MiMeDB: Showing metabocard for 4-Pyridoxic acid (MMDBc0000325)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2020-12-10 18:28:45 UTC

Update Date

2024-04-30 19:31:47 UTC

Metabolite ID

MMDBc0000325

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>
MMDBc0000325

> <DATABASE_NAME>
MIME

> <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

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

Molecular Formula

C₈H₉NO₄

Average Mass

183.1614

Monoisotopic Mass

183.053157781

IUPAC Name

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

Traditional Name

pyridoxic acid

CAS Registry Number

Not Available

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 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted 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

Spectra

Not Available

Biological Properties

Cellular Locations

Cytoplasm
Extracellular

Biospecimen Locations

Bladder
Blood
Cerebrospinal Fluid (CSF)
Erythrocyte
Feces
Kidney
Liver
Placenta
Urine

Tissue Locations

Bladder
Erythrocyte
Kidney
Liver
Placenta

Associated OMIM IDs

114500 (Colorectal cancer)
610247 (Eosinophilic esophagitis)

Human Proteins and Enzymes

Protein ID	Protein Name	Protein Type	Uniprot ID	Species
MMDBp0191797	Aldehyde oxidase	Unknown	Q06278	Homo sapiens

Human Pathways

Pathways

Name	SMPDB/PathBank

Metabolic Reactions

Reactions

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference
MMDBr0024551	4-Pyridoxic acid	5-formyl-3-hydroxy-2-methylpyridine-4-carboxylic acid	4-pyridoxate dehydrogenase	Dehydrogenation	RHEA	34755880

Health Effects and Bioactivity

Health Outcome/Bioactivity	Metabolite Response/Effect	Evidence Type	Host and Biospecimen	Data Source	Reference
Eosinophilic esophagitis		Association	Human Urine	HMDB	Slae, M., Huynh, H., Wishart, D.S. (2014). Analysis of 30 normal pediatric urine samples via NMR spectroscopy (unpublished work)

Microbial Sources

Superkingdom/Kingdom	Phylum	Total species	Hosts and Body Sites	Microbial Links
Bacteria/Eubacteria	Bacteroidetes	1		Indirect association between microbiota composition and metabolites measured in host biospecimen
Bacteria/Eubacteria	Proteobacteria	1	Human feces

Exposure Sources

Food Exposures

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
Human Feces	Detected but not Quantified									HMDB
Human Urine	Detected and Quantified	> 0.33				umol/mmol creatinine	Adult (>18 years old)	Female	Normal	HMDB	18230968
Human Urine	Detected and Quantified	> 3.0				umol/mmol creatinine	Children (1-13 years old)	Both	Normal	HMDB	12368406
Human Cerebrospinal fluid (csf)	Detected and Quantified			0.00009	0.00300	uM	Children (1-13 years old)	Not Specified	Normal	HMDB	27912044
Human Blood	Detected and Quantified	0.0071	0.005			uM	Adult (>18 years old)	Female	Normal	HMDB	11068702
Human Blood	Detected and Quantified	0.0097	0.00665			uM	Adult (>18 years old)	Male	Normal	HMDB	11068702
Human Blood	Detected and Quantified	0.027		0.0062	3.14	uM	Adult (>18 years old)	Both	Normal	HMDB	15450810
Human Urine	Detected and Quantified	0.157	0.0613			umol/mmol creatinine	Children (1 - 13 years old)	Both	Normal	HMDB	20576202
Human Urine	Detected and Quantified	0.245	0.0873			umol/mmol creatinine	Adult (>18 years old)	Both	Normal	HMDB	20502474
Human Urine	Detected and Quantified	0.407	0.173			umol/mmol creatinine	Adolescent (13-18 years old)	Female	Normal	HMDB	17349090
Human Urine	Detected and Quantified	0.420	0.187			umol/mmol creatinine	Adolescent (13-18 years old)	Male	Normal	HMDB	17349090
Human Urine	Detected and Quantified	0.78	0.45			umol/mmol creatinine	Adult (>18 years old)	Both	Normal	HMDB	6695847
Human Urine	Detected and Quantified	2.99	5.25			umol/mmol creatinine	Infant (0-1 year old)	Both	Normal	HMDB	2026685
Human Urine	Detected and Quantified	3.1		0.4	7.5	umol/mmol creatinine	Adult (>18 years old)	Both	Normal	HMDB	24023812
Human Urine	Detected and Quantified	5.701	3.878			umol/mmol creatinine	Children (1 - 13 years old)	Not Specified	Eosinophilic esophagitis	HMDB	Analysis of 30 normal pediatric urine samples via NMR spectroscopy (unpublished work)
Human Urine	Detected and Quantified	5.975	2.873			umol/mmol creatinine	Children (1 - 13 years old)	Not Specified	Normal	HMDB	Analysis of 30 normal pediatric urine samples via NMR spectroscopy (unpublished work)
Human Blood	Detected and Quantified	0.040	0.007			uM	Adult (>18 years old)	Both	Normal	HMDB	Geigy Scientific Tables, 8th Rev edition, pp. 130. Edited by C. Lentner, West Cadwell, N.J.: Medical education Div., Ciba-Geigy Corp. Basel, Switzerland c1981-1992.
Human Bladder	Detected but not Quantified						Not Specified	Not Specified	Normal	HMDB	34986597
Human Erythrocyte	Detected but not Quantified						Not Specified	Not Specified	Normal	HMDB	34986597
Human Kidney	Detected but not Quantified						Not Specified	Not Specified	Normal	HMDB	34986597
Human Liver	Detected but not Quantified						Not Specified	Not Specified	Normal	HMDB	34986597
Human Placenta	Detected but not Quantified						Not Specified	Not Specified	Normal	HMDB	34986597
Human Feces	Detected but not Quantified						Infant (0-1 year old)	Not Specified	Normal	HMDB	24628373
Human Feces	Detected but not Quantified						Infant (0-1 year old)	Not Specified	Normal	HMDB	24628373
Human Feces	Detected but not Quantified						Children (6 - 18 years old)	Not Specified	Normal	HMDB	27609529
Human Blood	Detected but not Quantified						Adult (>18 years old)	Both	Normal	HMDB	24740205
Human Blood	Detected but not Quantified						Adult (>18 years old)	Female	Normal	HMDB	27355821
Human Feces	Detected but not Quantified						Adult (>18 years old)	Both	Normal	HMDB	27543620
Human Feces	Detected but not Quantified						Adult (>18 years old)	Both	Normal	HMDB	25037050
Human Feces	Detected but not Quantified						Adult (>18 years old)	Both	Normal	HMDB	29808030
Human Urine	Detected but not Quantified						Adult (>18 years old)	Both	Normal	HMDB	32966057
Human Blood	Detected but not Quantified						Adult (>18 years old)	Both	Normal	HMDB	32966057

External Links

HMDB ID

HMDB0000017

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

References

Synthesis Reference

Not Available

General References

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. doi: 10.1002/bmc.1130050504. [PubMed:1742549 ]
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 ]
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. doi: 10.1038/sj.ejcn.1601321. [PubMed:12001008 ]
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. doi: 10.1093/jn/131.10.3130. [PubMed:12368406 ]
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. doi: 10.1007/s00394-003-0387-5. [PubMed:12638029 ]
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. doi: 10.1093/ajcn/80.4.946. [PubMed:15447904 ]
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. doi: 10.1016/j.ab.2004.06.036. [PubMed:15450810 ]
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. doi: 10.1016/j.nut.2004.11.013. [PubMed:15975484 ]
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. doi: 10.1373/clinchem.2005.051169. [PubMed:15976101 ]
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. doi: 10.1016/j.jchromb.2005.07.017. [PubMed:16054880 ]
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. doi: 10.1186/ar1821. Epub 2005 Sep 13. [PubMed:16277678 ]
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 ]

Showing metabocard for 4-Pyridoxic acid (MMDBc0000325)

MOL for #<Metabolite:0x00007f923118dc90>

3D MOL for #<Metabolite:0x00007f923118dc90>

3D SDF for #<Metabolite:0x00007f923118dc90>

3D-SDF for #<Metabolite:0x00007f923118dc90>

PDB for #<Metabolite:0x00007f923118dc90>

3D PDB for #<Metabolite:0x00007f923118dc90>

SMILES for #<Metabolite:0x00007f923118dc90>

INCHI for #<Metabolite:0x00007f923118dc90>

Structure for #<Metabolite:0x00007f923118dc90>

3D Structure for #<Metabolite:0x00007f923118dc90>