MiMeDB: Showing metabocard for Pyridoxamine 5'-phosphate (MMDBc0029671)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-11-17 23:36:54 UTC

Update Date

2024-10-06 18:34:20 UTC

Metabolite ID

MMDBc0029671

Metabolite Identification

Common Name

Pyridoxamine 5'-phosphate

Description

Pyradoxamine 5' phosphate or Vitamin B6 is a water-soluble compound that was discovered in 1930s during nutrition studies on rats. The vitamin was named pyridoxine to indicate its structural homology to pyridine. Later it was shown that vitamin B6 could exist in two other, slightly different, chemical forms, termed pyridoxal and pyridoxamine. All three forms of vitamin B6 are precursors of an activated compound known as pyridoxal 5-phosphate (PLP), which plays a vital role as the cofactor of a large number of essential enzymes.Vitamin B6 is a water-soluble vitamin. The three major forms of vitamin B6 are pyridoxine (also known as pyridoxol), pyridoxal, and pyridoxamine, which are all converted in to pyridoxal 5-phosphate (PLP) a cofactor in many reactions of amino acid metabolism. PLP also is necessary for the enzymatic reaction governing the release of glucose from glycogen.

Structure

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

HMDB0001555
     RDKit          3D
Pyridoxamine 5'-phosphate
 29 29  0  0  0  0  0  0  0  0999 V2000
   -3.7171   -1.6528    0.2919 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4014   -0.9865   -0.0087 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5604   -1.6473   -0.8186 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3566   -1.1901   -1.0993 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0340    0.0309   -0.5054 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4254    0.4555   -0.6029 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9507   -0.7480    0.0566 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5904   -0.7607    0.0502 P   0  0  0  0  0  5  0  0  0  0  0  0
    4.3101    0.5248    0.2457 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.1344   -1.9260    1.1799 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.9798   -1.3218   -1.5495 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8511    0.7545    0.2984 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3825    2.0592    0.7700 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2013    3.0226   -0.1022 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0708    0.2264    0.5748 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9610    0.8612    1.4227 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2159   -1.1033    1.0885 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4450   -2.6851    0.7116 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2767   -1.8760   -0.6190 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3205   -1.5986   -1.7958 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7289    1.3637   -0.2230 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7390    0.2317   -1.6776 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1747   -2.8158    0.8340 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.8445   -1.6867   -1.5881 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9123    2.3391    1.7505 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6187    2.3354    0.8274 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3098    2.4511   -1.0245 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4060    3.6810   -0.4753 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7153    1.6618    1.9875 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
 14 28  1  0
 16 29  1  0
M  END


  Mrv1652307092020582D          

 16 16  0  0  0  0            999 V2000
 9999.625210000.8709    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9998.910710000.4584    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9998.196310000.8709    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
 9998.607710001.5845    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9997.477710000.4563    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9997.782710001.5845    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9999.6252 9999.2204    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9998.9066 9999.6360    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
10001.0570 9998.3954    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10002.4822 9999.2204    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10001.054910000.8710    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10000.340510000.4585    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10000.3405 9999.6334    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10001.0549 9999.2209    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10001.7694 9999.6334    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10001.769410000.4585    0.0000 N   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  2  0  0  0  0
  3  5  1  0  0  0  0
  3  6  1  0  0  0  0
  7  8  1  0  0  0  0
 11 12  2  0  0  0  0
 12 13  1  0  0  0  0
 13 14  2  0  0  0  0
 14 15  1  0  0  0  0
 15 16  2  0  0  0  0
 16 11  1  0  0  0  0
  1 12  1  0  0  0  0
 13  7  1  0  0  0  0
 14  9  1  0  0  0  0
 15 10  1  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0029671

> <DATABASE_NAME>
MIME

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

> <INCHI_IDENTIFIER>
InChI=1S/C8H13N2O5P/c1-5-8(11)7(2-9)6(3-10-5)4-15-16(12,13)14/h3,11H,2,4,9H2,1H3,(H2,12,13,14)

> <INCHI_KEY>
ZMJGSOSNSPKHNH-UHFFFAOYSA-N

> <FORMULA>
C8H13N2O5P

> <MOLECULAR_WEIGHT>
248.173

> <EXACT_MASS>
248.056208048

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
29

> <JCHEM_AVERAGE_POLARIZABILITY>
22.149163667314372

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

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

> <ALOGPS_LOGP>
-0.99

> <JCHEM_LOGP>
-2.2240254392379724

> <ALOGPS_LOGS>
-1.57

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
6.741483417681486

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.7417589844386874

> <JCHEM_PKA_STRONGEST_BASIC>
9.905510964077699

> <JCHEM_POLAR_SURFACE_AREA>
125.9

> <JCHEM_REFRACTIVITY>
56.63570000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
6.61e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
pyridoxamine-5'-phosphate

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0001555
     RDKit          3D
Pyridoxamine 5'-phosphate
 29 29  0  0  0  0  0  0  0  0999 V2000
   -3.7171   -1.6528    0.2919 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4014   -0.9865   -0.0087 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5604   -1.6473   -0.8186 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3566   -1.1901   -1.0993 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0340    0.0309   -0.5054 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4254    0.4555   -0.6029 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9507   -0.7480    0.0566 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5904   -0.7607    0.0502 P   0  0  0  0  0  5  0  0  0  0  0  0
    4.3101    0.5248    0.2457 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.1344   -1.9260    1.1799 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.9798   -1.3218   -1.5495 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8511    0.7545    0.2984 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3825    2.0592    0.7700 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2013    3.0226   -0.1022 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0708    0.2264    0.5748 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9610    0.8612    1.4227 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2159   -1.1033    1.0885 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4450   -2.6851    0.7116 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2767   -1.8760   -0.6190 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3205   -1.5986   -1.7958 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7289    1.3637   -0.2230 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7390    0.2317   -1.6776 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1747   -2.8158    0.8340 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.8445   -1.6867   -1.5881 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9123    2.3391    1.7505 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6187    2.3354    0.8274 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3098    2.4511   -1.0245 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4060    3.6810   -0.4753 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7153    1.6618    1.9875 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
 14 28  1  0
 16 29  1  0
M  END

HEADER    PROTEIN                                 09-JUL-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   09-JUL-20         0                                  
HETATM    1  C   UNK     0    8665.9678668.292   0.000  0.00  0.00           C+0
HETATM    2  O   UNK     0    8664.6338667.522   0.000  0.00  0.00           O+0
HETATM    3  P   UNK     0    8663.3008668.292   0.000  0.00  0.00           P+0
HETATM    4  O   UNK     0    8664.0688669.624   0.000  0.00  0.00           O+0
HETATM    5  O   UNK     0    8661.9588667.518   0.000  0.00  0.00           O+0
HETATM    6  O   UNK     0    8662.5288669.624   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0    8665.9678665.211   0.000  0.00  0.00           C+0
HETATM    8  N   UNK     0    8664.6268665.987   0.000  0.00  0.00           N+0
HETATM    9  O   UNK     0    8668.6408663.671   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0    8671.3008665.211   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0    8668.6368668.293   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0    8667.3028667.523   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0    8667.3028665.982   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0    8668.6368665.212   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0    8669.9708665.982   0.000  0.00  0.00           C+0
HETATM   16  N   UNK     0    8669.9708667.523   0.000  0.00  0.00           N+0
CONECT    1    2   12                                                       
CONECT    2    1    3                                                       
CONECT    3    2    4    5    6                                             
CONECT    4    3                                                            
CONECT    5    3                                                            
CONECT    6    3                                                            
CONECT    7    8   13                                                       
CONECT    8    7                                                            
CONECT    9   14                                                            
CONECT   10   15                                                            
CONECT   11   12   16                                                       
CONECT   12   11   13    1                                                  
CONECT   13   12   14    7                                                  
CONECT   14   13   15    9                                                  
CONECT   15   14   16   10                                                  
CONECT   16   15   11                                                       
MASTER        0    0    0    0    0    0    0    0   16    0   32    0
END

COMPND    HMDB0001555
HETATM    1  C1  UNL     1      -3.717  -1.653   0.292  1.00  0.00           C  
HETATM    2  C2  UNL     1      -2.401  -0.987  -0.009  1.00  0.00           C  
HETATM    3  N1  UNL     1      -1.560  -1.647  -0.819  1.00  0.00           N  
HETATM    4  C3  UNL     1      -0.357  -1.190  -1.099  1.00  0.00           C  
HETATM    5  C4  UNL     1      -0.034   0.031  -0.505  1.00  0.00           C  
HETATM    6  C5  UNL     1       1.425   0.455  -0.603  1.00  0.00           C  
HETATM    7  O1  UNL     1       1.951  -0.748   0.057  1.00  0.00           O  
HETATM    8  P1  UNL     1       3.590  -0.761   0.050  1.00  0.00           P  
HETATM    9  O2  UNL     1       4.310   0.525   0.246  1.00  0.00           O  
HETATM   10  O3  UNL     1       4.134  -1.926   1.180  1.00  0.00           O  
HETATM   11  O4  UNL     1       3.980  -1.322  -1.550  1.00  0.00           O  
HETATM   12  C6  UNL     1      -0.851   0.754   0.298  1.00  0.00           C  
HETATM   13  C7  UNL     1      -0.382   2.059   0.770  1.00  0.00           C  
HETATM   14  N2  UNL     1      -1.201   3.023  -0.102  1.00  0.00           N  
HETATM   15  C8  UNL     1      -2.071   0.226   0.575  1.00  0.00           C  
HETATM   16  O5  UNL     1      -2.961   0.861   1.423  1.00  0.00           O  
HETATM   17  H1  UNL     1      -4.216  -1.103   1.088  1.00  0.00           H  
HETATM   18  H2  UNL     1      -3.445  -2.685   0.712  1.00  0.00           H  
HETATM   19  H3  UNL     1      -4.277  -1.876  -0.619  1.00  0.00           H  
HETATM   20  H4  UNL     1       0.320  -1.599  -1.796  1.00  0.00           H  
HETATM   21  H5  UNL     1       1.729   1.364  -0.223  1.00  0.00           H  
HETATM   22  H6  UNL     1       1.739   0.232  -1.678  1.00  0.00           H  
HETATM   23  H7  UNL     1       4.175  -2.816   0.834  1.00  0.00           H  
HETATM   24  H8  UNL     1       4.844  -1.687  -1.588  1.00  0.00           H  
HETATM   25  H9  UNL     1      -0.912   2.339   1.750  1.00  0.00           H  
HETATM   26  H10 UNL     1       0.619   2.335   0.827  1.00  0.00           H  
HETATM   27  H11 UNL     1      -1.310   2.451  -1.024  1.00  0.00           H  
HETATM   28  H12 UNL     1      -0.406   3.681  -0.475  1.00  0.00           H  
HETATM   29  H13 UNL     1      -2.715   1.662   1.987  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   28
CONECT   15   16
CONECT   16   29
END

HMDB0001555
     RDKit          3D
Pyridoxamine 5'-phosphate
 29 29  0  0  0  0  0  0  0  0999 V2000
   -3.7171   -1.6528    0.2919 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4014   -0.9865   -0.0087 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5604   -1.6473   -0.8186 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3566   -1.1901   -1.0993 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0340    0.0309   -0.5054 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4254    0.4555   -0.6029 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9507   -0.7480    0.0566 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5904   -0.7607    0.0502 P   0  0  0  0  0  5  0  0  0  0  0  0
    4.3101    0.5248    0.2457 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.1344   -1.9260    1.1799 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.9798   -1.3218   -1.5495 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8511    0.7545    0.2984 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3825    2.0592    0.7700 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2013    3.0226   -0.1022 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0708    0.2264    0.5748 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9610    0.8612    1.4227 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2159   -1.1033    1.0885 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4450   -2.6851    0.7116 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2767   -1.8760   -0.6190 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3205   -1.5986   -1.7958 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7289    1.3637   -0.2230 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7390    0.2317   -1.6776 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1747   -2.8158    0.8340 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.8445   -1.6867   -1.5881 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9123    2.3391    1.7505 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6187    2.3354    0.8274 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3098    2.4511   -1.0245 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4060    3.6810   -0.4753 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7153    1.6618    1.9875 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
 14 28  1  0
 16 29  1  0
M  END

Synonyms

Value	Source
4'-Deoxy-4'-aminopyridoxal-5'-phosphate	ChEBI
Pyridoxamine 5'-(dihydrogen phosphate)	ChEBI
Pyridoxamine 5'-phosphoric acid	ChEBI
Pyridoxamine 5-phosphate	ChEBI
Pyridoxamine 5-phosphoric acid	ChEBI
Pyridoxamine phosphate	ChEBI
4'-Deoxy-4'-aminopyridoxal-5'-phosphoric acid	Generator
Pyridoxamine 5'-(dihydrogen phosphoric acid)	Generator
Pyridoxamine phosphoric acid	Generator
Pyridoxamine-P	MeSH, HMDB
PMP	HMDB
Pyridoxamine 5'-phosphate	HMDB
Pyridoxamine 5’-phosphate	HMDB
4’-Deoxy-4’-aminopyridoxal-5’-phosphate	HMDB
4’-Deoxy-4’-aminopyridoxal-5’-phosphoric acid	HMDB

Molecular Formula

C₈H₁₃N₂O₅P

Average Mass

248.173

Monoisotopic Mass

248.056208048

IUPAC Name

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

Traditional Name

pyridoxamine-5'-phosphate

CAS Registry Number

529-96-4

SMILES

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

InChI Identifier

InChI=1S/C8H13N2O5P/c1-5-8(11)7(2-9)6(3-10-5)4-15-16(12,13)14/h3,11H,2,4,9H2,1H3,(H2,12,13,14)

InChI Key

ZMJGSOSNSPKHNH-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as pyridoxamine 5'-phosphates. These are heterocyclic aromatic compounds containing a pyridoxamine that carries a phosphate group at the 5'-position.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Pyridines and derivatives

Sub Class

Pyridoxamines

Direct Parent

Pyridoxamine 5'-phosphates

Alternative Parents

Substituents

Pyridoxamine 5'-phosphate
Monoalkyl phosphate
Aralkylamine
Hydroxypyridine
Methylpyridine
Organic phosphoric acid derivative
Alkyl phosphate
Phosphoric acid ester
Heteroaromatic compound
Azacycle
Primary aliphatic amine
Hydrocarbon derivative
Amine
Primary amine
Organooxygen compound
Organonitrogen compound
Organic nitrogen compound
Organic oxide
Organopnictogen compound
Organic oxygen compound
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

monohydroxypyridine (CHEBI:18335 )
methylpyridines (CHEBI:18335 )
aminoalkylpyridine (CHEBI:18335 )
vitamin B6 phosphate (CHEBI:18335 )

Functional Ontology

Not Available

Physical Properties

State

Solid

Predicted Properties

Property	Value	Source
Water Solubility	6.61 g/L	ALOGPS
logP	-0.99	ALOGPS
logP	-2.2	ChemAxon
logS	-1.6	ALOGPS
pKa (Strongest Acidic)	1.74	ChemAxon
pKa (Strongest Basic)	9.91	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	6	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	125.9 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	56.64 m³·mol⁻¹	ChemAxon
Polarizability	22.15 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

Mitochondria

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

Metabolic Reactions

Reactions

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference
MMDBr0018457	Pyridoxamine 5'-phosphate	Hydrogen peroxide	Pyridoxine/pyridoxamine 5'-phosphate oxidase	Oxidation	PathBank	31602464
MMDBr0018458	Pyridoxamine	Pyridoxamine 5'-phosphate	Pyridoxine/pyridoxal/pyridoxamine kinase	Phosphorylation	PathBank	31602464
MMDBr0019958	Pyridoxamine 5'-phosphate	Hydrogen peroxide	Unknown Protein		PathBank	31602464
MMDBr0019959	Pyridoxamine	Pyridoxamine 5'-phosphate	Unknown Protein		PathBank	31602464

Health Effects and Bioactivity

Health Outcome/Bioactivity	Metabolite Response/Effect	Evidence Type	Host and Biospecimen	Data Source	Reference

Microbial Sources

Superkingdom/Kingdom	Phylum	Total species	Hosts and Body Sites	Microbial Links
Bacteria	Proteobacteria	12	Human feces; Human sputum; Human ; Human unknown; Pig ; Human pleural fluid plaque; Human dental plaque; Human nasal swab; Human stool; Human feces; pleural fluid plaque; bal; Cattle ; River trout ; Turkey ; Sheep ; Dog	Unknown; Metabolic reconstruction
Bacteria/Eubacteria	Firmicutes	307	Human feces; Human pleural fluid plaque; Pig ; Human sputum; Human ; Human subgingival plaque; Human saliva; Human urine; Human mucosa; Cattle ; Human stool	Metabolic reconstruction
Bacteria/Eubacteria	Proteobacteria	414	Human feces; Human sputum; Human ; Human unknown; Pig ; Human pleural fluid plaque; Human dental plaque; Human nasal swab; Human stool; Human feces; pleural fluid plaque; bal; Cattle ; River trout ; Turkey ; Sheep ; Dog	Unknown; Metabolic reconstruction
Bacteria	Actinobacteria	14	Human feces; Human sputum; Human bronchial brush; Human nasopharyngeal swab; Human pleural fluid plaque; Human dental plaque; Human ; Human supragingival plaque; Human mucosa; Human subgingival plaque; Human saliva; Cattle	Metabolic reconstruction
Bacteria/Eubacteria	Actinobacteria	140	Human feces; Human sputum; Human bronchial brush; Human nasopharyngeal swab; Human pleural fluid plaque; Human dental plaque; Human ; Human supragingival plaque; Human mucosa; Human subgingival plaque; Human saliva; Cattle	Metabolic reconstruction
Bacteria/Eubacteria	Verrucomicrobia	1	Human ; Human feces	Metabolic reconstruction
Bacteria/Eubacteria	Bacteroidetes	114	Human feces; Human appendix biopsy; Human ; Human stool; Human saliva; Human supragingival plaque; Human subgingival plaque; Human gastric fluid; Human urine	Metabolic reconstruction
Bacteria	Firmicutes	23	Human feces; Human pleural fluid plaque; Pig ; Human sputum; Human ; Human subgingival plaque; Human saliva; Human urine; Human mucosa; Cattle ; Human stool	Metabolic reconstruction
Bacteria/Eubacteria	Spirochaetes	7	Human feces; Human	Metabolic reconstruction
Archaea	Thaumarchaeota	1		Metabolic reconstruction
Bacteria/Eubacteria	Synergistetes	2	Human feces	Metabolic reconstruction
Bacteria/Eubacteria	Fusobacteria	9	Human feces; Human	Metabolic reconstruction
Archaea	Euryarchaeota	3		Metabolic reconstruction
Bacteria/Eubacteria	Planctomycetes	2	Human feces	Metabolic reconstruction
Archaea	Crenarchaeota	1		Metabolic reconstruction
Eukaryota/Fungi	Ascomycota	3	Human feces; Human saliva	Unknown
Bacteria/Eubacteria	Cyanobacteria	12	Human
Bacteria/Eubacteria	Deinococcus-thermus	3
Bacteria	nah	1

Exposure Sources

Food Exposures

Other Exposures

Source Type	Data Source	Reference
Drugs - Antimicrobial	U.S. Environmental Protection Agency	CompTox
Cosmetics	U.S. Environmental Protection Agency	CompTox
Domestics	U.S. Environmental Protection Agency	CompTox

Host Biospecimen and Location

Host and Biospecimen	Status	Mean	Std	Units	Age	Sex	Health Condition	Data Source	Reference
Human Feces	Detected but not Quantified							HMDB
Human Blood	Detected and Quantified	0.00098	0.00019	uM	Adult (>18 years old)	Both	Normal	HMDB	1783639
Human Blood	Detected and Quantified	0.015	0.005	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.

External Links

HMDB ID

HMDB0001555

DrugBank ID

DB02142

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

Not Available

PubChem Compound

1053

PDB ID

Not Available

ChEBI ID

18335

Food Biomarker Ontology

Not Available

References

Synthesis Reference

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 Pyridoxamine 5'-phosphate (MMDBc0029671)

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Structure for #<Metabolite:0x00007f921b916c48>

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