

Structure

MOL SDF PDB SMILES InChI

Synonyms

Apolon B6
Biosechs
Codecarboxylase
Coenzyme B6
Hairoxal
Hexermin-P
Hi-Pyridoxin
Hiadelon
Himitan
PAL-P
Phosphopyridoxal
Phosphopyridoxal coenzyme
Pidopidon
Piodel
PLP
Pydoxal
Pyridoxal 5-phosphate
Pyridoxal 5'-phosphate
Pyridoxal 5'-phosphic acid
Pyridoxal P
Pyridoxal phosphate
Pyridoxal-P
Pyridoxyl phosphate
Pyromijin
Sechvitan
Vitahexin-P
Vitazechs
3-Hydroxy-2-methyl-5-[(phosphonooxy)methyl]-4-pyridinecarboxaldehyde
3-Hydroxy-5-(hydroxymethyl)-2-methylisonicotinaldehyde 5-phosphate
Phosphoric acid mono-(4-formyl-5-hydroxy-6-methyl-pyridin-3-ylmethyl) ester
Pyridoxal 5'-(dihydrogen phosphate)
Pyridoxal 5-monophosphoric acid ester
PYRIDOXAL-5'-phosphATE
3-Hydroxy-5-(hydroxymethyl)-2-methylisonicotinaldehyde 5-phosphoric acid
Phosphate mono-(4-formyl-5-hydroxy-6-methyl-pyridin-3-ylmethyl) ester
Pyridoxal 5'-(dihydrogen phosphoric acid)
Pyridoxal 5-monophosphate ester
Pyridoxal 5-phosphoric acid
Pyridoxal phosphoric acid
PYRIDOXAL-5'-phosphoric acid
Pyridoxal 5'-phosphoric acid
Phosphate, pyridoxal
Pyridoxal 5 phosphate

CAS number

54-47-7

Weight

Average: 247.1419
Monoisotopic: 247.024573569

InChI Key

NGVDGCNFYWLIFO-UHFFFAOYSA-N

InChI

InChI=1S/C8H10NO6P/c1-5-8(11)7(3-10)6(2-9-5)4-15-16(12,13)14/h2-3,11H,4H2,1H3,(H2,12,13,14)

IUPAC Name

[(4-formyl-5-hydroxy-6-methylpyridin-3-yl)methoxy]phosphonic acid

Traditional IUPAC Name

pyridoxal phosphate

Chemical Formula

C₈H₁₀NO₆P

SMILES

[H]OC1=C(C([H])=O)C(=C([H])N=C1C([H])([H])[H])C([H])([H])OP(=O)(O[H])O[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
Monoalkyl phosphate
Hydroxypyridine
Methylpyridine
Organic phosphoric acid derivative
Phosphoric acid ester
Alkyl phosphate
Vinylogous acid
Heteroaromatic compound
Azacycle
Organopnictogen compound
Aldehyde
Organic oxygen compound
Organic nitrogen compound
Organooxygen compound
Organonitrogen compound
Hydrocarbon derivative
Organic oxide
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

monohydroxypyridine (CHEBI:18405 )
pyridinecarbaldehyde (CHEBI:18405 )
methylpyridines (CHEBI:18405 )
vitamin B6 phosphate (CHEBI:18405 )

Physical Properties

State

Solid

Charge

Melting point

255 °C

Experimental Properties

Property	Value	Reference
Water Solubility	28 mg/mL [HMP experimental]	PhysProp
LogP	Not Available	PhysProp

Predicted Properties

Property	Value	Source
Water Solubility	5.7 g/L	ALOGPS
logP	-0.55	ALOGPS
logP	-2.1	ChemAxon
logS	-1.6	ALOGPS
pKa (Strongest Acidic)	1.68	ChemAxon
pKa (Strongest Basic)	4.11	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	6	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	116.95 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	54.75 m³·mol⁻¹	ChemAxon
Polarizability	20.9 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

Porphyrin Metabolism	PW002462
Sphingolipid metabolism	PW002479
Starch and sucrose metabolism	PW002481
Sulfur metabolism	PW002483
Vitamin B6	PW002488

KEGG Pathways

Sphingolipid metabolism	ec00600
Starch and sucrose metabolism	ec00500
Sulfur metabolism	ec00920
Vitamin B6 metabolism	ec00750

SMPDB Reactions

Pyridoxal 5'-phosphate → 4-amino-2-methyl-5-diphosphomethylpyrimidine

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

Pyridoxine 5'-phosphate + oxygen → Pyridoxal 5'-phosphate + Hydrogen peroxide

Pyridoxamine 5'-phosphate + oxygen + water → Pyridoxal 5'-phosphate + Hydrogen peroxide + Ammonium

KEGG Reactions

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

water + Pyridoxamine 5'-phosphate + oxygen → Pyridoxal 5'-phosphate + Hydrogen peroxide + Ammonium

Pyridoxine 5'-phosphate + oxygen ↔ Pyridoxal 5'-phosphate + Hydrogen peroxide

Concentrations

Intracellular Concentrations

Not Available

Extracellular Concentrations

Not Available

Spectra

Spectrum Type	Description	Splash Key	View
GC-MS	GC-MS Spectrum - GC-MS (1 MEOX; 3 TMS)	splash10-0gb9-2690000000-c9bacb7e657461e28407	JSpectraViewer \| MoNA
GC-MS	GC-MS Spectrum - GC-MS (Non-derivatized)	splash10-0gb9-2690000000-c9bacb7e657461e28407	JSpectraViewer \| MoNA
GC-MS	GC-MS Spectrum - GC-EI-TOF (Non-derivatized)	splash10-004j-0910000000-0408f3957221fc9882cd	JSpectraViewer \| MoNA
GC-MS	GC-MS Spectrum - GC-EI-TOF (Non-derivatized)	splash10-0gb9-1790000000-b01115fa8b4cfd3612c7	JSpectraViewer \| MoNA
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	splash10-0002-9520000000-bfd574b2e5355694902a	JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (1 TMS) - 70eV, Positive	splash10-006t-9152000000-26c9f631195663322986	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)	splash10-0f6t-0690000000-4aa57f3f28f0bdef9dcf	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 25V, Positive (Annotated)	splash10-0fxx-8900000000-ee972556340c61650528	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 40V, Positive (Annotated)	splash10-014l-9100000000-3cc29fb51820adecd59c	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 10V, Negative	splash10-0002-0090000000-9b86e80a9dd0de14ab59	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 20V, Negative	splash10-03dj-9800000000-9313aa9cbf19bc6311c5	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 30V, Negative	splash10-0002-9500000000-7ce120a58879e2214ce5	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 40V, Negative	splash10-004j-9200000000-7e6bd8c298613e59fb5d	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 50V, Negative	splash10-004i-9000000000-4c05178b1645bf01f3fa	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QTOF (UPLC Q-Tof Premier, Waters) , Positive	splash10-0udi-3920000000-6c5e6106f5658d1d6c50	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QTOF (UPLC Q-Tof Premier, Waters) , Positive	splash10-0udi-3920000000-f96097815e6922356131	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QTOF (UPLC Q-Tof Premier, Waters) , Negative	splash10-002b-9000000000-2c4e243699a95e3a0f88	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QTOF (UPLC Q-Tof Premier, Waters) , Negative	splash10-002b-9000000000-8aa111485891af9f0d02	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ , negative	splash10-0002-0090000000-9b86e80a9dd0de14ab59	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ , negative	splash10-03dj-9800000000-9313aa9cbf19bc6311c5	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ , negative	splash10-0002-9500000000-7ce120a58879e2214ce5	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ , negative	splash10-004j-9200000000-7e6bd8c298613e59fb5d	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ , negative	splash10-004i-9000000000-4c05178b1645bf01f3fa	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QTOF , negative	splash10-002b-9000000000-2c4e243699a95e3a0f88	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QTOF , negative	splash10-002b-9000000000-8aa111485891af9f0d02	JSpectraViewer \| MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-0f6t-1790000000-1dcb07cd1110c71f7005	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0udi-0900000000-ca6aab7f31a36863a417	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0udi-9800000000-053802b9c0533d7943ea	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-0002-9080000000-12ca63d34d39d59f6b42	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-004i-9000000000-144099ec201adbbc4684	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-004i-9000000000-70a9559d65e78c488e7e	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	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
2D NMR	[1H,1H] 2D 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:

Not Available

External Links:

Resource	Link
CHEBI ID	18405
HMDB ID	HMDB01491
Pubchem Compound ID	1051
Kegg ID	C00018
ChemSpider ID	1022
FOODB ID	FDB021820
Wikipedia	Pyridoxal_phosphate
BioCyc ID	PYRIDOXAL_PHOSPHATE

Enzymes

Protein Details

1. 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

2. 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

3. 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:0xa760c0b4>

Enzymes

Reactions

Reactions

Reactions