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Showing metabocard for Pyridoxine 5'-phosphate (HMDB0001319)

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enzymes (4) Show 4 proteins
Record Information
Version5.0
StatusDetected and Quantified
Creation Date2005-11-16 15:48:42 UTC
Update Date2020-09-15 18:18:14 UTC
HMDB IDHMDB0001319
Secondary Accession Numbers
  • HMDB01319
Metabolite Identification
Common NamePyridoxine 5'-phosphate
DescriptionPyridoxine 5'-phosphate, also known as pyridoxine-5P or pyridoxine phosphoric acid, belongs to the class of organic compounds known as pyridoxine-5'-phosphates. These are pyridoxines that carry a phosphate group at the 5-position. Pyridoxine 5'-phosphate is a very strong basic compound (based on its pKa). Pyridoxine 5'-phosphate exists in all living species, ranging from bacteria to humans. Within humans, pyridoxine 5'-phosphate participates in a number of enzymatic reactions. In particular, pyridoxine 5'-phosphate can be biosynthesized from pyridoxine through its interaction with the enzyme pyridoxal kinase. In addition, pyridoxine 5'-phosphate can be converted into pyridoxal 5'-phosphate through its interaction with the enzyme pyridoxine-5'-phosphate oxidase. In humans, pyridoxine 5'-phosphate is involved in vitamin B6 metabolism. Outside of the human body, Pyridoxine 5'-phosphate has been detected, but not quantified in, several different foods, such as welsh onions, sweet marjorams, mango, kales, and oil-seed camellia. This could make pyridoxine 5'-phosphate a potential biomarker for the consumption of these foods.
Structure
Data?1600193894
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0001319 (Pyridoxine 5'-phosphate)


  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
Download

3D MOL for HMDB0001319 (Pyridoxine 5'-phosphate)

HMDB0001319
     RDKit          3D
Pyridoxine 5'-phosphate
 28 28  0  0  0  0  0  0  0  0999 V2000
    2.9616   -1.6383    1.6528 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7941   -1.0802    0.8815 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7117   -1.7998    0.6192 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3487   -1.2965   -0.0802 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3539   -0.0146   -0.5510 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4511    0.5658   -1.3342 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5339   -0.2311   -1.4972 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3774   -0.6425   -0.1179 P   0  0  0  0  0  5  0  0  0  0  0  0
   -4.6643    0.2001   -0.1393 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5965   -0.2502    1.3159 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8814   -2.2472   -0.0688 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7955    0.7837   -0.2857 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7582    2.1463   -0.8033 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8658    2.8923   -0.5401 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.8211    0.2537    0.4060 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9819    0.9129    0.7278 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.0305   -1.1258    2.6312 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9032   -2.7330    1.7167 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8906   -1.3386    1.0890 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1813   -1.9538   -0.2692 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8187    1.4784   -0.7600 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0768    1.0166   -2.2846 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4811   -1.0452    1.8682 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8555   -2.6949   -0.9282 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7030    2.0573   -1.9373 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1955    2.6790   -0.5510 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2992    3.3123   -1.3198 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2997    1.7934    0.5593 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  0
  3  4  1  0
  4  5  2  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  2  0
  8 10  1  0
  8 11  1  0
  5 12  1  0
 12 13  1  0
 13 14  1  0
 12 15  2  0
 15 16  1  0
 15  2  1  0
  1 17  1  0
  1 18  1  0
  1 19  1  0
  4 20  1  0
  6 21  1  0
  6 22  1  0
 10 23  1  0
 11 24  1  0
 13 25  1  0
 13 26  1  0
 14 27  1  0
 16 28  1  0
M  END
Download

3D SDF for HMDB0001319 (Pyridoxine 5'-phosphate)


  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>
HMDB0001319

> <DATABASE_NAME>
hmdb

> <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

$$$$
Download

3D-SDF for HMDB0001319 (Pyridoxine 5'-phosphate)

HMDB0001319
     RDKit          3D
Pyridoxine 5'-phosphate
 28 28  0  0  0  0  0  0  0  0999 V2000
    2.9616   -1.6383    1.6528 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7941   -1.0802    0.8815 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7117   -1.7998    0.6192 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3487   -1.2965   -0.0802 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3539   -0.0146   -0.5510 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4511    0.5658   -1.3342 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5339   -0.2311   -1.4972 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3774   -0.6425   -0.1179 P   0  0  0  0  0  5  0  0  0  0  0  0
   -4.6643    0.2001   -0.1393 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5965   -0.2502    1.3159 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8814   -2.2472   -0.0688 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7955    0.7837   -0.2857 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7582    2.1463   -0.8033 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8658    2.8923   -0.5401 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.8211    0.2537    0.4060 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9819    0.9129    0.7278 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.0305   -1.1258    2.6312 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9032   -2.7330    1.7167 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8906   -1.3386    1.0890 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1813   -1.9538   -0.2692 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8187    1.4784   -0.7600 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0768    1.0166   -2.2846 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4811   -1.0452    1.8682 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8555   -2.6949   -0.9282 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7030    2.0573   -1.9373 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1955    2.6790   -0.5510 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2992    3.3123   -1.3198 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2997    1.7934    0.5593 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  0
  3  4  1  0
  4  5  2  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  2  0
  8 10  1  0
  8 11  1  0
  5 12  1  0
 12 13  1  0
 13 14  1  0
 12 15  2  0
 15 16  1  0
 15  2  1  0
  1 17  1  0
  1 18  1  0
  1 19  1  0
  4 20  1  0
  6 21  1  0
  6 22  1  0
 10 23  1  0
 11 24  1  0
 13 25  1  0
 13 26  1  0
 14 27  1  0
 16 28  1  0
M  END
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PDB for HMDB0001319 (Pyridoxine 5'-phosphate)

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
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3D PDB for HMDB0001319 (Pyridoxine 5'-phosphate)

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
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SMILES for HMDB0001319 (Pyridoxine 5'-phosphate)

CC1=NC=C(COP(O)(O)=O)C(CO)=C1O
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INCHI for HMDB0001319 (Pyridoxine 5'-phosphate)

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)
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View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
ValueSource
Pyridoxine 5'-(dihydrogen phosphate)ChEBI
Pyridoxine 5-phosphateChEBI
Pyridoxine phosphateChEBI
PYRIDOXINE-5'-phosphATEChEBI
Pyridoxol 5'-phosphateChEBI
Pyridoxol 5-phosphateChEBI
Pyridoxyl-5-phosphateChEBI
Pyridoxine 5'-(dihydrogen phosphoric acid)Generator
Pyridoxine 5-phosphoric acidGenerator
Pyridoxine phosphoric acidGenerator
PYRIDOXINE-5'-phosphoric acidGenerator
Pyridoxol 5'-phosphoric acidGenerator
Pyridoxol 5-phosphoric acidGenerator
Pyridoxyl-5-phosphoric acidGenerator
Pyridoxine 5'-phosphoric acidGenerator
5-Hydroxy-4-(hydroxymethyl)-6-methyl-3-pyridylmethyl dihydrogen phosphateHMDB
5-Hydroxy-6-methyl-3,4-pyridinedimethanol alpha( 3)-(dihydrogen phosphate)HMDB
Pyridoxine-5PHMDB
Pyridoxine-pHMDB
Pyridoxine-phosphateHMDB
Pyridoxine 5-phosphate hydrochlorideHMDB
5-PhosphopyridoxineHMDB
Chemical FormulaC8H12NO6P
Average Molecular Weight249.1577
Monoisotopic Molecular Weight249.040223633
IUPAC Name{[5-hydroxy-4-(hydroxymethyl)-6-methylpyridin-3-yl]methoxy}phosphonic acid
Traditional Namepyridoxine-5'-phosphate
CAS Registry Number447-05-2
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 KeyWHOMFKWHIQZTHY-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.
KingdomOrganic compounds
Super ClassOrganoheterocyclic compounds
ClassPyridines and derivatives
Sub ClassPyridoxines
Direct ParentPyridoxine-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 FrameworkAromatic heteromonocyclic compounds
External Descriptors
Ontology
Physiological effectNot Available
Disposition
Biological locationSource
Process
Naturally occurring process
RoleNot Available
Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Experimental Chromatographic Properties

Experimental Collision Cross Sections

Adduct TypeData SourceCCS Value (Å2)Reference
[M+H]+Not Available150.628http://allccs.zhulab.cn/database/detail?ID=AllCCS00000469
Predicted Molecular Properties
PropertyValueSource
Water Solubility9.41 g/LALOGPS
logP-0.8ALOGPS
logP-3.6ChemAxon
logS-1.4ALOGPS
pKa (Strongest Acidic)1.74ChemAxon
pKa (Strongest Basic)5.55ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count6ChemAxon
Hydrogen Donor Count4ChemAxon
Polar Surface Area120.11 ŲChemAxon
Rotatable Bond Count4ChemAxon
Refractivity54.98 m³·mol⁻¹ChemAxon
Polarizability21.73 ųChemAxon
Number of Rings1ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
DarkChem[M+H]+156.97831661259
DarkChem[M-H]-152.84431661259
AllCCS[M+H]+153.66332859911
AllCCS[M-H]-149.11532859911
DeepCCS[M+H]+151.23430932474
DeepCCS[M-H]-148.87630932474
DeepCCS[M-2H]-183.12730932474
DeepCCS[M+Na]+157.76630932474
AllCCS[M+H]+153.732859911
AllCCS[M+H-H2O]+149.932859911
AllCCS[M+NH4]+157.132859911
AllCCS[M+Na]+158.132859911
AllCCS[M-H]-149.132859911
AllCCS[M+Na-2H]-149.632859911
AllCCS[M+HCOO]-150.232859911

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
Pyridoxine 5'-phosphateCC1=NC=C(COP(O)(O)=O)C(CO)=C1O2904.0Standard polar33892256
Pyridoxine 5'-phosphateCC1=NC=C(COP(O)(O)=O)C(CO)=C1O2136.9Standard non polar33892256
Pyridoxine 5'-phosphateCC1=NC=C(COP(O)(O)=O)C(CO)=C1O2319.8Semi standard non polar33892256

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
Pyridoxine 5'-phosphate,1TMS,isomer #1CC1=NC=C(COP(=O)(O)O)C(CO[Si](C)(C)C)=C1O2331.4Semi standard non polar33892256
Pyridoxine 5'-phosphate,1TMS,isomer #2CC1=NC=C(COP(=O)(O)O)C(CO)=C1O[Si](C)(C)C2250.6Semi standard non polar33892256
Pyridoxine 5'-phosphate,1TMS,isomer #3CC1=NC=C(COP(=O)(O)O[Si](C)(C)C)C(CO)=C1O2329.5Semi standard non polar33892256
Pyridoxine 5'-phosphate,2TMS,isomer #1CC1=NC=C(COP(=O)(O)O)C(CO[Si](C)(C)C)=C1O[Si](C)(C)C2262.9Semi standard non polar33892256
Pyridoxine 5'-phosphate,2TMS,isomer #2CC1=NC=C(COP(=O)(O)O[Si](C)(C)C)C(CO[Si](C)(C)C)=C1O2322.3Semi standard non polar33892256
Pyridoxine 5'-phosphate,2TMS,isomer #3CC1=NC=C(COP(=O)(O)O[Si](C)(C)C)C(CO)=C1O[Si](C)(C)C2259.0Semi standard non polar33892256
Pyridoxine 5'-phosphate,2TMS,isomer #4CC1=NC=C(COP(=O)(O[Si](C)(C)C)O[Si](C)(C)C)C(CO)=C1O2298.4Semi standard non polar33892256
Pyridoxine 5'-phosphate,3TMS,isomer #1CC1=NC=C(COP(=O)(O)O[Si](C)(C)C)C(CO[Si](C)(C)C)=C1O[Si](C)(C)C2316.8Semi standard non polar33892256
Pyridoxine 5'-phosphate,3TMS,isomer #1CC1=NC=C(COP(=O)(O)O[Si](C)(C)C)C(CO[Si](C)(C)C)=C1O[Si](C)(C)C2244.2Standard non polar33892256
Pyridoxine 5'-phosphate,3TMS,isomer #1CC1=NC=C(COP(=O)(O)O[Si](C)(C)C)C(CO[Si](C)(C)C)=C1O[Si](C)(C)C2720.5Standard polar33892256
Pyridoxine 5'-phosphate,3TMS,isomer #2CC1=NC=C(COP(=O)(O[Si](C)(C)C)O[Si](C)(C)C)C(CO[Si](C)(C)C)=C1O2313.4Semi standard non polar33892256
Pyridoxine 5'-phosphate,3TMS,isomer #2CC1=NC=C(COP(=O)(O[Si](C)(C)C)O[Si](C)(C)C)C(CO[Si](C)(C)C)=C1O2297.8Standard non polar33892256
Pyridoxine 5'-phosphate,3TMS,isomer #2CC1=NC=C(COP(=O)(O[Si](C)(C)C)O[Si](C)(C)C)C(CO[Si](C)(C)C)=C1O2596.9Standard polar33892256
Pyridoxine 5'-phosphate,3TMS,isomer #3CC1=NC=C(COP(=O)(O[Si](C)(C)C)O[Si](C)(C)C)C(CO)=C1O[Si](C)(C)C2243.6Semi standard non polar33892256
Pyridoxine 5'-phosphate,3TMS,isomer #3CC1=NC=C(COP(=O)(O[Si](C)(C)C)O[Si](C)(C)C)C(CO)=C1O[Si](C)(C)C2269.7Standard non polar33892256
Pyridoxine 5'-phosphate,3TMS,isomer #3CC1=NC=C(COP(=O)(O[Si](C)(C)C)O[Si](C)(C)C)C(CO)=C1O[Si](C)(C)C2508.2Standard polar33892256
Pyridoxine 5'-phosphate,4TMS,isomer #1CC1=NC=C(COP(=O)(O[Si](C)(C)C)O[Si](C)(C)C)C(CO[Si](C)(C)C)=C1O[Si](C)(C)C2327.4Semi standard non polar33892256
Pyridoxine 5'-phosphate,4TMS,isomer #1CC1=NC=C(COP(=O)(O[Si](C)(C)C)O[Si](C)(C)C)C(CO[Si](C)(C)C)=C1O[Si](C)(C)C2278.9Standard non polar33892256
Pyridoxine 5'-phosphate,4TMS,isomer #1CC1=NC=C(COP(=O)(O[Si](C)(C)C)O[Si](C)(C)C)C(CO[Si](C)(C)C)=C1O[Si](C)(C)C2457.1Standard polar33892256
Pyridoxine 5'-phosphate,1TBDMS,isomer #1CC1=NC=C(COP(=O)(O)O)C(CO[Si](C)(C)C(C)(C)C)=C1O2568.8Semi standard non polar33892256
Pyridoxine 5'-phosphate,1TBDMS,isomer #2CC1=NC=C(COP(=O)(O)O)C(CO)=C1O[Si](C)(C)C(C)(C)C2520.0Semi standard non polar33892256
Pyridoxine 5'-phosphate,1TBDMS,isomer #3CC1=NC=C(COP(=O)(O)O[Si](C)(C)C(C)(C)C)C(CO)=C1O2577.1Semi standard non polar33892256
Pyridoxine 5'-phosphate,2TBDMS,isomer #1CC1=NC=C(COP(=O)(O)O)C(CO[Si](C)(C)C(C)(C)C)=C1O[Si](C)(C)C(C)(C)C2726.6Semi standard non polar33892256
Pyridoxine 5'-phosphate,2TBDMS,isomer #2CC1=NC=C(COP(=O)(O)O[Si](C)(C)C(C)(C)C)C(CO[Si](C)(C)C(C)(C)C)=C1O2762.4Semi standard non polar33892256
Pyridoxine 5'-phosphate,2TBDMS,isomer #3CC1=NC=C(COP(=O)(O)O[Si](C)(C)C(C)(C)C)C(CO)=C1O[Si](C)(C)C(C)(C)C2734.4Semi standard non polar33892256
Pyridoxine 5'-phosphate,2TBDMS,isomer #4CC1=NC=C(COP(=O)(O[Si](C)(C)C(C)(C)C)O[Si](C)(C)C(C)(C)C)C(CO)=C1O2772.7Semi standard non polar33892256
Pyridoxine 5'-phosphate,3TBDMS,isomer #1CC1=NC=C(COP(=O)(O)O[Si](C)(C)C(C)(C)C)C(CO[Si](C)(C)C(C)(C)C)=C1O[Si](C)(C)C(C)(C)C2982.1Semi standard non polar33892256
Pyridoxine 5'-phosphate,3TBDMS,isomer #1CC1=NC=C(COP(=O)(O)O[Si](C)(C)C(C)(C)C)C(CO[Si](C)(C)C(C)(C)C)=C1O[Si](C)(C)C(C)(C)C2798.8Standard non polar33892256
Pyridoxine 5'-phosphate,3TBDMS,isomer #1CC1=NC=C(COP(=O)(O)O[Si](C)(C)C(C)(C)C)C(CO[Si](C)(C)C(C)(C)C)=C1O[Si](C)(C)C(C)(C)C2985.4Standard polar33892256
Pyridoxine 5'-phosphate,3TBDMS,isomer #2CC1=NC=C(COP(=O)(O[Si](C)(C)C(C)(C)C)O[Si](C)(C)C(C)(C)C)C(CO[Si](C)(C)C(C)(C)C)=C1O2976.9Semi standard non polar33892256
Pyridoxine 5'-phosphate,3TBDMS,isomer #2CC1=NC=C(COP(=O)(O[Si](C)(C)C(C)(C)C)O[Si](C)(C)C(C)(C)C)C(CO[Si](C)(C)C(C)(C)C)=C1O2831.4Standard non polar33892256
Pyridoxine 5'-phosphate,3TBDMS,isomer #2CC1=NC=C(COP(=O)(O[Si](C)(C)C(C)(C)C)O[Si](C)(C)C(C)(C)C)C(CO[Si](C)(C)C(C)(C)C)=C1O2911.1Standard polar33892256
Pyridoxine 5'-phosphate,3TBDMS,isomer #3CC1=NC=C(COP(=O)(O[Si](C)(C)C(C)(C)C)O[Si](C)(C)C(C)(C)C)C(CO)=C1O[Si](C)(C)C(C)(C)C2927.8Semi standard non polar33892256
Pyridoxine 5'-phosphate,3TBDMS,isomer #3CC1=NC=C(COP(=O)(O[Si](C)(C)C(C)(C)C)O[Si](C)(C)C(C)(C)C)C(CO)=C1O[Si](C)(C)C(C)(C)C2764.9Standard non polar33892256
Pyridoxine 5'-phosphate,3TBDMS,isomer #3CC1=NC=C(COP(=O)(O[Si](C)(C)C(C)(C)C)O[Si](C)(C)C(C)(C)C)C(CO)=C1O[Si](C)(C)C(C)(C)C2821.3Standard polar33892256
Pyridoxine 5'-phosphate,4TBDMS,isomer #1CC1=NC=C(COP(=O)(O[Si](C)(C)C(C)(C)C)O[Si](C)(C)C(C)(C)C)C(CO[Si](C)(C)C(C)(C)C)=C1O[Si](C)(C)C(C)(C)C3186.1Semi standard non polar33892256
Pyridoxine 5'-phosphate,4TBDMS,isomer #1CC1=NC=C(COP(=O)(O[Si](C)(C)C(C)(C)C)O[Si](C)(C)C(C)(C)C)C(CO[Si](C)(C)C(C)(C)C)=C1O[Si](C)(C)C(C)(C)C2910.0Standard non polar33892256
Pyridoxine 5'-phosphate,4TBDMS,isomer #1CC1=NC=C(COP(=O)(O[Si](C)(C)C(C)(C)C)O[Si](C)(C)C(C)(C)C)C(CO[Si](C)(C)C(C)(C)C)=C1O[Si](C)(C)C(C)(C)C2847.5Standard polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - Pyridoxine 5'-phosphate GC-MS (Non-derivatized) - 70eV, Positivesplash10-0002-9530000000-1e967afad92165e82bee2016-09-22Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Pyridoxine 5'-phosphate GC-MS (2 TMS) - 70eV, Positivesplash10-00di-9226000000-49f5293644ca681d401b2017-10-06Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Pyridoxine 5'-phosphate GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Pyridoxine 5'-phosphate GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart LabView Spectrum

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Pyridoxine 5'-phosphate 10V, Positive-QTOFsplash10-0ue9-0590000000-68640055ed308d852fd02015-09-15Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Pyridoxine 5'-phosphate 20V, Positive-QTOFsplash10-0f89-0900000000-1450b9f084acf6421d592015-09-15Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Pyridoxine 5'-phosphate 40V, Positive-QTOFsplash10-001i-4900000000-8fd6492e6f2a6bea98792015-09-15Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Pyridoxine 5'-phosphate 10V, Negative-QTOFsplash10-0002-8090000000-65f73f2c7a460a3fca232015-09-15Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Pyridoxine 5'-phosphate 20V, Negative-QTOFsplash10-004i-9010000000-5b0859a6a40a458fcc9f2015-09-15Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Pyridoxine 5'-phosphate 40V, Negative-QTOFsplash10-004i-9000000000-a6fead236e12d88986b82015-09-15Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Pyridoxine 5'-phosphate 10V, Positive-QTOFsplash10-0udi-0290000000-da88c1789911b79c03622021-09-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Pyridoxine 5'-phosphate 20V, Positive-QTOFsplash10-0ff0-0910000000-366dc9237952c888f4b82021-09-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Pyridoxine 5'-phosphate 40V, Positive-QTOFsplash10-001i-2900000000-cd37cb30cd544c5f866a2021-09-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Pyridoxine 5'-phosphate 10V, Negative-QTOFsplash10-002b-9010000000-64a9d47104102ec4486f2021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Pyridoxine 5'-phosphate 20V, Negative-QTOFsplash10-004i-9000000000-ef724d5177083af378f02021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Pyridoxine 5'-phosphate 40V, Negative-QTOFsplash10-004i-9000000000-a5e502a2627af2048a1f2021-09-24Wishart LabView Spectrum

NMR Spectra

Spectrum TypeDescriptionDeposition DateSourceView
Predicted 1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Biological Properties
Cellular Locations
  • Cytoplasm (predicted from logP)
Biospecimen Locations
  • Blood
Tissue LocationsNot Available
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodDetected and Quantified0.003 (0.0-0.01) uMAdult (>18 years old)FemaleObesity details
Associated Disorders and Diseases
Disease References
Obesity
  1. Driskell JA, Chrisley BM, Reynolds LK, Moak SW: Plasma B6 vitamer and plasma and urinary 4-pyridoxic acid concentrations of middle-aged obese black women. J Chromatogr. 1991 Aug 23;568(2):333-40. [PubMed:1783639 ]
Associated OMIM IDs
DrugBank IDDB02209
Phenol Explorer Compound IDNot Available
FooDB IDFDB031140
KNApSAcK IDC00007505
Chemspider ID1026
KEGG Compound IDC00627
BioCyc IDPYRIDOXINE-5P
BiGG ID35527
Wikipedia LinkNot Available
METLIN ID6156
PubChem Compound1055
PDB IDNot Available
ChEBI ID28803
Food Biomarker OntologyNot Available
VMH IDPDX5P
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceArgoudelis, Chris J. Preparation of crystalline pyridoxine 5'-phosphate and some of its properties. Journal of Agricultural and Food Chemistry (1986), 34(6), 995-8.
Material Safety Data Sheet (MSDS)Not Available
General ReferencesNot Available

Enzymes

Enzyme Details
1. Pyridoxine-5'-phosphate oxidase
General function:
Involved in pyridoxamine-phosphate oxidase activity
Specific function:
Catalyzes the oxidation of either pyridoxine 5'-phosphate (PNP) or pyridoxamine 5'-phosphate (PMP) into pyridoxal 5'-phosphate (PLP).
Gene Name:
PNPO
Uniprot ID:
Q9NVS9
Molecular weight:
29987.79
Reactions
Pyridoxine 5'-phosphate + Oxygen → Pyridoxal 5'-phosphate + Hydrogen peroxidedetails
Enzyme Details
2. Pyridoxal kinase
General function:
Involved in pyridoxal kinase activity
Specific function:
Required for synthesis of pyridoxal-5-phosphate from vitamin B6.
Gene Name:
PDXK
Uniprot ID:
O00764
Molecular weight:
35102.105
Reactions
Adenosine triphosphate + Pyridoxine → ADP + Pyridoxine 5'-phosphatedetails
Enzyme Details
3. Pyridoxal phosphate phosphatase
General function:
Involved in catalytic activity
Specific function:
Protein serine phosphatase that dephosphorylates 'Ser-3' in cofilin and probably also dephosphorylates phospho-serine residues in DSTN. Regulates cofilin-dependent actin cytoskeleton reorganization. Required for normal progress through mitosis and normal cytokinesis. Does not dephosphorylate phospho-threonines in LIMK1. Does not dephosphorylate peptides containing phospho-tyrosine. Pyridoxal phosphate phosphatase. Has some activity towards pyridoxal 5'-phosphate (PLP), pyridoxine 5'-phosphate (PMP) and pyridoxine 5'-phosphate (PNP), with a highest activity with PLP followed by PNP.
Gene Name:
PDXP
Uniprot ID:
Q96GD0
Molecular weight:
31697.735
Reactions
Pyridoxine + Phosphate → Pyridoxine 5'-phosphate + Waterdetails
Enzyme Details
4. Pyridoxal phosphate phosphatase PHOSPHO2
General function:
Involved in phosphatase activity
Specific function:
Phosphatase that has high activity toward pyridoxal 5'-phosphate (PLP). Also active at much lower level toward pyrophosphate, phosphoethanolamine (PEA), phosphocholine (PCho), phospho-l-tyrosine, fructose-6-phosphate, p-nitrophenyl phosphate, and h-glycerophosphate.
Gene Name:
PHOSPHO2
Uniprot ID:
Q8TCD6
Molecular weight:
27768.72
Reactions
Pyridoxine + Phosphate → Pyridoxine 5'-phosphate + Waterdetails