MiMeDB: Showing metabocard for sn-glycero-3-phosphocholine (MMDBc0032168)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-11-18 02:05:15 UTC

Update Date

2024-04-30 19:54:28 UTC

Metabolite ID

MMDBc0032168

Metabolite Identification

Common Name

sn-glycero-3-phosphocholine

Description

sn-Glycero-3-phosphocholine (GPC) is a choline derivative and one of the two major forms of choline storage (along with phosphocholine) in the cytosol. Glycerophosphorylcholine is also osmolyte. GPC is an intermediate of glycerophospholipid metabolism. It is converted from both 2-acyl-sn-glycero-3-phosphocholine and 1-acyl-sn-glycero-3-phosphocholine by lysophospholipase L2 (EC:3.1.1.5). It is converted to choline and sn-glycerol 3-phosphate by glycerophosphodiester phosphodiesterase (EC:3.1.4.46). (KEGG)

Structure

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

HMDB0252858
     RDKit          3D
Glycerylphosphorylcholine
 36 35  0  0  0  0  0  0  0  0999 V2000
   -3.4587   -0.4540   -1.7173 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4371   -0.2028   -0.2908 N   0  0  0  0  0  4  0  0  0  0  0  0
   -3.8347    1.1590   -0.0501 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4595   -1.0673    0.2917 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1810   -0.5610    0.3042 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1552    0.5375    0.2739 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1035   -0.0848    0.3018 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1544    0.7814   -0.6801 P   0  0  0  0  0  5  0  0  0  0  0  0
    1.2189    2.1891   -0.1610 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5126    0.8183   -2.2539 O   0  0  0  0  0  1  0  0  0  0  0  0
    2.6572    0.0402   -0.7757 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.2333   -0.0307    0.4840 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6007   -0.6546    0.4494 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6806   -1.6982   -0.4544 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.6925    0.3321    0.1216 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.6074    0.7930   -1.1902 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1245   -1.4676   -1.9846 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7858    0.2650   -2.2263 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4771   -0.3303   -2.1120 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8733    1.3251    1.0392 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1645    1.8667   -0.5811 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8387    1.2909   -0.5011 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0284   -2.0957    0.2922 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4106   -1.0016   -0.2629 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5800   -0.7519    1.3585 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3835   -0.8229    1.3672 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7647   -1.4290   -0.2312 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2364    1.2046   -0.5985 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1962    1.1471    1.2120 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5801   -0.6824    1.1026 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2525    0.9576    0.9620 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.8100   -1.0407    1.4727 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1971   -2.4794   -0.0795 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.7194    1.1924    0.8150 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.6626   -0.2004    0.2605 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.7072    1.1553   -1.3325 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  2  4  1  0
  2  5  1  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
 11 12  1  0
 12 13  1  0
 13 14  1  0
 13 15  1  0
 15 16  1  0
  1 17  1  0
  1 18  1  0
  1 19  1  0
  3 20  1  0
  3 21  1  0
  3 22  1  0
  4 23  1  0
  4 24  1  0
  4 25  1  0
  5 26  1  0
  5 27  1  0
  6 28  1  0
  6 29  1  0
 12 30  1  0
 12 31  1  0
 13 32  1  0
 14 33  1  0
 15 34  1  0
 15 35  1  0
 16 36  1  0
M  CHG  2   2   1  10  -1
M  END


  Mrv1652305221920472D          

 16 15  0  0  0  0            999 V2000
   -2.8875    2.1434    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1895    1.0164    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7605    1.8414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0625    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2375    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4750   -1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375   -0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0625   -0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4750    1.4289    0.0000 N   0  3  0  0  0  0  0  0  0  0  0  0
    3.3000   -1.4289    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4750   -0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0000    0.8250    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
   -0.8250   -0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
  5  4  1  0  0  0  0
  8  6  1  0  0  0  0
  8  7  1  0  0  0  0
  9  1  1  0  0  0  0
  9  2  1  0  0  0  0
  9  3  1  0  0  0  0
  9  4  1  0  0  0  0
 10  6  1  0  0  0  0
 11  8  1  0  0  0  0
 14  5  1  0  0  0  0
 15  7  1  0  0  0  0
 16 12  2  0  0  0  0
 16 13  1  0  0  0  0
 16 14  1  0  0  0  0
 16 15  1  0  0  0  0
M  CHG  2   9   1  13  -1
M  END
> <DATABASE_ID>
MMDBc0032168

> <DATABASE_NAME>
MIME

> <SMILES>
C[N+](C)(C)CCOP([O-])(=O)OCC(O)CO

> <INCHI_IDENTIFIER>
InChI=1S/C8H20NO6P/c1-9(2,3)4-5-14-16(12,13)15-7-8(11)6-10/h8,10-11H,4-7H2,1-3H3

> <INCHI_KEY>
SUHOQUVVVLNYQR-UHFFFAOYSA-N

> <FORMULA>
C8H20NO6P

> <MOLECULAR_WEIGHT>
257.2213

> <EXACT_MASS>
257.102823889

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
36

> <JCHEM_AVERAGE_POLARIZABILITY>
24.818047498402308

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
{2-[(2,3-dihydroxypropyl phosphono)oxy]ethyl}trimethylazanium

> <ALOGPS_LOGP>
-2.56

> <JCHEM_LOGP>
-5.728311425471745

> <ALOGPS_LOGS>
-1.54

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
13.641245557329462

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.8553451472945346

> <JCHEM_PKA_STRONGEST_BASIC>
-2.9689647678822215

> <JCHEM_POLAR_SURFACE_AREA>
99.05000000000001

> <JCHEM_REFRACTIVITY>
68.6823

> <JCHEM_ROTATABLE_BOND_COUNT>
8

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
8.96e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
{2-[(2,3-dihydroxypropyl phosphono)oxy]ethyl}trimethylazanium

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0252858
     RDKit          3D
Glycerylphosphorylcholine
 36 35  0  0  0  0  0  0  0  0999 V2000
   -3.4587   -0.4540   -1.7173 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4371   -0.2028   -0.2908 N   0  0  0  0  0  4  0  0  0  0  0  0
   -3.8347    1.1590   -0.0501 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4595   -1.0673    0.2917 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1810   -0.5610    0.3042 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1552    0.5375    0.2739 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1035   -0.0848    0.3018 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1544    0.7814   -0.6801 P   0  0  0  0  0  5  0  0  0  0  0  0
    1.2189    2.1891   -0.1610 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5126    0.8183   -2.2539 O   0  0  0  0  0  1  0  0  0  0  0  0
    2.6572    0.0402   -0.7757 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.2333   -0.0307    0.4840 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6007   -0.6546    0.4494 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6806   -1.6982   -0.4544 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.6925    0.3321    0.1216 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.6074    0.7930   -1.1902 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1245   -1.4676   -1.9846 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7858    0.2650   -2.2263 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4771   -0.3303   -2.1120 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8733    1.3251    1.0392 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1645    1.8667   -0.5811 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8387    1.2909   -0.5011 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0284   -2.0957    0.2922 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4106   -1.0016   -0.2629 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5800   -0.7519    1.3585 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3835   -0.8229    1.3672 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7647   -1.4290   -0.2312 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2364    1.2046   -0.5985 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1962    1.1471    1.2120 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5801   -0.6824    1.1026 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2525    0.9576    0.9620 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.8100   -1.0407    1.4727 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1971   -2.4794   -0.0795 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.7194    1.1924    0.8150 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.6626   -0.2004    0.2605 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.7072    1.1553   -1.3325 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  2  4  1  0
  2  5  1  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
 11 12  1  0
 12 13  1  0
 13 14  1  0
 13 15  1  0
 15 16  1  0
  1 17  1  0
  1 18  1  0
  1 19  1  0
  3 20  1  0
  3 21  1  0
  3 22  1  0
  4 23  1  0
  4 24  1  0
  4 25  1  0
  5 26  1  0
  5 27  1  0
  6 28  1  0
  6 29  1  0
 12 30  1  0
 12 31  1  0
 13 32  1  0
 14 33  1  0
 15 34  1  0
 15 35  1  0
 16 36  1  0
M  CHG  2   2   1  10  -1
M  END

HEADER    PROTEIN                                 22-MAY-19   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   22-MAY-19         0                                  
HETATM    1  C   UNK     0      -5.390   4.001   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -5.954   1.897   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -3.286   3.437   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -3.850   1.334   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -2.310   1.334   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       4.620  -2.667   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       2.310  -1.334   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       3.850  -1.334   0.000  0.00  0.00           C+0
HETATM    9  N   UNK     0      -4.620   2.667   0.000  0.00  0.00           N+1
HETATM   10  O   UNK     0       6.160  -2.667   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0       4.620  -0.000   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0       0.000  -1.540   0.000  0.00  0.00           O+0
HETATM   13  O   UNK     0      -0.000   1.540   0.000  0.00  0.00           O-1
HETATM   14  O   UNK     0      -1.540  -0.000   0.000  0.00  0.00           O+0
HETATM   15  O   UNK     0       1.540   0.000   0.000  0.00  0.00           O+0
HETATM   16  P   UNK     0       0.000   0.000   0.000  0.00  0.00           P+0
CONECT    1    9                                                            
CONECT    2    9                                                            
CONECT    3    9                                                            
CONECT    4    5    9                                                       
CONECT    5    4   14                                                       
CONECT    6    8   10                                                       
CONECT    7    8   15                                                       
CONECT    8    6    7   11                                                  
CONECT    9    1    2    3    4                                             
CONECT   10    6                                                            
CONECT   11    8                                                            
CONECT   12   16                                                            
CONECT   13   16                                                            
CONECT   14    5   16                                                       
CONECT   15    7   16                                                       
CONECT   16   12   13   14   15                                             
MASTER        0    0    0    0    0    0    0    0   16    0   30    0
END

COMPND    HMDB0252858
HETATM    1  C1  UNL     1      -3.459  -0.454  -1.717  1.00  0.00           C  
HETATM    2  N1  UNL     1      -3.437  -0.203  -0.291  1.00  0.00           N1+
HETATM    3  C2  UNL     1      -3.835   1.159  -0.050  1.00  0.00           C  
HETATM    4  C3  UNL     1      -4.459  -1.067   0.292  1.00  0.00           C  
HETATM    5  C4  UNL     1      -2.181  -0.561   0.304  1.00  0.00           C  
HETATM    6  C5  UNL     1      -1.155   0.538   0.274  1.00  0.00           C  
HETATM    7  O1  UNL     1       0.103  -0.085   0.302  1.00  0.00           O  
HETATM    8  P1  UNL     1       1.154   0.781  -0.680  1.00  0.00           P  
HETATM    9  O2  UNL     1       1.219   2.189  -0.161  1.00  0.00           O  
HETATM   10  O3  UNL     1       0.513   0.818  -2.254  1.00  0.00           O1-
HETATM   11  O4  UNL     1       2.657   0.040  -0.776  1.00  0.00           O  
HETATM   12  C6  UNL     1       3.233  -0.031   0.484  1.00  0.00           C  
HETATM   13  C7  UNL     1       4.601  -0.655   0.449  1.00  0.00           C  
HETATM   14  O5  UNL     1       4.681  -1.698  -0.454  1.00  0.00           O  
HETATM   15  C8  UNL     1       5.692   0.332   0.122  1.00  0.00           C  
HETATM   16  O6  UNL     1       5.607   0.793  -1.190  1.00  0.00           O  
HETATM   17  H1  UNL     1      -3.125  -1.468  -1.985  1.00  0.00           H  
HETATM   18  H2  UNL     1      -2.786   0.265  -2.226  1.00  0.00           H  
HETATM   19  H3  UNL     1      -4.477  -0.330  -2.112  1.00  0.00           H  
HETATM   20  H4  UNL     1      -3.873   1.325   1.039  1.00  0.00           H  
HETATM   21  H5  UNL     1      -3.164   1.867  -0.581  1.00  0.00           H  
HETATM   22  H6  UNL     1      -4.839   1.291  -0.501  1.00  0.00           H  
HETATM   23  H7  UNL     1      -4.028  -2.096   0.292  1.00  0.00           H  
HETATM   24  H8  UNL     1      -5.411  -1.002  -0.263  1.00  0.00           H  
HETATM   25  H9  UNL     1      -4.580  -0.752   1.359  1.00  0.00           H  
HETATM   26  H10 UNL     1      -2.384  -0.823   1.367  1.00  0.00           H  
HETATM   27  H11 UNL     1      -1.765  -1.429  -0.231  1.00  0.00           H  
HETATM   28  H12 UNL     1      -1.236   1.205  -0.598  1.00  0.00           H  
HETATM   29  H13 UNL     1      -1.196   1.147   1.212  1.00  0.00           H  
HETATM   30  H14 UNL     1       2.580  -0.682   1.103  1.00  0.00           H  
HETATM   31  H15 UNL     1       3.253   0.958   0.962  1.00  0.00           H  
HETATM   32  H16 UNL     1       4.810  -1.041   1.473  1.00  0.00           H  
HETATM   33  H17 UNL     1       4.197  -2.479  -0.080  1.00  0.00           H  
HETATM   34  H18 UNL     1       5.719   1.192   0.815  1.00  0.00           H  
HETATM   35  H19 UNL     1       6.663  -0.200   0.261  1.00  0.00           H  
HETATM   36  H20 UNL     1       4.707   1.155  -1.333  1.00  0.00           H  
CONECT    1    2   17   18   19
CONECT    2    3    4    5
CONECT    3   20   21   22
CONECT    4   23   24   25
CONECT    5    6   26   27
CONECT    6    7   28   29
CONECT    7    8
CONECT    8    9    9   10   11
CONECT   11   12
CONECT   12   13   30   31
CONECT   13   14   15   32
CONECT   14   33
CONECT   15   16   34   35
CONECT   16   36
END

HMDB0252858
     RDKit          3D
Glycerylphosphorylcholine
 36 35  0  0  0  0  0  0  0  0999 V2000
   -3.4587   -0.4540   -1.7173 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4371   -0.2028   -0.2908 N   0  0  0  0  0  4  0  0  0  0  0  0
   -3.8347    1.1590   -0.0501 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4595   -1.0673    0.2917 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1810   -0.5610    0.3042 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1552    0.5375    0.2739 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1035   -0.0848    0.3018 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1544    0.7814   -0.6801 P   0  0  0  0  0  5  0  0  0  0  0  0
    1.2189    2.1891   -0.1610 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5126    0.8183   -2.2539 O   0  0  0  0  0  1  0  0  0  0  0  0
    2.6572    0.0402   -0.7757 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.2333   -0.0307    0.4840 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6007   -0.6546    0.4494 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6806   -1.6982   -0.4544 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.6925    0.3321    0.1216 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.6074    0.7930   -1.1902 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1245   -1.4676   -1.9846 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7858    0.2650   -2.2263 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4771   -0.3303   -2.1120 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8733    1.3251    1.0392 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1645    1.8667   -0.5811 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8387    1.2909   -0.5011 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0284   -2.0957    0.2922 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4106   -1.0016   -0.2629 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5800   -0.7519    1.3585 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3835   -0.8229    1.3672 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7647   -1.4290   -0.2312 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2364    1.2046   -0.5985 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1962    1.1471    1.2120 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5801   -0.6824    1.1026 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2525    0.9576    0.9620 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.8100   -1.0407    1.4727 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1971   -2.4794   -0.0795 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.7194    1.1924    0.8150 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.6626   -0.2004    0.2605 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.7072    1.1553   -1.3325 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  2  4  1  0
  2  5  1  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
 11 12  1  0
 12 13  1  0
 13 14  1  0
 13 15  1  0
 15 16  1  0
  1 17  1  0
  1 18  1  0
  1 19  1  0
  3 20  1  0
  3 21  1  0
  3 22  1  0
  4 23  1  0
  4 24  1  0
  4 25  1  0
  5 26  1  0
  5 27  1  0
  6 28  1  0
  6 29  1  0
 12 30  1  0
 12 31  1  0
 13 32  1  0
 14 33  1  0
 15 34  1  0
 15 35  1  0
 16 36  1  0
M  CHG  2   2   1  10  -1
M  END

Synonyms

Value	Source
Choline alfosceric acid	Generator
Glycerophosphate, choline	MeSH
Alphoscerate, choline	MeSH
Choline glycerophosphate	MeSH
Glycerol 3 phosphocholine	MeSH
3-Phosphocholine, glycerol	MeSH
Glycerophosphorylcholine	MeSH
L alpha Glycerylphosphorylcholine	MeSH
Glycerol 3-phosphocholine	MeSH
Choline alphoscerate	MeSH
Alfoscerate, choline	MeSH
L-alpha-Glycerylphosphorylcholine	MeSH

Molecular Formula

C₈H₂₀NO₆P

Average Mass

257.2213

Monoisotopic Mass

257.102823889

IUPAC Name

{2-[(2,3-dihydroxypropyl phosphono)oxy]ethyl}trimethylazanium

Traditional Name

{2-[(2,3-dihydroxypropyl phosphono)oxy]ethyl}trimethylazanium

CAS Registry Number

Not Available

SMILES

C[N+](C)(C)CCOP([O-])(=O)OCC(O)CO

InChI Identifier

InChI=1S/C8H20NO6P/c1-9(2,3)4-5-14-16(12,13)15-7-8(11)6-10/h8,10-11H,4-7H2,1-3H3

InChI Key

SUHOQUVVVLNYQR-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as glycerophosphocholines. These are lipids containing a glycerol moiety carrying a phosphocholine at the 3-position.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Glycerophospholipids

Sub Class

Glycerophosphocholines

Direct Parent

Glycerophosphocholines

Alternative Parents

Substituents

Glycero-3-phosphocholine
Phosphocholine
Dialkyl phosphate
Organic phosphoric acid derivative
Phosphoric acid ester
Alkyl phosphate
Tetraalkylammonium salt
Quaternary ammonium salt
1,2-diol
Secondary alcohol
Organic nitrogen compound
Organic salt
Hydrocarbon derivative
Primary alcohol
Organic oxide
Organopnictogen compound
Organooxygen compound
Organonitrogen compound
Organic oxygen compound
Amine
Alcohol
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

a small molecule (L-1-GLYCERO-PHOSPHORYLCHOLINE )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	8.96 g/L	ALOGPS
logP	-2.6	ALOGPS
logP	-5.7	ChemAxon
logS	-1.5	ALOGPS
pKa (Strongest Acidic)	1.86	ChemAxon
pKa (Strongest Basic)	-3	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	99.05 Å²	ChemAxon
Rotatable Bond Count	8	ChemAxon
Refractivity	68.68 m³·mol⁻¹	ChemAxon
Polarizability	24.82 Å³	ChemAxon
Number of Rings	0	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

Not Available

Biospecimen Locations

Not Available

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

Human Pathways

Pathways

Name	SMPDB/PathBank

Metabolic Reactions

Reactions

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference
MMDBr0018537	sn-glycero-3-phosphocholine	Benzyl alcohol	Glycerophosphodiester phosphodiesterase, periplasmic	Formation of 2'-nucleotide products from 2',3'-cyclic substrates	PathBank	31602464
MMDBr0025591	Glycerophosphocholine	CoA	Glycerophosphocholine acyltransferase 1	Acylation	RHEA	34755880
MMDBr0025592	Glycerophosphocholine	CoA	Glycerophosphocholine acyltransferase 1	Acylation	RHEA	34755880
MMDBr0025593	Glycerophosphocholine	CoA	Glycerophosphocholine acyltransferase 1	Acylation	RHEA	34755880
MMDBr0025594	Glycerophosphocholine	CoA	Glycerophosphocholine acyltransferase 1	Acylation	RHEA	34755880
MMDBr0025595	Glycerophosphocholine	CoA	Glycerophosphocholine acyltransferase 1	Acylation	RHEA	34755880
MMDBr0025596	Glycerophosphocholine	CoA	Glycerophosphocholine acyltransferase 1	Acylation	RHEA	34755880
MMDBr0025599	Glycerophosphocholine	CoA	Glycerophosphocholine acyltransferase 1	Acylation	RHEA	34755880
MMDBr0025600	Glycerophosphocholine	CoA	Glycerophosphocholine acyltransferase 1	Acylation	RHEA	34755880
MMDBr0025601	Glycerophosphocholine	CoA	Glycerophosphocholine acyltransferase 1	Acylation	RHEA	34755880
MMDBr0025602	Glycerophosphocholine	CoA	Glycerophosphocholine acyltransferase 1	Acylation	RHEA	34755880
MMDBr0025607	Glycerophosphocholine	sn-glycero-3-phosphoethanolamine	Glycerophosphocholine acyltransferase 1	Acylation	RHEA	34755880
MMDBr0025608	Glycerophosphocholine	sn-glycero-3-phosphoethanolamine	Glycerophosphocholine acyltransferase 1	Acylation	RHEA	34755880
MMDBr0025661	Glycerophosphocholine	CoA	Glycerophosphocholine acyltransferase 1	Acylation	RHEA	34755880

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/Eubacteria	Proteobacteria	1	Human ; Human feces; Human feces; pleural fluid plaque; bal; Human stool	Unknown
Eukaryota/Fungi	Ascomycota	5	Human feces; Human saliva	Unknown

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

External Links

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

FDB021802

KNApSAcK ID

Not Available

Chemspider ID

Not Available

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Alpha-GPC

METLIN ID

Not Available

PubChem Compound

11234

PDB ID

Not Available

ChEBI ID

Not Available

Food Biomarker Ontology

Not Available

References

Synthesis Reference

Not Available

General References

Barupal DK, Fiehn O: Generating the Blood Exposome Database Using a Comprehensive Text Mining and Database Fusion Approach. Environ Health Perspect. 2019 Sep;127(9):97008. doi: 10.1289/EHP4713. Epub 2019 Sep 26. [PubMed:31557052 ]

Showing metabocard for sn-glycero-3-phosphocholine (MMDBc0032168)

MOL for #<Metabolite:0x00007f923fde8b08>

3D MOL for #<Metabolite:0x00007f923fde8b08>

3D SDF for #<Metabolite:0x00007f923fde8b08>

3D-SDF for #<Metabolite:0x00007f923fde8b08>

PDB for #<Metabolite:0x00007f923fde8b08>

3D PDB for #<Metabolite:0x00007f923fde8b08>

SMILES for #<Metabolite:0x00007f923fde8b08>

INCHI for #<Metabolite:0x00007f923fde8b08>

Structure for #<Metabolite:0x00007f923fde8b08>

3D Structure for #<Metabolite:0x00007f923fde8b08>