MiMeDB: Showing metabocard for 4-deoxypyridoxine (MMDBc0034224)

Record Information

Version

2.0

Status

Detected and Quantified

Creation Date

2021-11-19 05:21:23 UTC

Update Date

2025-10-07 16:04:12 UTC

Metabolite ID

MMDBc0034224

Metabolite Identification

Common Name

4-deoxypyridoxine

Description

4-deoxypyridoxine is a pyridoxine analog and a member of the vitamin B6 chemical class. Its chemical structure features a pyridine ring with a hydroxymethyl group, which is crucial for its function as a pyridoxal 5'-phosphate (PLP) antagonist. Biologically, 4-deoxypyridoxine is involved in various metabolic pathways, particularly in the inhibition of sphingosine 1-phosphate (S1P) lyase, which has been shown to reduce white gonadal adipose tissue mass and adipocyte size in mice subjected to a high-fat diet (PMID:40193069 ). Additionally, it has been utilized to induce vitamin B6 deficiency in Drosophila, highlighting its role as a PLP antagonist (PMID:40123014 ). The compound has also been implicated in promoting tumorigenesis in larval eye discs by enhancing the aggressiveness of RasV12 tumors when PLP is deficient (PMID:38830901 ). Furthermore, 4-deoxypyridoxine facilitates the replication of BmNPV gDNA, contrasting with the inhibitory effects of exogenous PLP (PMID:38335442 ). Overall, 4-deoxypyridoxine serves as a significant metabolic regulator in various biological contexts.

Structure

MOL 3D MOL SDF 3D SDF PDB 3D PDB SMILES InChI

Synonyms

Value	Source
4-Deoxypyridoxal	ChEBI
4-Deoxypyridoxol	ChEBI
4-Deoxypyridoxine hydrochloride	MeSH
4'-Deoxypyridoxine	MeSH

Molecular Formula

C₈H₁₁NO₂

Average Mass

153.1784

Monoisotopic Mass

153.078978601

IUPAC Name

5-(hydroxymethyl)-2,4-dimethylpyridin-3-ol

Traditional Name

4-deoxypyridoxine

CAS Registry Number

61-67-6

SMILES

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

InChI Identifier

InChI=1S/C8H11NO2/c1-5-7(4-10)3-9-6(2)8(5)11/h3,10-11H,4H2,1-2H3

InChI Key

KKOWAYISKWGDBG-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as methylpyridines. These are organic compounds containing a pyridine ring substituted at one or more positions by a methyl group.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Pyridines and derivatives

Sub Class

Methylpyridines

Direct Parent

Methylpyridines

Alternative Parents

Substituents

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:65083 )
methylpyridines (CHEBI:65083 )
hydroxymethylpyridine (CHEBI:65083 )
a small molecule (CPD0-1605 )

Functional Ontology

Not Available

Physical Properties

State

Not Available

Predicted Properties

Property	Value	Source
Water Solubility	26.3 g/L	ALOGPS
logP	0.38	ALOGPS
logP	0.33	ChemAxon
logS	-0.76	ALOGPS
pKa (Strongest Acidic)	9.41	ChemAxon
pKa (Strongest Basic)	6.67	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	3	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	53.35 Å²	ChemAxon
Rotatable Bond Count	1	ChemAxon
Refractivity	42.33 m³·mol⁻¹	ChemAxon
Polarizability	16.24 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

Spectrum Type	Description	Splash Key	Deposition Date	View
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	splash10-0fki-2900000000-a3edcef5c69870e573df	2016-09-22	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_1) - 70eV, Positive	Not Available	2021-11-03	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_2) - 70eV, Positive	Not Available	2021-11-03	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_1) - 70eV, Positive	Not Available	2021-11-03	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_1_1) - 70eV, Positive	Not Available	2021-11-03	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_1_2) - 70eV, Positive	Not Available	2021-11-03	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_2_1) - 70eV, Positive	Not Available	2021-11-03	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-0udr-0900000000-62a8d714d322b0cdb8e8	2016-09-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-000i-0900000000-19ca6ebc25595510c2f8	2016-09-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-000i-8900000000-079638c46f89394afb44	2016-09-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-0udi-0900000000-25a3c61fd43aa1153bc7	2016-09-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-00di-1900000000-ced02b30c4af935e937c	2016-09-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0a4l-9400000000-ebe23da130757602666e	2016-09-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-0udi-0900000000-e0734431831e40cae6ea	2021-10-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-000i-1900000000-1d9b31b8ff6d0488c995	2021-10-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0159-9500000000-b418894e2a51f092a978	2021-10-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-0ul0-0900000000-c0d52586faf96092b02f	2021-10-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-00di-1900000000-de42a01e1aa5fedc36ca	2021-10-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0aor-9700000000-b0890434768e750df593	2021-10-12	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)		2021-10-13	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, D₂O, predicted)		2021-10-13	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)		2021-10-13	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, D₂O, predicted)		2021-10-13	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)		2021-10-13	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, D₂O, predicted)		2021-10-13	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)		2021-10-13	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, D₂O, predicted)		2021-10-13	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)		2021-10-13	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, D₂O, predicted)		2021-10-13	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, predicted)		2021-10-13	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)		2021-10-13	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, D₂O, predicted)		2021-10-13	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)		2021-10-13	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, D₂O, predicted)		2021-10-13	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)		2021-10-13	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)		2021-10-13	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, D₂O, predicted)		2021-10-13	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)		2021-10-13	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, predicted)		2021-10-13	View Spectrum

Chromatographic Retention Times and Retention Indices

Retention Times

Chromatography Type	Technique	Column	Deposition Date	Retention Time (s)
Liquid Chromatography	HILIC	Waters Acquity UPLC-BEH Amide column (eluted)	2025-10-24	177.9
Liquid Chromatography	HILIC	Accucore 150 Amide HILIC (eluted)	2025-10-24	75.7
Liquid Chromatography	Reversed-phase	Hypersil Gold 1.9 µm C18 (void)	2025-10-24	49.5
Liquid Chromatography	Reversed-phase	Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) (eluted)	2025-10-24	287.8
Liquid Chromatography	Reversed-phase	XBridge C18 3.5u 2.1x50 mm (eluted)	2025-10-24	268.5
Liquid Chromatography	Reversed-phase	Ascentis Express C18 (void)	2025-10-24	284.6
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (eluted)	2025-10-24	449.3
Liquid Chromatography	HILIC	Merck SeQuant ZIC-HILIC (void)	2025-10-24	330.1
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC (eluted)	2025-10-24	398.7
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (eluted)	2025-10-24	160.9
Liquid Chromatography	HILIC	Merck SeQuant ZIC-HILIC (eluted)	2025-10-24	374.7
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (eluted)	2025-10-24	159.8
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (eluted)	2025-10-24	91.2
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC column (eluted)	2025-10-24	327.0
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC column (eluted)	2025-10-24	442.3
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (eluted)	2025-10-24	44.6
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (void)	2025-10-24	214.9
Liquid Chromatography	Reversed-phase	Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex (eluted)	2025-10-24	866.3
Liquid Chromatography	Reversed-phase	Waters Atlantis T3 (2.1 x 150 mm, 5 um) (eluted)	2025-10-24	628.5

Retention Indices

Chromatography Type	Peak Label	SMILES	Stationary Phase	Deposition Date	Retention Index
Gas Chromatography	4-deoxypyridoxine_TMS_1	CC1=NC=C(CO[Si](C)(C)C)C(C)=C1O	standard non polar	2025-10-24	2197.82
Gas Chromatography	4-deoxypyridoxine_TMS_2	CC1=NC=C(CO)C(C)=C1O[Si](C)(C)C	standard non polar	2025-10-24	1941.28
Gas Chromatography	4-deoxypyridoxine_TMS_3	CC1=NC=C(CO[Si](C)(C)C)C(C)=C1O[Si](C)(C)C	standard non polar	2025-10-24	1600.09
Gas Chromatography	4-deoxypyridoxine_TMS_1	CC1=NC=C(CO[Si](C)(C)C)C(C)=C1O	standard polar	2025-10-24	2040.33
Gas Chromatography	4-deoxypyridoxine_TMS_2	CC1=NC=C(CO)C(C)=C1O[Si](C)(C)C	standard polar	2025-10-24	1937.44
Gas Chromatography	4-deoxypyridoxine_TMS_3	CC1=NC=C(CO[Si](C)(C)C)C(C)=C1O[Si](C)(C)C	standard polar	2025-10-24	2050.08

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Not Available

Tissue Locations

Not Available

Associated OMIM IDs

114500 (Colorectal cancer)
610247 (Eosinophilic esophagitis)

Human Proteins and Enzymes

Protein ID	Protein Name	Protein Type	Uniprot ID	Species

Human Pathways

Pathways

Name	SMPDB/PathBank

Microbial Pathways

Pathways

Not Available

Metabolic Reactions

Reactions

This table shows at most 20 reactions. For the full list of associated reactions:

See All Associated Reactions

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference

Health Effects and Bioactivity

Health Outcome/Bioactivity	Metabolite Response/Effect	Evidence Type	Host and Biospecimen	Data Source	Reference

Microbial Sources

Superkingdom/Kingdom	Phylum	Total species	Hosts and Body Sites	Microbial Links
Eukaryota/Fungi	Ascomycota	1	Human feces; Human saliva	Unknown

Exposure Sources

Other Exposures

Source Type	Data Source	Reference

Host Biospecimen and Location

Host and Biospecimen	Status	Mean	Std	Min	Max	Units	Age	Sex	Health Condition	Data Source	Reference

External Links

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

5869

KEGG Compound ID

Not Available

BioCyc ID

CPD0-1605

BiGG ID

Not Available

Wikipedia Link

4-Deoxypyridoxine

METLIN ID

Not Available

PubChem Compound

Not Available

PDB ID

Not Available

ChEBI ID

65083

Food Biomarker Ontology

Not Available

CMMC Knowledgebase

Not Available

General References

Barupal DK, Fiehn O: Generating the Blood Exposome Database Using a Comprehensive Text Mining and Database Fusion Approach. Environ Health Perspect. 2019 Sep;127(9):97008. doi: 10.1289/EHP4713. Epub 2019 Sep 26. [PubMed:31557052 ]

Showing metabocard for 4-deoxypyridoxine (MMDBc0034224)

MOL for #<Metabolite:0x00007f9ab714afb0>

3D MOL for #<Metabolite:0x00007f9ab714afb0>

3D SDF for #<Metabolite:0x00007f9ab714afb0>

3D-SDF for #<Metabolite:0x00007f9ab714afb0>

PDB for #<Metabolite:0x00007f9ab714afb0>

3D PDB for #<Metabolite:0x00007f9ab714afb0>

SMILES for #<Metabolite:0x00007f9ab714afb0>

INCHI for #<Metabolite:0x00007f9ab714afb0>

Structure for #<Metabolite:0x00007f9ab714afb0>

3D Structure for #<Metabolite:0x00007f9ab714afb0>