MiMeDB: Showing metabocard for Pyridoxine 5'-phosphate (MMDBc0029617)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-11-17 23:34:43 UTC

Update Date

2022-08-31 13:59:48 UTC

Metabolite ID

MMDBc0029617

Metabolite Identification

Common Name

Pyridoxine 5'-phosphate

Description

Pyridoxine 5'-phosphate is a substrate for Pyridoxine-5'-phosphate oxidase and Pyridoxal kinase.

Structure

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


  Mrv1652309042000212D          

 16 16  0  0  0  0            999 V2000
    2.1434    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.0000    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434   -0.4125    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8579   -0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5559    0.3020    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7309   -1.1270    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    2.0625    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    2.0625    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  2  0  0  0  0
  3  4  1  0  0  0  0
  4  5  2  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  8 10  1  0  0  0  0
  8 11  2  0  0  0  0
  5 12  1  0  0  0  0
 12 13  1  0  0  0  0
 13 14  1  0  0  0  0
 12 15  2  0  0  0  0
  2 15  1  0  0  0  0
 15 16  1  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0029617

> <DATABASE_NAME>
MIME

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

> <INCHI_IDENTIFIER>
InChI=1S/C8H12NO6P/c1-5-8(11)7(3-10)6(2-9-5)4-15-16(12,13)14/h2,10-11H,3-4H2,1H3,(H2,12,13,14)

> <INCHI_KEY>
WHOMFKWHIQZTHY-UHFFFAOYSA-N

> <FORMULA>
C8H12NO6P

> <MOLECULAR_WEIGHT>
249.1577

> <EXACT_MASS>
249.040223633

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
28

> <JCHEM_AVERAGE_POLARIZABILITY>
21.726701172777485

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
{[5-hydroxy-4-(hydroxymethyl)-6-methylpyridin-3-yl]methoxy}phosphonic acid

> <ALOGPS_LOGP>
-0.80

> <JCHEM_LOGP>
-3.640999575634358

> <ALOGPS_LOGS>
-1.42

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
6.798869153656689

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.7391293357611506

> <JCHEM_PKA_STRONGEST_BASIC>
5.554512423881395

> <JCHEM_POLAR_SURFACE_AREA>
120.11000000000001

> <JCHEM_REFRACTIVITY>
54.97820000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
9.41e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
pyridoxine-5'-phosphate

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 04-SEP-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   04-SEP-20         0                                  
HETATM    1  C   UNK     0       4.001   2.310   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
HETATM    3  N   UNK     0       2.667   0.000   0.000  0.00  0.00           N+0
HETATM    4  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0      -2.667   0.000   0.000  0.00  0.00           O+0
HETATM    8  P   UNK     0      -4.001  -0.770   0.000  0.00  0.00           P+0
HETATM    9  O   UNK     0      -5.335  -1.540   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0      -4.771   0.564   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0      -3.231  -2.104   0.000  0.00  0.00           O+0
HETATM   12  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      -1.334   2.310   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0      -1.334   3.850   0.000  0.00  0.00           O+0
HETATM   15  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0       1.334   3.850   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3   15                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6   12                                                  
CONECT    6    5    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7    9   10   11                                             
CONECT    9    8                                                            
CONECT   10    8                                                            
CONECT   11    8                                                            
CONECT   12    5   13   15                                                  
CONECT   13   12   14                                                       
CONECT   14   13                                                            
CONECT   15   12    2   16                                                  
CONECT   16   15                                                            
MASTER        0    0    0    0    0    0    0    0   16    0   32    0
END

COMPND    HMDB0001319
HETATM    1  C1  UNL     1       2.962  -1.638   1.653  1.00  0.00           C  
HETATM    2  C2  UNL     1       1.794  -1.080   0.882  1.00  0.00           C  
HETATM    3  N1  UNL     1       0.712  -1.800   0.619  1.00  0.00           N  
HETATM    4  C3  UNL     1      -0.349  -1.296  -0.080  1.00  0.00           C  
HETATM    5  C4  UNL     1      -0.354  -0.015  -0.551  1.00  0.00           C  
HETATM    6  C5  UNL     1      -1.451   0.566  -1.334  1.00  0.00           C  
HETATM    7  O1  UNL     1      -2.534  -0.231  -1.497  1.00  0.00           O  
HETATM    8  P1  UNL     1      -3.377  -0.642  -0.118  1.00  0.00           P  
HETATM    9  O2  UNL     1      -4.664   0.200  -0.139  1.00  0.00           O  
HETATM   10  O3  UNL     1      -2.597  -0.250   1.316  1.00  0.00           O  
HETATM   11  O4  UNL     1      -3.881  -2.247  -0.069  1.00  0.00           O  
HETATM   12  C6  UNL     1       0.796   0.784  -0.286  1.00  0.00           C  
HETATM   13  C7  UNL     1       0.758   2.146  -0.803  1.00  0.00           C  
HETATM   14  O5  UNL     1       1.866   2.892  -0.540  1.00  0.00           O  
HETATM   15  C8  UNL     1       1.821   0.254   0.406  1.00  0.00           C  
HETATM   16  O6  UNL     1       2.982   0.913   0.728  1.00  0.00           O  
HETATM   17  H1  UNL     1       3.030  -1.126   2.631  1.00  0.00           H  
HETATM   18  H2  UNL     1       2.903  -2.733   1.717  1.00  0.00           H  
HETATM   19  H3  UNL     1       3.891  -1.339   1.089  1.00  0.00           H  
HETATM   20  H4  UNL     1      -1.181  -1.954  -0.269  1.00  0.00           H  
HETATM   21  H5  UNL     1      -1.819   1.478  -0.760  1.00  0.00           H  
HETATM   22  H6  UNL     1      -1.077   1.017  -2.285  1.00  0.00           H  
HETATM   23  H7  UNL     1      -2.481  -1.045   1.868  1.00  0.00           H  
HETATM   24  H8  UNL     1      -3.855  -2.695  -0.928  1.00  0.00           H  
HETATM   25  H9  UNL     1       0.703   2.057  -1.937  1.00  0.00           H  
HETATM   26  H10 UNL     1      -0.195   2.679  -0.551  1.00  0.00           H  
HETATM   27  H11 UNL     1       2.299   3.312  -1.320  1.00  0.00           H  
HETATM   28  H12 UNL     1       3.300   1.793   0.559  1.00  0.00           H  
CONECT    1    2   17   18   19
CONECT    2    3    3   15
CONECT    3    4
CONECT    4    5    5   20
CONECT    5    6   12
CONECT    6    7   21   22
CONECT    7    8
CONECT    8    9    9   10   11
CONECT   10   23
CONECT   11   24
CONECT   12   13   15   15
CONECT   13   14   25   26
CONECT   14   27
CONECT   15   16
CONECT   16   28
END

Synonyms

Value	Source
Pyridoxine 5'-(dihydrogen phosphate)	ChEBI
Pyridoxine 5-phosphate	ChEBI
Pyridoxine phosphate	ChEBI
PYRIDOXINE-5'-phosphATE	ChEBI
Pyridoxol 5'-phosphate	ChEBI
Pyridoxol 5-phosphate	ChEBI
Pyridoxyl-5-phosphate	ChEBI
Pyridoxine 5'-(dihydrogen phosphoric acid)	Generator
Pyridoxine 5-phosphoric acid	Generator
Pyridoxine phosphoric acid	Generator
PYRIDOXINE-5'-phosphoric acid	Generator
Pyridoxol 5'-phosphoric acid	Generator
Pyridoxol 5-phosphoric acid	Generator
Pyridoxyl-5-phosphoric acid	Generator
Pyridoxine 5'-phosphoric acid	Generator
5-Hydroxy-4-(hydroxymethyl)-6-methyl-3-pyridylmethyl dihydrogen phosphate	HMDB
5-Hydroxy-6-methyl-3,4-pyridinedimethanol alpha( 3)-(dihydrogen phosphate)	HMDB
Pyridoxine-5P	HMDB
Pyridoxine-p	HMDB
Pyridoxine-phosphate	HMDB
Pyridoxine 5-phosphate hydrochloride	HMDB
5-Phosphopyridoxine	HMDB

Molecular Formula

C₈H₁₂NO₆P

Average Mass

249.1577

Monoisotopic Mass

249.040223633

IUPAC Name

{[5-hydroxy-4-(hydroxymethyl)-6-methylpyridin-3-yl]methoxy}phosphonic acid

Traditional Name

pyridoxine-5'-phosphate

CAS Registry Number

447-05-2

SMILES

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

InChI Identifier

InChI=1S/C8H12NO6P/c1-5-8(11)7(3-10)6(2-9-5)4-15-16(12,13)14/h2,10-11H,3-4H2,1H3,(H2,12,13,14)

InChI Key

WHOMFKWHIQZTHY-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as pyridoxine-5'-phosphates. These are pyridoxines that carry a phosphate group at the 5-position.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Pyridines and derivatives

Sub Class

Pyridoxines

Direct Parent

Pyridoxine-5'-phosphates

Alternative Parents

Substituents

Pyridoxine-5'-phosphate
Monoalkyl phosphate
Hydroxypyridine
Methylpyridine
Organic phosphoric acid derivative
Alkyl phosphate
Phosphoric acid ester
Heteroaromatic compound
Azacycle
Hydrocarbon derivative
Alcohol
Aromatic alcohol
Organic nitrogen compound
Primary alcohol
Organooxygen compound
Organonitrogen compound
Organic oxide
Organopnictogen compound
Organic oxygen compound
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

vitamin B6 phosphate (CHEBI:28803 )

Functional Ontology

Not Available

Physical Properties

State

Solid

Predicted Properties

Property	Value	Source
Water Solubility	9.41 g/L	ALOGPS
logP	-0.8	ALOGPS
logP	-3.6	ChemAxon
logS	-1.4	ALOGPS
pKa (Strongest Acidic)	1.74	ChemAxon
pKa (Strongest Basic)	5.55	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	6	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	120.11 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	54.98 m³·mol⁻¹	ChemAxon
Polarizability	21.73 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

Chromatographic Retention Times and Retention Indices

Retention Times

Not Available

Retention Indices

Not Available

Chromatographic Retention Times and Retention Indices

Retention Times

Not Available

Retention Indices

Not Available

Biological Properties

Cellular Locations

Cytoplasm

Biospecimen Locations

Blood
Feces

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
MMDBp0192313	Pyridoxine-5'-phosphate oxidase	Unknown	Q9NVS9	Homo_sapiens
MMDBp0192664	Pyridoxal kinase	Unknown	O00764	Homo_sapiens
MMDBp0193940	Pyridoxal phosphate phosphatase	Unknown	Q96GD0	Homo_sapiens
MMDBp0195556	Pyridoxal phosphate phosphatase PHOSPHO2	Unknown	Q8TCD6	Homo_sapiens

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
Obesity		Association	Human Blood	HMDB	1783639

Microbial Sources

Superkingdom/Kingdom	Phylum	Total species	Hosts and Body Sites	Microbial Links
Bacteria	Proteobacteria	497	Human feces; Human sputum; Human ; Human unknown; Pig ; Human pleural fluid plaque; Human dental plaque; Human nasal swab; Human feces; pleural fluid plaque; bal; Cattle ; River trout ; Turkey ; Sheep ; Dog ; Lion	Unknown; Metabolic reconstruction
Bacteria	Firmicutes	338	Human feces; Human pleural fluid plaque; Pig ; Human ; Cattle	Metabolic reconstruction
Bacteria	Actinobacteria	155	Human feces; Human sputum; Human bronchial brush; Human nasopharyngeal swab; Human pleural fluid plaque; Human dental plaque; Human ; Cattle	Metabolic reconstruction
Bacteria	Verrucomicrobia	2	Human ; Human feces	Metabolic reconstruction
Bacteria	Bacteroidetes	118	Human feces; Human appendix biopsy; Human	Metabolic reconstruction
Bacteria	Spirochaetes	7	Human feces; Human	Metabolic reconstruction
Archaea	Thaumarchaeota	1	Human feces	Metabolic reconstruction
Bacteria	Synergistetes	2	Human feces	Metabolic reconstruction
Bacteria	Fusobacteria	9	Human feces; Human	Metabolic reconstruction
Archaea	Euryarchaeota	3	Human feces; Cattle	Metabolic reconstruction
Bacteria	Candidatus Melainabacteria	1	Human feces	Metabolic reconstruction
Bacteria	Planctomycetes	2	Human feces	Metabolic reconstruction
Archaea	Crenarchaeota	1	Human feces	Metabolic reconstruction
Eukaryota/Fungi	Ascomycota	3	Human feces	Unknown
Bacteria	Cyanobacteria	33	Human
Bacteria	Deinococcus-Thermus	3
Bacteria	nah	1
Bacteria/NULL	Proteobacteria	2	Human feces; Human sputum; Human ; Human unknown; Pig ; Human pleural fluid plaque; Human dental plaque; Human nasal swab; Human feces; pleural fluid plaque; bal; Cattle ; River trout ; Turkey ; Sheep ; Dog ; Lion	Unknown; Metabolic reconstruction
Bacteria	Aquificae	4
Bacteria/NULL	Aquificae	1
Bacteria	Chlorobi	10
Bacteria	Elusimicrobia	1
Bacteria	Nitrospirae	1

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
Human Feces	Detected but not Quantified									HMDB
Human	Detected and Quantified	0.003		0.0	0.01		Adult (>18 years old)	Female	Obesity	HMDB	1783639

External Links

HMDB ID

HMDB0001319

DrugBank ID

DB02209

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

6156

PubChem Compound

1055

PDB ID

Not Available

ChEBI ID

28803

Food Biomarker Ontology

Not Available

CMMC Knowledgebase

Not Available

General References

Noronha A, Modamio J, Jarosz Y, Guerard E, Sompairac N, Preciat G, Danielsdottir AD, Krecke M, Merten D, Haraldsdottir HS, Heinken A, Heirendt L, Magnusdottir S, Ravcheev DA, Sahoo S, Gawron P, Friscioni L, Garcia B, Prendergast M, Puente A, Rodrigues M, Roy A, Rouquaya M, Wiltgen L, Zagare A, John E, Krueger M, Kuperstein I, Zinovyev A, Schneider R, Fleming RMT, Thiele I: The Virtual Metabolic Human database: integrating human and gut microbiome metabolism with nutrition and disease. Nucleic Acids Res. 2019 Jan 8;47(D1):D614-D624. doi: 10.1093/nar/gky992. [PubMed:30371894 ]

Showing metabocard for Pyridoxine 5'-phosphate (MMDBc0029617)

MOL for #<Metabolite:0x00007f12407ca8b8>

3D MOL for #<Metabolite:0x00007f12407ca8b8>

3D SDF for #<Metabolite:0x00007f12407ca8b8>

3D-SDF for #<Metabolite:0x00007f12407ca8b8>

PDB for #<Metabolite:0x00007f12407ca8b8>

3D PDB for #<Metabolite:0x00007f12407ca8b8>

SMILES for #<Metabolite:0x00007f12407ca8b8>

INCHI for #<Metabolite:0x00007f12407ca8b8>

Structure for #<Metabolite:0x00007f12407ca8b8>

3D Structure for #<Metabolite:0x00007f12407ca8b8>