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Record Information

Version

5.0

Status

Detected but not Quantified

Creation Date

2021-09-10 23:25:49 UTC

Update Date

2021-09-26 22:55:28 UTC

HMDB ID

HMDB0246408

Secondary Accession Numbers

None

Metabolite Identification

Common Name

4-Deoxypyridoxine

Description

4-deoxypyridoxine 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. 4-deoxypyridoxine is a secondary metabolite. Secondary metabolites are metabolically or physiologically non-essential metabolites that may serve a role as defense or signalling molecules. In some cases they are simply molecules that arise from the incomplete metabolism of other secondary metabolites. Based on a literature review very few articles have been published on 4-deoxypyridoxine. This compound has been identified in human blood as reported by (PMID: 31557052 ). 4-deoxypyridoxine is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically 4-Deoxypyridoxine is part of the human exposome. The exposome can be defined as the collection of all the exposures of an individual in a lifetime and how those exposures relate to health. An individual's exposure begins before birth and includes insults from environmental and occupational sources.

Structure

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

View in JSmol View NMR Assignments View Stereo Labels

Synonyms

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

Chemical Formula

C₈H₁₁NO₂

Average Molecular Weight

153.1784

Monoisotopic Molecular Weight

153.078978601

IUPAC Name

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

Traditional Name

4-deoxypyridoxine

CAS Registry Number

Not Available

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 )

Ontology

Physiological effect

Not Available

Disposition

Biological location

Non-excretory biofluid

Biofluid or Excreta

Blood (PMID: 31557052)

Process

Not Available

Role

Not Available

Physical Properties

State

Not Available

Experimental Molecular Properties

Property	Value	Reference
Melting Point	Not Available	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	Not Available	Not Available
LogP	Not Available	Not Available

Experimental Chromatographic Properties

Not Available

Predicted Molecular Properties

Property	Value	Source
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

Predicted Chromatographic Properties

Predicted Collision Cross Sections

Predictor	Adduct Type	CCS Value (Å²)	Reference
DeepCCS	[M+H]+	138.982	30932474
DeepCCS	[M-H]-	136.415	30932474
DeepCCS	[M-2H]-	172.772	30932474
DeepCCS	[M+Na]+	148.065	30932474
AllCCS	[M+H]+	135.9	32859911
AllCCS	[M+H-H2O]+	131.6	32859911
AllCCS	[M+NH4]+	139.8	32859911
AllCCS	[M+Na]+	140.9	32859911
AllCCS	[M-H]-	131.9	32859911
AllCCS	[M+Na-2H]-	133.6	32859911
AllCCS	[M+HCOO]-	135.5	32859911

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
4-Deoxypyridoxine	CC1=NC=C(CO)C(C)=C1O	2567.9	Standard polar	33892256
4-Deoxypyridoxine	CC1=NC=C(CO)C(C)=C1O	1460.2	Standard non polar	33892256
4-Deoxypyridoxine	CC1=NC=C(CO)C(C)=C1O	1561.2	Semi standard non polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted GC-MS	Predicted GC-MS Spectrum - 4-Deoxypyridoxine GC-MS (Non-derivatized) - 70eV, Positive	splash10-0fki-2900000000-a3edcef5c69870e573df	2016-09-22	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 4-Deoxypyridoxine GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 4-Deoxypyridoxine GC-MS (TMS_1_1) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 4-Deoxypyridoxine GC-MS (TMS_1_2) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 4-Deoxypyridoxine GC-MS (TMS_2_1) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 4-Deoxypyridoxine GC-MS (TBDMS_1_1) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 4-Deoxypyridoxine GC-MS (TBDMS_1_2) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 4-Deoxypyridoxine GC-MS (TBDMS_2_1) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum

MS/MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 4-Deoxypyridoxine 10V, Positive-QTOF	splash10-0udr-0900000000-62a8d714d322b0cdb8e8	2016-09-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 4-Deoxypyridoxine 20V, Positive-QTOF	splash10-000i-0900000000-19ca6ebc25595510c2f8	2016-09-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 4-Deoxypyridoxine 40V, Positive-QTOF	splash10-000i-8900000000-079638c46f89394afb44	2016-09-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 4-Deoxypyridoxine 10V, Negative-QTOF	splash10-0udi-0900000000-25a3c61fd43aa1153bc7	2016-09-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 4-Deoxypyridoxine 20V, Negative-QTOF	splash10-00di-1900000000-ced02b30c4af935e937c	2016-09-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 4-Deoxypyridoxine 40V, Negative-QTOF	splash10-0a4l-9400000000-ebe23da130757602666e	2016-09-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 4-Deoxypyridoxine 10V, Positive-QTOF	splash10-0udi-0900000000-e0734431831e40cae6ea	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 4-Deoxypyridoxine 20V, Positive-QTOF	splash10-000i-1900000000-1d9b31b8ff6d0488c995	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 4-Deoxypyridoxine 40V, Positive-QTOF	splash10-0159-9500000000-b418894e2a51f092a978	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 4-Deoxypyridoxine 10V, Negative-QTOF	splash10-0ul0-0900000000-c0d52586faf96092b02f	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 4-Deoxypyridoxine 20V, Negative-QTOF	splash10-00di-1900000000-de42a01e1aa5fedc36ca	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 4-Deoxypyridoxine 40V, Negative-QTOF	splash10-0aor-9700000000-b0890434768e750df593	2021-10-12	Wishart Lab	View Spectrum

NMR Spectra

Spectrum Type	Description	Deposition Date	Source	View
Predicted 1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Blood

Tissue Locations

Not Available

Pathways

Not Available

Name	SMPDB/PathBank	KEGG

Normal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Blood	Detected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	31557052	details

Abnormal Concentrations

Not Available

Associated Disorders and Diseases

Disease References

None

Associated OMIM IDs

None

External Links

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

VMH ID

Not Available

MarkerDB ID

Not Available

Good Scents ID

Not Available

References

Synthesis Reference

Not Available

Material Safety Data Sheet (MSDS)

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 (HMDB0246408)

MOL for HMDB0246408 (4-Deoxypyridoxine)

3D MOL for HMDB0246408 (4-Deoxypyridoxine)

3D SDF for HMDB0246408 (4-Deoxypyridoxine)

3D-SDF for HMDB0246408 (4-Deoxypyridoxine)

PDB for HMDB0246408 (4-Deoxypyridoxine)

3D PDB for HMDB0246408 (4-Deoxypyridoxine)

SMILES for HMDB0246408 (4-Deoxypyridoxine)

INCHI for HMDB0246408 (4-Deoxypyridoxine)

Structure for HMDB0246408 (4-Deoxypyridoxine)

3D Structure for HMDB0246408 (4-Deoxypyridoxine)

Predicted Collision Cross Sections

Predicted Kovats Retention Indices

Underivatized

GC-MS Spectra

MS/MS Spectra

NMR Spectra