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Record Information

Version

5.0

Status

Detected and Quantified

Creation Date

2005-11-16 15:48:42 UTC

Update Date

2023-02-21 17:14:27 UTC

HMDB ID

HMDB0000017

Secondary Accession Numbers

HMDB00017

Metabolite Identification

Common Name

4-Pyridoxic acid

Description

4-Pyridoxic acid is a member of the class of compounds known as methylpyridines. More specifically it is a 2-methylpyridine derivative substituted by a hydroxy group at C-3, a carboxy group at C-4, and a hydroxymethyl group at C-5. 4-Pyridoxic acid is the catabolic product of vitamin B6 (also known as pyridoxine, pyridoxal and pyradoxamine) and is excreted in the urine. Urinary levels of 4-pyridoxic acid are lower in females than in males and will be reduced even further in persons with a riboflavin deficiency. 4-Pyridoxic acid is formed by the action of aldehyde oxidase I (an endogenous enzyme) and by microbial enzymes (pyridoxal 4-dehydrogenase), an NAD-dependent aldehyde dehydrogenase. 4-pyridoxic acid can be further broken down by the gut microflora via the enzyme known as 4-pyridoxic acid dehydrogenase. This enzyme catalyzes the four-electron oxidation of 4-pyridoxic acid to 3-hydroxy-2-methylpyridine-4,5-dicarboxylate, using nicotinamide adenine dinucleotide (NAD) as a cofactor.

Structure

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

4-Pyridoxic acid.mol
  Mrv1652303182019222D          

 13 13  0  0  0  0            999 V2000
   -0.3582    1.0316    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3574    0.2066    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3574   -0.2052    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0715    0.2080    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7864   -0.2038    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3582   -1.0302    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3558   -1.4434    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0707   -1.0316    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7848   -1.4448    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0715   -0.2066    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7864    0.2052    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0731    1.4434    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3558    1.4448    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  3  6  2  0  0  0  0
  6  7  1  0  0  0  0
  7  8  2  0  0  0  0
  8  9  1  0  0  0  0
  8 10  1  0  0  0  0
 10 11  1  0  0  0  0
  2 10  2  0  0  0  0
  1 12  2  0  0  0  0
  1 13  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0000017

> <DATABASE_NAME>
hmdb

> <SMILES>
CC1=NC=C(CO)C(C(O)=O)=C1O

> <INCHI_IDENTIFIER>
InChI=1S/C8H9NO4/c1-4-7(11)6(8(12)13)5(3-10)2-9-4/h2,10-11H,3H2,1H3,(H,12,13)

> <INCHI_KEY>
HXACOUQIXZGNBF-UHFFFAOYSA-N

> <FORMULA>
C8H9NO4

> <MOLECULAR_WEIGHT>
183.1614

> <EXACT_MASS>
183.053157781

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
22

> <JCHEM_AVERAGE_POLARIZABILITY>
17.185817118123126

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
3-hydroxy-5-(hydroxymethyl)-2-methylpyridine-4-carboxylic acid

> <ALOGPS_LOGP>
-0.08

> <JCHEM_LOGP>
-0.7503333510578963

> <ALOGPS_LOGS>
-1.32

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
11.91317833557911

> <JCHEM_PKA_STRONGEST_ACIDIC>
2.5470192618835608

> <JCHEM_PKA_STRONGEST_BASIC>
4.090673374822506

> <JCHEM_POLAR_SURFACE_AREA>
90.65000000000002

> <JCHEM_REFRACTIVITY>
44.5456

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
8.71e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
pyridoxic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 18-MAR-20   NONE
TITLE     NULL                                                        
COMPND    MOLECULE: 4-Pyridoxic acid.mol                              
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   18-MAR-20         0                                  
HETATM    1  C   UNK     0      -0.669   1.926   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -0.667   0.386   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.667  -0.383   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       2.000   0.388   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0       3.335  -0.380   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0       0.669  -1.923   0.000  0.00  0.00           C+0
HETATM    7  N   UNK     0      -0.664  -2.694   0.000  0.00  0.00           N+0
HETATM    8  C   UNK     0      -1.999  -1.926   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -3.332  -2.697   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -2.000  -0.386   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0      -3.335   0.383   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0      -2.003   2.694   0.000  0.00  0.00           O+0
HETATM   13  O   UNK     0       0.664   2.697   0.000  0.00  0.00           O+0
CONECT    1    2   12   13                                                  
CONECT    2    1    3   10                                                  
CONECT    3    2    4    6                                                  
CONECT    4    3    5                                                       
CONECT    5    4                                                            
CONECT    6    3    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7    9   10                                                  
CONECT    9    8                                                            
CONECT   10    8   11    2                                                  
CONECT   11   10                                                            
CONECT   12    1                                                            
CONECT   13    1                                                            
MASTER        0    0    0    0    0    0    0    0   13    0   26    0
END

View in JSmol View Stereo Labels

Synonyms

Value	Source
2-Methyl-3-hydroxy-4-carboxy-5-hydroxymethylpyridine	ChEBI
3-Hydroxy-5-(hydroxymethyl)-2-methyl-4-pyridinecarboxylic acid	ChEBI
3-Hydroxy-5-(hydroxymethyl)-2-methylisonicotinic acid	ChEBI
4-Pyridoxinecarboxylic acid	ChEBI
4-Pyridoxinic acid	ChEBI
4-Pyridoxinsaeure	ChEBI
4-Pyridoxylic acid	ChEBI
Pyridoxic acid	ChEBI
3-Hydroxy-5-(hydroxymethyl)-2-methyl-4-pyridinecarboxylate	Generator
3-Hydroxy-5-(hydroxymethyl)-2-methylisonicotinate	Generator
4-Pyridoxinecarboxylate	Generator
4-Pyridoxinate	Generator
4-Pyridoxylate	Generator
Pyridoxate	Generator
4-Pyridoxate	Generator
3-Hydroxy-5-(hydroxymethyl)-2-methyl-isonicotinate	HMDB
3-Hydroxy-5-(hydroxymethyl)-2-methyl-isonicotinic acid	HMDB
3-Hydroxy-5-hydroxymethyl-2-methyl-isonicotinate	HMDB
3-Hydroxy-5-hydroxymethyl-2-methyl-isonicotinic acid	HMDB
3-Hydroxy-5-hydroxymethyl-2-methyl-isonicotinsaeure	HMDB
4 Pyridoxinic acid	MeSH, HMDB
Pyridoxinecarboxylic acid	MeSH, HMDB
4 Pyridoxylic acid	MeSH, HMDB
4 Pyridoxic acid	MeSH, HMDB

Chemical Formula

C₈H₉NO₄

Average Molecular Weight

183.1614

Monoisotopic Molecular Weight

183.053157781

IUPAC Name

3-hydroxy-5-(hydroxymethyl)-2-methylpyridine-4-carboxylic acid

Traditional Name

pyridoxic acid

CAS Registry Number

82-82-6

SMILES

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

InChI Identifier

InChI=1S/C8H9NO4/c1-4-7(11)6(8(12)13)5(3-10)2-9-4/h2,10-11H,3H2,1H3,(H,12,13)

InChI Key

HXACOUQIXZGNBF-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as pyridinecarboxylic acids. Pyridinecarboxylic acids are compounds containing a pyridine ring bearing a carboxylic acid group.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Pyridines and derivatives

Sub Class

Pyridinecarboxylic acids and derivatives

Direct Parent

Pyridinecarboxylic acids

Alternative Parents

Substituents

Pyridine carboxylic acid
Hydroxypyridine
Methylpyridine
Vinylogous acid
Heteroaromatic compound
Azacycle
Monocarboxylic acid or derivatives
Carboxylic acid
Carboxylic acid derivative
Organic oxygen compound
Hydrocarbon derivative
Alcohol
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:17405 )
methylpyridines (CHEBI:17405 )
vitamin B6 (CHEBI:17405 )
hydroxymethylpyridine (CHEBI:17405 )

Ontology

Physiological effect

Not Available

Disposition

Biological location

Non-excretory biofluid

Biofluid or Excreta

Blood (PMID: 11068702)
Saliva (HMDB: HMDB0000017)
Cerebrospinal Fluid (CSF) (PMID: 27912044)

Organ

Cell

Erythrocyte (HMDB: HMDB0000017)

Excreta

Biofluid or Excreta

Urine (PMID: 12001008)
Feces (PMID: 24628373)

Cellular substructure

Cytoplasm (HMDB: HMDB0000017)
Extracellular (HMDB: HMDB0000017)

Source

Endogenous

Endogenous (HMDB: HMDB0000017)

Pheasant (FooDB: FOOD00430)
Squab (FooDB: FOOD00481)
Turkey (FooDB: FOOD00494)
Quail (FooDB: FOOD00541)
Anatidae (FooDB: FOOD00576)
Rock ptarmigan (FooDB: FOOD00597)
Columbidae (Dove, Pigeon) (FooDB: FOOD00610)
Chicken (FooDB: FOOD00329)
Mallard duck (FooDB: FOOD00353)
Emu (FooDB: FOOD00360)
Greylag goose (FooDB: FOOD00368)
Guinea hen (FooDB: FOOD00373)
Ostrich (FooDB: FOOD00422)
Velvet duck (FooDB: FOOD00427)

Lagomorph

Ovis

Sheep (Mutton, Lamb) (FooDB: FOOD00473)

Bovine

Venison

Deer (FooDB: FOOD00524)
Mule deer (FooDB: FOOD00348)
Elk (FooDB: FOOD00359)

Caprae

Domestic goat (FooDB: FOOD00529)

Swine

Domestic pig (FooDB: FOOD00536)
Wild boar (FooDB: FOOD00307)

Equine

Horse (FooDB: FOOD00378)

Beverage

Fermented beverage

Beer (FooDB: FOOD00268)

Process

Naturally occurring process

Biological process

Biochemical pathway

Metabolic pathway

Vitamin B6 Metabolism (PathBank: SMP0087395)
Vitamin B6 Metabolism (HMDB: HMDB0000017)

Disease pathway

Hypophosphatasia (HMDB: HMDB0000017)
Hypophosphatasia (PathBank: SMP0120568)

Role

Industrial application

Pharmaceutical industry

Biomarker

Vitamin B6 Consumption (MarkerDB: MDB00000008)

Physical Properties

State

Solid

Experimental Molecular Properties

Property	Value	Reference
Melting Point	247 - 248 °C	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	4337 mg/L @ 25 °C (est)	The Good Scents Company Information System
LogP	Not Available	Not Available

Experimental Chromatographic Properties

Experimental Collision Cross Sections

Adduct Type	Data Source	CCS Value (Å²)	Reference
[M+H]+	Astarita_pos	130.0	30932474
[M+H]+	MetCCS_test_pos	135.297	30932474
[M+H]+	MetCCS_train_pos	135.797	30932474
[M-H]-	Not Available	130.4	http://allccs.zhulab.cn/database/detail?ID=AllCCS00000363
[M+H]+	Not Available	136.2	http://allccs.zhulab.cn/database/detail?ID=AllCCS00000363

Predicted Molecular Properties

Property	Value	Source
Water Solubility	8.71 g/L	ALOGPS
logP	-0.08	ALOGPS
logP	-0.75	ChemAxon
logS	-1.3	ALOGPS
pKa (Strongest Acidic)	2.55	ChemAxon
pKa (Strongest Basic)	4.09	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	90.65 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	44.55 m³·mol⁻¹	ChemAxon
Polarizability	17.19 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
DarkChem	[M+H]+	139.958	31661259
DarkChem	[M-H]-	136.706	31661259
AllCCS	[M+H]+	139.149	32859911
AllCCS	[M-H]-	135.649	32859911
DeepCCS	[M+H]+	141.832	30932474
DeepCCS	[M-H]-	139.197	30932474
DeepCCS	[M-2H]-	175.663	30932474
DeepCCS	[M+Na]+	150.881	30932474
AllCCS	[M+H]+	139.1	32859911
AllCCS	[M+H-H2O]+	134.9	32859911
AllCCS	[M+NH4]+	143.1	32859911
AllCCS	[M+Na]+	144.3	32859911
AllCCS	[M-H]-	135.6	32859911
AllCCS	[M+Na-2H]-	136.5	32859911
AllCCS	[M+HCOO]-	137.5	32859911

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
4-Pyridoxic acid	CC1=NC=C(CO)C(C(O)=O)=C1O	2644.3	Standard polar	33892256
4-Pyridoxic acid	CC1=NC=C(CO)C(C(O)=O)=C1O	1768.2	Standard non polar	33892256
4-Pyridoxic acid	CC1=NC=C(CO)C(C(O)=O)=C1O	1786.8	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
4-Pyridoxic acid,1TMS,isomer #1	CC1=NC=C(CO[Si](C)(C)C)C(C(=O)O)=C1O	1856.0	Semi standard non polar	33892256
4-Pyridoxic acid,1TMS,isomer #2	CC1=NC=C(CO)C(C(=O)O[Si](C)(C)C)=C1O	1837.4	Semi standard non polar	33892256
4-Pyridoxic acid,1TMS,isomer #3	CC1=NC=C(CO)C(C(=O)O)=C1O[Si](C)(C)C	1805.1	Semi standard non polar	33892256
4-Pyridoxic acid,2TMS,isomer #1	CC1=NC=C(CO[Si](C)(C)C)C(C(=O)O[Si](C)(C)C)=C1O	1875.8	Semi standard non polar	33892256
4-Pyridoxic acid,2TMS,isomer #2	CC1=NC=C(CO[Si](C)(C)C)C(C(=O)O)=C1O[Si](C)(C)C	1831.9	Semi standard non polar	33892256
4-Pyridoxic acid,2TMS,isomer #3	CC1=NC=C(CO)C(C(=O)O[Si](C)(C)C)=C1O[Si](C)(C)C	1863.9	Semi standard non polar	33892256
4-Pyridoxic acid,3TMS,isomer #1	CC1=NC=C(CO[Si](C)(C)C)C(C(=O)O[Si](C)(C)C)=C1O[Si](C)(C)C	1952.4	Semi standard non polar	33892256
4-Pyridoxic acid,1TBDMS,isomer #1	CC1=NC=C(CO[Si](C)(C)C(C)(C)C)C(C(=O)O)=C1O	2113.2	Semi standard non polar	33892256
4-Pyridoxic acid,1TBDMS,isomer #2	CC1=NC=C(CO)C(C(=O)O[Si](C)(C)C(C)(C)C)=C1O	2099.9	Semi standard non polar	33892256
4-Pyridoxic acid,1TBDMS,isomer #3	CC1=NC=C(CO)C(C(=O)O)=C1O[Si](C)(C)C(C)(C)C	2064.3	Semi standard non polar	33892256
4-Pyridoxic acid,2TBDMS,isomer #1	CC1=NC=C(CO[Si](C)(C)C(C)(C)C)C(C(=O)O[Si](C)(C)C(C)(C)C)=C1O	2330.2	Semi standard non polar	33892256
4-Pyridoxic acid,2TBDMS,isomer #2	CC1=NC=C(CO[Si](C)(C)C(C)(C)C)C(C(=O)O)=C1O[Si](C)(C)C(C)(C)C	2338.8	Semi standard non polar	33892256
4-Pyridoxic acid,2TBDMS,isomer #3	CC1=NC=C(CO)C(C(=O)O[Si](C)(C)C(C)(C)C)=C1O[Si](C)(C)C(C)(C)C	2350.0	Semi standard non polar	33892256
4-Pyridoxic acid,3TBDMS,isomer #1	CC1=NC=C(CO[Si](C)(C)C(C)(C)C)C(C(=O)O[Si](C)(C)C(C)(C)C)=C1O[Si](C)(C)C(C)(C)C	2591.1	Semi standard non polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Experimental GC-MS	GC-MS Spectrum - 4-Pyridoxic acid GC-MS (3 TMS)	splash10-0600-1594000000-399002a1b2bc22455c9f	2014-06-16	HMDB team, MONA, MassBank	View Spectrum
Experimental GC-MS	GC-MS Spectrum - 4-Pyridoxic acid GC-MS (Non-derivatized)	splash10-0600-1594000000-399002a1b2bc22455c9f	2017-09-12	HMDB team, MONA, MassBank	View Spectrum
Experimental GC-MS	GC-MS Spectrum - 4-Pyridoxic acid GC-EI-TOF (Non-derivatized)	splash10-0002-0963000000-5ea1f1ffe15dc2478b63	2017-09-12	HMDB team, MONA, MassBank	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 4-Pyridoxic acid GC-MS (Non-derivatized) - 70eV, Positive	splash10-0uxr-0900000000-fa35397acddd7c3351b8	2017-09-01	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 4-Pyridoxic acid GC-MS (3 TMS) - 70eV, Positive	splash10-00c0-6029000000-e59f960993866934b8cc	2017-10-06	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 4-Pyridoxic acid GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 4-Pyridoxic acid GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 4-Pyridoxic acid GC-MS (TMS_1_1) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 4-Pyridoxic acid GC-MS (TMS_1_2) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 4-Pyridoxic acid GC-MS (TMS_1_3) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 4-Pyridoxic acid GC-MS (TMS_2_1) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 4-Pyridoxic acid GC-MS (TMS_2_2) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 4-Pyridoxic acid GC-MS (TMS_2_3) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 4-Pyridoxic acid GC-MS (TBDMS_1_1) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 4-Pyridoxic acid GC-MS (TBDMS_1_2) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 4-Pyridoxic acid GC-MS (TBDMS_1_3) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 4-Pyridoxic acid GC-MS (TBDMS_2_1) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 4-Pyridoxic acid GC-MS (TBDMS_2_2) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 4-Pyridoxic acid GC-MS (TBDMS_2_3) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 4-Pyridoxic acid GC-MS (TBDMS_3_1) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum

MS/MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Experimental LC-MS/MS	LC-MS/MS Spectrum - 4-Pyridoxic acid LC-ESI-QQ (API3000, Applied Biosystems) 10V, Positive-QTOF	splash10-001i-0900000000-4f9434fb63b0ad0ce994	2012-08-31	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - 4-Pyridoxic acid LC-ESI-QQ (API3000, Applied Biosystems) 20V, Positive-QTOF	splash10-014i-0900000000-99753fc7dd56422dd423	2012-08-31	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - 4-Pyridoxic acid LC-ESI-QQ (API3000, Applied Biosystems) 30V, Positive-QTOF	splash10-0002-0900000000-6e2e1f60d8bebc0b3340	2012-08-31	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - 4-Pyridoxic acid LC-ESI-QQ (API3000, Applied Biosystems) 40V, Positive-QTOF	splash10-0002-6900000000-8c038db01c62f9d4e87b	2012-08-31	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - 4-Pyridoxic acid LC-ESI-QQ (API3000, Applied Biosystems) 50V, Positive-QTOF	splash10-014i-9200000000-a94133cf31fe1f8b7938	2012-08-31	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - 4-Pyridoxic acid LC-ESI-QTOF (UPLC Q-Tof Premier, Waters) , Positive-QTOF	splash10-00kb-0900000000-d57234d89d8c011abfb4	2012-08-31	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - 4-Pyridoxic acid LC-ESI-QTOF (UPLC Q-Tof Premier, Waters) 30V, Positive-QTOF	splash10-00kb-7900000000-a99b8437514399d65aba	2012-08-31	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - 4-Pyridoxic acid LC-ESI-QTOF (UPLC Q-Tof Premier, Waters) , Negative-QTOF	splash10-052r-0900000000-725f61f22b0bc1a28b93	2012-08-31	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - 4-Pyridoxic acid LC-ESI-IT , negative-QTOF	splash10-000i-0900000000-79e29b063e250dd7037b	2017-09-14	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - 4-Pyridoxic acid LC-ESI-QTOF , negative-QTOF	splash10-052r-0900000000-725f61f22b0bc1a28b93	2017-09-14	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - 4-Pyridoxic acid , negative-QTOF	splash10-000i-0900000000-f82707706c2653c46393	2017-09-14	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - 4-Pyridoxic acid LC-ESI-QQ , positive-QTOF	splash10-001i-0900000000-4f9434fb63b0ad0ce994	2017-09-14	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - 4-Pyridoxic acid LC-ESI-QQ , positive-QTOF	splash10-014i-0900000000-2c70b549625fa141234a	2017-09-14	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - 4-Pyridoxic acid LC-ESI-QQ , positive-QTOF	splash10-0002-0900000000-2a37bda24c0b0f98132b	2017-09-14	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - 4-Pyridoxic acid LC-ESI-QQ , positive-QTOF	splash10-0002-6900000000-d3f955b006cc32330edd	2017-09-14	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - 4-Pyridoxic acid LC-ESI-QQ , positive-QTOF	splash10-014i-9200000000-8f0fa7a53eb7325318ba	2017-09-14	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - 4-Pyridoxic acid LC-ESI-QTOF , positive-QTOF	splash10-00kb-0900000000-d57234d89d8c011abfb4	2017-09-14	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - 4-Pyridoxic acid LC-ESI-QTOF , positive-QTOF	splash10-00kb-7900000000-a99b8437514399d65aba	2017-09-14	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - 4-Pyridoxic acid , positive-QTOF	splash10-014i-0900000000-df0aa00e8733225ac266	2017-09-14	HMDB team, MONA	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 4-Pyridoxic acid 10V, Positive-QTOF	splash10-0159-0900000000-5860f1285218e1907916	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 4-Pyridoxic acid 20V, Positive-QTOF	splash10-01ba-0900000000-463662790c3d6c47c8d1	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 4-Pyridoxic acid 40V, Positive-QTOF	splash10-00di-6900000000-eda84db35c5bfbd25ceb	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 4-Pyridoxic acid 10V, Negative-QTOF	splash10-001r-0900000000-cdc1e6701650ec6b77f1	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 4-Pyridoxic acid 20V, Negative-QTOF	splash10-0a4i-0900000000-fd70f5eeff9dec054259	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 4-Pyridoxic acid 40V, Negative-QTOF	splash10-0a4i-7900000000-ff1dc4213c27146d1751	2017-09-01	Wishart Lab	View Spectrum

NMR Spectra

Spectrum Type	Description	Deposition Date	Source	View
Experimental 1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, experimental)	2021-10-10	Wishart Lab	View Spectrum
Experimental 1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, experimental)	2021-10-10	Wishart Lab	View Spectrum
Experimental 1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, experimental)	2021-10-10	Wishart Lab	View Spectrum
Experimental 2D NMR	[¹H, ¹³C]-HSQC NMR Spectrum (2D, 600 MHz, H₂O, experimental)	2012-12-04	Wishart Lab	View Spectrum

IR Spectra

Spectrum Type	Description	Deposition Date	Source	View
Predicted IR Spectrum	IR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M-H]-)	2023-02-03	FELIX lab	View Spectrum
Predicted IR Spectrum	IR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M+H]+)	2023-02-03	FELIX lab	View Spectrum
Predicted IR Spectrum	IR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M+Na]+)	2023-02-03	FELIX lab	View Spectrum

Biological Properties

Cellular Locations

Cytoplasm
Extracellular

Biospecimen Locations

Blood
Cerebrospinal Fluid (CSF)
Feces
Saliva
Urine

Tissue Locations

Bladder
Erythrocyte
Kidney
Liver
Placenta

Pathways

Name	SMPDB/PathBank	KEGG
Vitamin B6 Metabolism
Hypophosphatasia		Not Available

Normal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Blood	Detected and Quantified	0.027 (0.0062-3.14) uM	Adult (>18 years old)	Both	Normal	15450810	details
Blood	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Both	Normal	32966057	details
Blood	Detected and Quantified	0.040 +/- 0.007 uM	Adult (>18 years old)	Both	Normal	Geigy Scientific ...	details
Blood	Detected and Quantified	0.0071 +/- 0.005 uM	Adult (>18 years old)	Female	Normal	11068702	details
Blood	Detected and Quantified	0.0097 +/- 0.00665 uM	Adult (>18 years old)	Male	Normal	11068702	details
Blood	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Both	Normal	24740205	details
Blood	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Female	Normal	27355821	details
Cerebrospinal Fluid (CSF)	Detected and Quantified	0.00009-0.00300 uM	Children (1-13 years old)	Not Specified	Normal	27912044	details
Feces	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Both	Normal	27543620	details
Feces	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Both	Normal	29808030	details
Feces	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Both	Normal	25037050	details
Feces	Detected but not Quantified	Not Quantified	Children (6 - 18 years old)	Not Specified	Normal	27609529	details
Feces	Detected but not Quantified	Not Quantified	Infant (0-1 year old)	Not Specified	Normal	24628373	details
Feces	Detected but not Quantified	Not Quantified	Infant (0-1 year old)	Not Specified	Normal	24628373	details
Saliva	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Both	Normal	Zerihun T. Dame, ...	details
Urine	Detected and Quantified	> 0.33 umol/mmol creatinine	Adult (>18 years old)	Female	Normal	18230968	details
Urine	Detected and Quantified	0.78 +/- 0.45 umol/mmol creatinine	Adult (>18 years old)	Both	Normal	6695847	details
Urine	Detected and Quantified	3.1 (0.4-7.5) umol/mmol creatinine	Adult (>18 years old)	Both	Normal	24023812	details
Urine	Detected and Quantified	5.975 +/- 2.873 umol/mmol creatinine	Children (1 - 13 years old)	Not Specified	Normal	Analysis of 30 no...	details
Urine	Detected and Quantified	0.157 +/- 0.0613 umol/mmol creatinine	Children (1 - 13 years old)	Both	Normal	20576202	details
Urine	Detected and Quantified	0.245 +/- 0.0873 umol/mmol creatinine	Adult (>18 years old)	Both	Normal	20502474	details
Urine	Detected and Quantified	0.407 +/- 0.173 umol/mmol creatinine	Adolescent (13-18 years old)	Female	Normal	17349090	details
Urine	Detected and Quantified	0.420 +/- 0.187 umol/mmol creatinine	Adolescent (13-18 years old)	Male	Normal	17349090	details
Urine	Detected and Quantified	> 3.0 umol/mmol creatinine	Children (1-13 years old)	Both	Normal	12368406	details
Urine	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Both	Normal	32966057	details
Urine	Detected and Quantified	2.99 +/- 5.25 umol/mmol creatinine	Infant (0-1 year old)	Both	Normal	2026685	details

Abnormal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Blood	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Both	Colorectal adenoma	27510537	details
Feces	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Both	Colorectal cancer	27015276	details
Feces	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Both	Crohns disease	26848182	details
Feces	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Both	Iron deficiency	26848182	details
Feces	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Both	Colorectal cancer	25037050	details
Feces	Detected but not Quantified	Not Quantified	Children (6 - 18 years old)	Both	Crohns disease	27609529	details
Feces	Detected but not Quantified	Not Quantified	Children (6 - 18 years old)	Both	Ulcerative colitis	27609529	details
Feces	Detected but not Quantified	Not Quantified	Children (6 - 18 years old)	Not Specified	Crohns disease	27609529	details
Feces	Detected but not Quantified	Not Quantified	Children (6 - 18 years old)	Not Specified	Ulcerative colitis	27609529	details
Feces	Detected but not Quantified	Not Quantified	Children (6 - 18 years old)	Not Specified	Unclassified IBD	27609529	details
Feces	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Both	Colorectal Cancer	27275383	details
Urine	Detected and Quantified	5.701 +/- 3.878 umol/mmol creatinine	Children (1 - 13 years old)	Not Specified	Eosinophilic esophagitis	Analysis of 30 no...	details
Urine	Detected and Quantified	1414.9 +/- 737.8 umol/mmol creatinine	Adult (>18 years old)	Both	Critically ill	12001008	details
Urine	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Both	Colorectal adenoma	27510537	details

Associated Disorders and Diseases

Disease References

Crohn's disease
Lee T, Clavel T, Smirnov K, Schmidt A, Lagkouvardos I, Walker A, Lucio M, Michalke B, Schmitt-Kopplin P, Fedorak R, Haller D: Oral versus intravenous iron replacement therapy distinctly alters the gut microbiota and metabolome in patients with IBD. Gut. 2017 May;66(5):863-871. doi: 10.1136/gutjnl-2015-309940. Epub 2016 Feb 4. [PubMed:26848182 ] Kolho KL, Pessia A, Jaakkola T, de Vos WM, Velagapudi V: Faecal and Serum Metabolomics in Paediatric Inflammatory Bowel Disease. J Crohns Colitis. 2017 Mar 1;11(3):321-334. doi: 10.1093/ecco-jcc/jjw158. [PubMed:27609529 ]
Iron deficiency
Lee T, Clavel T, Smirnov K, Schmidt A, Lagkouvardos I, Walker A, Lucio M, Michalke B, Schmitt-Kopplin P, Fedorak R, Haller D: Oral versus intravenous iron replacement therapy distinctly alters the gut microbiota and metabolome in patients with IBD. Gut. 2017 May;66(5):863-871. doi: 10.1136/gutjnl-2015-309940. Epub 2016 Feb 4. [PubMed:26848182 ]
Colorectal cancer
Brown DG, Rao S, Weir TL, O'Malia J, Bazan M, Brown RJ, Ryan EP: Metabolomics and metabolic pathway networks from human colorectal cancers, adjacent mucosa, and stool. Cancer Metab. 2016 Jun 6;4:11. doi: 10.1186/s40170-016-0151-y. eCollection 2016. [PubMed:27275383 ] Sinha R, Ahn J, Sampson JN, Shi J, Yu G, Xiong X, Hayes RB, Goedert JJ: Fecal Microbiota, Fecal Metabolome, and Colorectal Cancer Interrelations. PLoS One. 2016 Mar 25;11(3):e0152126. doi: 10.1371/journal.pone.0152126. eCollection 2016. [PubMed:27015276 ] Goedert JJ, Sampson JN, Moore SC, Xiao Q, Xiong X, Hayes RB, Ahn J, Shi J, Sinha R: Fecal metabolomics: assay performance and association with colorectal cancer. Carcinogenesis. 2014 Sep;35(9):2089-96. doi: 10.1093/carcin/bgu131. Epub 2014 Jul 18. [PubMed:25037050 ]
Ulcerative colitis
Kolho KL, Pessia A, Jaakkola T, de Vos WM, Velagapudi V: Faecal and Serum Metabolomics in Paediatric Inflammatory Bowel Disease. J Crohns Colitis. 2017 Mar 1;11(3):321-334. doi: 10.1093/ecco-jcc/jjw158. [PubMed:27609529 ]
Eosinophilic esophagitis
Slae, M., Huynh, H., Wishart, D.S. (2014). Analysis of 30 normal pediatric urine samples via NMR spectroscopy (unpublished work). NA.

Associated OMIM IDs

266600 (Crohn's disease)
114500 (Colorectal cancer)
610247 (Eosinophilic esophagitis)

External Links

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

KNApSAcK ID

Chemspider ID

KEGG Compound ID

BioCyc ID

BiGG ID

Wikipedia Link

Not Available

METLIN ID

239

PubChem Compound

6723

PDB ID

Not Available

ChEBI ID

17405

Food Biomarker Ontology

Not Available

VMH ID

4PYRDX

MarkerDB ID

MDB00000008

Good Scents ID

rw1699441

References

Synthesis Reference

Senkuma, Masahiko; Imada, Katsumi; Sato, Masatada. Preparation of 4-pyridoxic acid. Jpn. Kokai Tokkyo Koho (1992), 2 pp.

Material Safety Data Sheet (MSDS)

Download (PDF)

General References

Huang YC, Lan PH, Cheng CH, Lee BJ, Kan MN: Vitamin B6 intakes and status of mechanically ventilated critically ill patients in Taiwan. Eur J Clin Nutr. 2002 May;56(5):387-92. [PubMed:12001008 ]
Kodentsova VM, Vrzhesinskaia OA, Sokol'nikov AA, Beketova NA, Spirichev VB: [The effect of riboflavin supply on metabolism of water-soluble vitamins]. Vopr Med Khim. 1993 Sep-Oct;39(5):29-33. [PubMed:8279138 ]
Masse PG, Mahuren JD, Tranchant C, Dosy J: B-6 vitamers and 4-pyridoxic acid in the plasma, erythrocytes, and urine of postmenopausal women. Am J Clin Nutr. 2004 Oct;80(4):946-51. [PubMed:15447904 ]
Huang YC, Chang HH, Huang SC, Cheng CH, Lee BJ, Cheng SY, Su KH: Plasma pyridoxal 5'-phosphate is a significant indicator of immune responses in the mechanically ventilated critically ill. Nutrition. 2005 Jul-Aug;21(7-8):779-85. [PubMed:15975484 ]
Ericson KL, Mahuren JD, Zubovic YM, Coburn SP: Use of chlorite to improve HPLC detection of pyridoxal 5'-phosphate. J Chromatogr B Analyt Technol Biomed Life Sci. 2005 Sep 5;823(2):218-20. [PubMed:16054880 ]
Driskell JA, Chrisley BM: Plasma B-6 vitamer and plasma and urinary 4-pyridoxic acid concentrations in young women as determined using high performance liquid chromatography. Biomed Chromatogr. 1991 Sep;5(5):198-201. [PubMed:1742549 ]
Chiang EP, Smith DE, Selhub J, Dallal G, Wang YC, Roubenoff R: Inflammation causes tissue-specific depletion of vitamin B6. Arthritis Res Ther. 2005;7(6):R1254-62. Epub 2005 Sep 13. [PubMed:16277678 ]
Rybak ME, Pfeiffer CM: Clinical analysis of vitamin B(6): determination of pyridoxal 5'-phosphate and 4-pyridoxic acid in human serum by reversed-phase high-performance liquid chromatography with chlorite postcolumn derivatization. Anal Biochem. 2004 Oct 15;333(2):336-44. [PubMed:15450810 ]
Huang YC, Chang SJ, Chiu YT, Chang HH, Cheng CH: The status of plasma homocysteine and related B-vitamins in healthy young vegetarians and nonvegetarians. Eur J Nutr. 2003 Apr;42(2):84-90. [PubMed:12638029 ]
Midttun O, Hustad S, Solheim E, Schneede J, Ueland PM: Multianalyte quantification of vitamin B6 and B2 species in the nanomolar range in human plasma by liquid chromatography-tandem mass spectrometry. Clin Chem. 2005 Jul;51(7):1206-16. [PubMed:15976101 ]
Chang SJ, Huang YC, Hsiao LJ, Lee YC, Hsuen SY: Determination of vitamin B-6 estimated average requirement and recommended dietary allowance for children aged 7-12 years using vitamin B-6 intake, nutritional status and anthropometry. J Nutr. 2002 Oct;132(10):3130-4. [PubMed:12368406 ]
Elshenawy S, Pinney SE, Stuart T, Doulias PT, Zura G, Parry S, Elovitz MA, Bennett MJ, Bansal A, Strauss JF 3rd, Ischiropoulos H, Simmons RA: The Metabolomic Signature of the Placenta in Spontaneous Preterm Birth. Int J Mol Sci. 2020 Feb 4;21(3). pii: ijms21031043. doi: 10.3390/ijms21031043. [PubMed:32033212 ]

Enzymes

Enzyme Details

1. Aldehyde oxidase

General function:: Involved in oxidoreductase activity
Specific function:: Not Available
Gene Name:: AOX1
Uniprot ID:: Q06278
Molecular weight:: 147916.735

Reactions

Pyridoxal + Oxygen + Water → 4-Pyridoxic acid + Hydrogen peroxide	details

References

Stanulovic M, Jeremic V, Leskovac V, Chaykin S: New pathway of conversion of pyridoxal to 4-pyridoxic acid. Enzyme. 1976;21(4):357-69. [PubMed:939227 ]

Showing metabocard for 4-Pyridoxic acid (HMDB0000017)

MOL for HMDB0000017 (4-Pyridoxic acid)

3D MOL for HMDB0000017 (4-Pyridoxic acid)

3D SDF for HMDB0000017 (4-Pyridoxic acid)

3D-SDF for HMDB0000017 (4-Pyridoxic acid)

PDB for HMDB0000017 (4-Pyridoxic acid)

3D PDB for HMDB0000017 (4-Pyridoxic acid)

SMILES for HMDB0000017 (4-Pyridoxic acid)

INCHI for HMDB0000017 (4-Pyridoxic acid)

Structure for HMDB0000017 (4-Pyridoxic acid)

3D Structure for HMDB0000017 (4-Pyridoxic acid)

Experimental Collision Cross Sections

Predicted Collision Cross Sections

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra

NMR Spectra

IR Spectra

Enzymes

Reactions

References