Cannabis Compound Database: Showing Compound Card for Pyridoxine (CDB005285)

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Record Information

Version

1.0

Created at

2020-04-17 19:27:51 UTC

Updated at

2020-12-07 19:11:54 UTC

CannabisDB ID

CDB005285

Secondary Accession Numbers

Not Available

Cannabis Compound Identification

Common Name

Pyridoxine

Description

Pyridoxine, also known as pyridoxol or vitamin B6, belongs to the class of organic compounds known as pyridoxines. These are pyridoxal derivatives in which the carbaldehyde group at position 2 of the pyridoxal moiety is replaced by a hydroxymethyl group. Pyridoxine is a very strong basic compound (based on its pKa). Pyridoxine exists in all living species, ranging from bacteria to humans. Within humans, pyridoxine participates in a number of enzymatic reactions. In particular, pyridoxine can be converted into pyridoxal; which is catalyzed by the enzyme pyridoxine-5'-phosphate oxidase. In addition, pyridoxine can be converted into pyridoxine 5'-phosphate through its interaction with the enzyme pyridoxal kinase. In humans, pyridoxine is involved in vitamin B6 metabolism. Outside of the human body, Pyridoxine is found, on average, in the highest concentration within a few different foods, such as common sages, tarragons, and summer savories and in a lower concentration in hushpuppies, alaska pollocks, and clupeinae (herring, sardine, sprat). Pyridoxine has also been detected, but not quantified in, several different foods, such as ucuhuba, pikeperchs, whiskies, fruit gums, and ginsengs. This could make pyridoxine a potential biomarker for the consumption of these foods. Pyridoxine is a potentially toxic compound. Pyridoxine is expected to be in Cannabis as all living plants are known to produce and metabolize it.

Structure

MOL SDF PDB SMILES InChI

Synonyms

Value	Source
2-Methyl-3-hydroxy-4,5-dihydroxymethylpyridine	ChEBI
3-Hydroxy-4,5-bis(hydroxymethyl)-2-methylpyridine	ChEBI
3-Hydroxy-4,5-dimethylol-alpha-picoline	ChEBI
5-Hydroxy-6-methyl-3,4-pyridinedimethanol	ChEBI
Pyridoxol	ChEBI
Vitamin b6	ChEBI
3-Hydroxy-4,5-dimethylol-a-picoline	Generator
3-Hydroxy-4,5-dimethylol-α-picoline	Generator
2-Methyl-3-hydroxy-4,5-bis(hydroxymethyl)pyridine	HMDB
2-Methyl-3-hydroxy-4,5-di(hydroxymethyl)pyridine	HMDB
2-Methyl-4,5-bis(hydroxymethyl)-3-hydroxypyridine	HMDB
3-Hydroxy-2-picoline-4,5-dimethanol	HMDB
Adermine	HMDB
Gravidox	HMDB
Hydoxin	HMDB
Piridossina	HMDB
Piridoxina	HMDB
Pyridoxin	HMDB
Pyridoxinum	HMDB
Pyridoxolum	HMDB
Pyridoxol hydrochloride	HMDB
Rodex	HMDB
Pyridoxine hydrochloride	HMDB

Chemical Formula

C₈H₁₁NO₃

Average Molecular Weight

169.18

Monoisotopic Molecular Weight

169.0739

IUPAC Name

4,5-bis(hydroxymethyl)-2-methylpyridin-3-ol

Traditional Name

pyridoxine

CAS Registry Number

65-23-6

SMILES

CC1=C(O)C(CO)=C(CO)C=N1

InChI Identifier

InChI=1S/C8H11NO3/c1-5-8(12)7(4-11)6(3-10)2-9-5/h2,10-12H,3-4H2,1H3

InChI Key

LXNHXLLTXMVWPM-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as pyridoxines. These are pyridoxal derivatives in which the carbaldehyde group at position 2 of the pyridoxal moiety is replaced by a hydroxymethyl group.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Pyridines and derivatives

Sub Class

Pyridoxines

Direct Parent

Pyridoxines

Alternative Parents

Substituents

Pyridoxine
Methylpyridine
Hydroxypyridine
Heteroaromatic compound
Azacycle
Organic nitrogen compound
Organic oxygen compound
Organopnictogen compound
Hydrocarbon derivative
Aromatic alcohol
Primary alcohol
Organooxygen compound
Organonitrogen compound
Alcohol
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

monohydroxypyridine (CHEBI:16709 )
methylpyridines (CHEBI:16709 )
vitamin B6 (CHEBI:16709 )
hydroxymethylpyridine (CHEBI:16709 )
Water-soluble vitamins (C00314 )
a vitamin B6 (PYRIDOXINE )

Ontology

Physiological effect

Health effect:

Health condition:

Homozygous sickle cell disease

Gastrointestinal disorders:

Diarrhea

Musculoskeletal and connective tissue disorders:

Muscle weakness

Intramuscular

Source:

Synthetic:

Personal care product

Biological:

Animal

Plant:

Biological location:

Organ and components:

Liver

Biofluid and excreta:

Cell and elements:

Extracellular

Role

Industrial application:

Pharmaceutical industry:

Pharmaceutical

Physical Properties

State

Solid

Experimental Properties

Property	Value	Reference
Melting Point	159 - 162 °C	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	79 mg/mL	Not Available
logP	-0.77	SANGSTER (1993)

Predicted Properties

Property	Value	Source
logP	-0.57	ALOGPS
logP	-0.95	ChemAxon
logS	-1	ALOGPS
pKa (Strongest Acidic)	9.4	ChemAxon
pKa (Strongest Basic)	5.58	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	73.58 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	44.11 m³·mol⁻¹	ChemAxon
Polarizability	17.11 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

EI-MS/GC-MS

Type	Description	Splash Key	View
EI-MS	Mass Spectrum (Electron Ionization)	splash10-1003-6900000000-1237eaf82dfadfd54d4b	2014-09-20	View Spectrum
GC-MS	Pyridoxine, 3 TMS, GC-MS Spectrum	splash10-000t-0940000000-30b4702623a6d8fcb4bb	Spectrum
GC-MS	Pyridoxine, non-derivatized, GC-MS Spectrum	splash10-001j-0690000000-0581e2b42fa48c1ea498	Spectrum
GC-MS	Pyridoxine, 3 TMS, GC-MS Spectrum	splash10-00di-9330000000-32929ff06762b9f5887f	Spectrum
GC-MS	Pyridoxine, 3 TMS, GC-MS Spectrum	splash10-001i-0490000000-34a09ddbbb462aeb02a6	Spectrum
GC-MS	Pyridoxine, non-derivatized, GC-MS Spectrum	splash10-0f6x-9400000000-486db54a30b61c2eb9d4	Spectrum
GC-MS	Pyridoxine, non-derivatized, GC-MS Spectrum	splash10-000t-0940000000-30b4702623a6d8fcb4bb	Spectrum
GC-MS	Pyridoxine, non-derivatized, GC-MS Spectrum	splash10-001j-0690000000-0581e2b42fa48c1ea498	Spectrum
GC-MS	Pyridoxine, non-derivatized, GC-MS Spectrum	splash10-00di-9330000000-32929ff06762b9f5887f	Spectrum
GC-MS	Pyridoxine, non-derivatized, GC-MS Spectrum	splash10-001i-0490000000-34a09ddbbb462aeb02a6	Spectrum
GC-MS	Pyridoxine, non-derivatized, GC-MS Spectrum	splash10-001j-0790000000-6f8f6e679e03f9119a65	Spectrum
Predicted GC-MS	Pyridoxine, non-derivatized, Predicted GC-MS Spectrum - 70eV, Positive	splash10-0f79-0900000000-0f727b3e23c2481951e8	Spectrum
Predicted GC-MS	Pyridoxine, 3 TMS, Predicted GC-MS Spectrum - 70eV, Positive	splash10-00di-7079000000-2f143e187cb8c078f936	Spectrum
Predicted GC-MS	Pyridoxine, non-derivatized, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Pyridoxine, non-derivatized, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Pyridoxine, TMS_1_1, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Pyridoxine, TMS_1_2, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Pyridoxine, TMS_1_3, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Pyridoxine, TMS_2_1, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Pyridoxine, TMS_2_2, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Pyridoxine, TMS_2_3, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Pyridoxine, TBDMS_1_1, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Pyridoxine, TBDMS_1_2, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Pyridoxine, TBDMS_1_3, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Pyridoxine, TBDMS_2_1, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Pyridoxine, TBDMS_2_2, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum

MS/MS

Type	Description	Splash Key	View
MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 10V, Positive (Annotated)	splash10-0vi0-0900000000-bd0de86c072765a5caad	2012-07-24	View Spectrum
MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 25V, Positive (Annotated)	splash10-001i-3900000000-2018b406a3c75213b733	2012-07-24	View Spectrum
MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 40V, Positive (Annotated)	splash10-0059-9200000000-e69bb531deb2a103a476	2012-07-24	View Spectrum
MS/MS	LC-MS/MS Spectrum - EI-B (HITACHI M-80) , Positive	splash10-0f6x-9400000000-77c43a946c4ae1abf3b9	2012-08-31	View Spectrum
MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 10V, Negative	splash10-014i-0900000000-479d4492cc8d634fa366	2012-08-31	View Spectrum
MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 20V, Negative	splash10-0udi-0900000000-486d6a4e5e1a731b7c54	2012-08-31	View Spectrum
MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 30V, Negative	splash10-05fr-0900000000-4ef09ce9c04561a1085e	2012-08-31	View Spectrum
MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 40V, Negative	splash10-0ab9-1900000000-3298adf6db36689d5d43	2012-08-31	View Spectrum
MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 50V, Negative	splash10-0a6r-7900000000-6711954ee96f08344434	2012-08-31	View Spectrum
MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 10V, Positive	splash10-00di-0900000000-234e90d43a7febd7a098	2012-08-31	View Spectrum
MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 20V, Positive	splash10-0udi-0900000000-137080765c0035b45258	2012-08-31	View Spectrum
MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 30V, Positive	splash10-001i-0900000000-882ee900a8bba08e2c7c	2012-08-31	View Spectrum
MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 40V, Positive	splash10-003r-8900000000-e0e11797b63cea991d81	2012-08-31	View Spectrum
MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 50V, Positive	splash10-0059-9100000000-c25384179219411af02c	2012-08-31	View Spectrum
MS/MS	LC-MS/MS Spectrum - LC-ESI-QTOF (UPLC Q-Tof Premier, Waters) , Positive	splash10-0ue9-0900000000-c0e149ce890192397b7f	2012-08-31	View Spectrum
MS/MS	LC-MS/MS Spectrum - LC-ESI-QTOF (UPLC Q-Tof Premier, Waters) , Negative	splash10-0v4i-0900000000-f9f378af3d47ab006806	2012-08-31	View Spectrum
MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ , negative	splash10-014i-0900000000-479d4492cc8d634fa366	2017-09-14	View Spectrum
MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ , negative	splash10-0udi-0900000000-486d6a4e5e1a731b7c54	2017-09-14	View Spectrum
MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ , negative	splash10-05fr-0900000000-4ef09ce9c04561a1085e	2017-09-14	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-0uk9-0900000000-eab5b3411261744df750	2015-05-26	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0ue9-0900000000-cc4dc8719602182ef1eb	2015-05-26	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-001i-5900000000-1c2637733578fcdd7c6a	2015-05-26	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-014i-0900000000-e89cc69d8b21012ff982	2015-05-27	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-059i-0900000000-0ad8d09e042015cb2e33	2015-05-27	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0a4i-9500000000-577a3d87899ca47d539f	2015-05-27	View Spectrum

NMR

Type	Description	View
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, experimental)	Spectrum
1D NMR	¹H NMR Spectrum (1D, D₂O, experimental)	Spectrum
1D NMR	¹³C NMR Spectrum (1D, D₂O, experimental)	Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	Spectrum
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, D₂O, predicted)	Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, D₂O, predicted)	Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	Spectrum
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, D₂O, predicted)	Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, D₂O, predicted)	Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	Spectrum
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, predicted)	Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	Spectrum
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, D₂O, predicted)	Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	Spectrum
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, D₂O, predicted)	Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	Spectrum
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, D₂O, predicted)	Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, predicted)	Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	Spectrum
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	Spectrum
2D NMR	[¹H, ¹H]-TOCSY. Unexported temporarily by An Chi on Oct 15, 2021 until json or nmrML file is generated. 2D NMR Spectrum (experimental)	Spectrum
2D NMR	[¹H, ¹³C]-HSQC NMR Spectrum (2D, 600 MHz, H₂O, experimental)	Spectrum

Pathways

Name	SMPDB/Pathwhiz	KEGG
Vitamin B6 Metabolism
Hypophosphatasia		Not Available

Protein Targets

Enzymes

Protein Name	Gene Name	Locus	Uniprot ID	Details
Methylenetetrahydrofolate reductase	MTHFR	1p36.3	P42898	details
Alpha-aminoadipic semialdehyde dehydrogenase	ALDH7A1	5q31	P49419	details
Pyridoxine-5'-phosphate oxidase	PNPO	17q21.32	Q9NVS9	details
Cystathionine beta-synthase	CBS	21q22.3	P35520	details
Phosphoserine aminotransferase	PSAT1	9q21.2	Q9Y617	details
Pyridoxal kinase	PDXK	21q22.3	O00764	details
Pyridoxal phosphate phosphatase	PDXP	22q12.3	Q96GD0	details
Pyridoxal phosphate phosphatase PHOSPHO2	PHOSPHO2	2q31.1	Q8TCD6	details

Transporters

Not Available

Metal Bindings

Protein Name	Gene Name	Locus	Uniprot ID	Details
Cystathionine beta-synthase	CBS	21q22.3	P35520	details
Pyridoxal phosphate phosphatase	PDXP	22q12.3	Q96GD0	details
Pyridoxal phosphate phosphatase PHOSPHO2	PHOSPHO2	2q31.1	Q8TCD6	details

Receptors

Not Available

Transcriptional Factors

Not Available

Concentrations Data

Not Available

External Links

HMDB ID

HMDB0000239

DrugBank ID

DB00165

Phenol Explorer Compound ID

Not Available

FoodDB ID

KNApSAcK ID

Chemspider ID

KEGG Compound ID

BioCyc ID

BiGG ID

Not Available

Wikipedia Link

Pyridoxine

METLIN ID

Not Available

PubChem Compound

1054

PDB ID

Not Available

ChEBI ID

16709

References

General References

Not Available

Only showing the first 10 proteins. There are 11 proteins in total.

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Enzymes

Enzyme Details

1. Methylenetetrahydrofolate reductase

General function:: Involved in methylenetetrahydrofolate reductase (NADPH) activity
Specific function:: Catalyzes the conversion of 5,10-methylenetetrahydrofolate to 5-methyltetrahydrofolate, a co-substrate for homocysteine remethylation to methionine.
Gene Name:: MTHFR
Uniprot ID:: P42898
Molecular weight:: 74595.895

Enzyme Details

2. Alpha-aminoadipic semialdehyde dehydrogenase

General function:: Involved in oxidoreductase activity
Specific function:: Multifunctional enzyme mediating important protective effects. Metabolizes betaine aldehyde to betaine, an important cellular osmolyte and methyl donor. Protects cells from oxidative stress by metabolizing a number of lipid peroxidation-derived aldehydes. Involved in lysine catabolism.
Gene Name:: ALDH7A1
Uniprot ID:: P49419
Molecular weight:: 58486.74

Enzyme Details

3. Pyridoxine-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:: PNPO
Uniprot ID:: Q9NVS9
Molecular weight:: 29987.79

Enzyme Details

4. Cystathionine beta-synthase

General function:: Involved in cysteine biosynthetic process from serine
Specific function:: Only known pyridoxal phosphate-dependent enzyme that contains heme. Important regulator of hydrogen sulfide, especially in the brain, utilizing cysteine instead of serine to catalyze the formation of hydrogen sulfide. Hydrogen sulfide is a gastratransmitter with signaling and cytoprotective effects such as acting as a neuromodulator in the brain to protect neurons against hypoxic injury (By similarity).
Gene Name:: CBS
Uniprot ID:: P35520
Molecular weight:: 60586.05

Enzyme Details

5. Phosphoserine aminotransferase

General function:: Involved in metabolic process
Specific function:: Catalyzes the reversible conversion of 3-phosphohydroxypyruvate to phosphoserine and of 3-hydroxy-2-oxo-4-phosphonooxybutanoate to phosphohydroxythreonine (By similarity).
Gene Name:: PSAT1
Uniprot ID:: Q9Y617
Molecular weight:: 35188.305

Enzyme Details

6. Pyridoxal kinase

General function:: Involved in pyridoxal kinase activity
Specific function:: Required for synthesis of pyridoxal-5-phosphate from vitamin B6.
Gene Name:: PDXK
Uniprot ID:: O00764
Molecular weight:: 35102.105

Enzyme Details

7. Pyridoxal phosphate phosphatase

General function:: Involved in catalytic activity
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. Pyridoxal phosphate phosphatase. Has some activity towards pyridoxal 5'-phosphate (PLP), pyridoxine 5'-phosphate (PMP) and pyridoxine 5'-phosphate (PNP), with a highest activity with PLP followed by PNP.
Gene Name:: PDXP
Uniprot ID:: Q96GD0
Molecular weight:: 31697.735

Enzyme Details

8. Pyridoxal phosphate phosphatase PHOSPHO2

General function:: Involved in phosphatase activity
Specific function:: Phosphatase that has high activity toward pyridoxal 5'-phosphate (PLP). Also active at much lower level toward pyrophosphate, phosphoethanolamine (PEA), phosphocholine (PCho), phospho-l-tyrosine, fructose-6-phosphate, p-nitrophenyl phosphate, and h-glycerophosphate.
Gene Name:: PHOSPHO2
Uniprot ID:: Q8TCD6
Molecular weight:: 27768.72

Only showing the first 10 proteins. There are 11 proteins in total.

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Showing Compound Card for Pyridoxine (CDB005285)

Structure for CDB005285 (Pyridoxine)

Enzymes