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Record Information

Version

5.0

Status

Expected but not Quantified

Creation Date

2012-09-11 18:54:00 UTC

Update Date

2022-03-07 02:53:59 UTC

HMDB ID

HMDB0034105

Secondary Accession Numbers

HMDB34105

Metabolite Identification

Common Name

Glycinol

Description

Glycinol belongs to the class of organic compounds known as pterocarpans. These are benzo-pyrano-furano-benzene compounds, containing the 6H-[1]benzofuro[3,2-c]chromene skeleton. They are derivatives of isoflavonoids. Glycinol has been detected, but not quantified in, several different foods, such as gram beans (Vigna mungo), pulses, scarlet beans (Phaseolus coccineus), and soy beans (Glycine max). This could make glycinol a potential biomarker for the consumption of these foods. Glycinol is a primary metabolite. Primary metabolites are metabolically or physiologically essential metabolites. They are directly involved in an organism’s growth, development or reproduction. Based on a literature review a significant number of articles have been published on Glycinol.

Structure

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

HMDB0034105
     RDKit          3D
Glycinol
 32 35  0  0  0  0  0  0  0  0999 V2000
   -4.7213    1.1374   -1.3597 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5936    0.8035   -0.5937 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8651    1.7573    0.0842 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7580    1.4509    0.8398 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3358    0.1268    0.9391 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0555   -0.8331    0.2662 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1750   -0.5066   -0.4950 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6042   -2.1478    0.3873 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1994   -2.3494    0.3088 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5937   -1.3577    1.0714 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3758   -1.9935    2.0436 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.5240   -0.5676    0.1893 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2611   -0.8836   -0.9221 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0511    0.0585   -1.5486 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0955    1.3374   -1.0431 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8930    2.2561   -1.6897 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.3624    1.6972    0.0822 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5843    0.7313    0.6825 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7575    0.8417    1.8208 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1680   -0.2636    1.7365 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6558    1.1477   -0.9236 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1646    2.7894    0.0283 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1725    2.1778    1.3785 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7225   -1.2969   -1.0132 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0236   -3.3787    0.6558 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1248   -2.3342   -0.7720 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9060   -2.7467    1.6546 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1832   -1.9170   -1.2751 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6018   -0.2701   -2.4198 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.8758    2.4204   -1.4648 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4404    2.7159    0.4286 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4627   -0.6029    2.7444 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  2  0
  6  8  1  0
  8  9  1  0
  9 10  1  0
 10 11  1  0
 10 12  1  0
 12 13  2  0
 13 14  1  0
 14 15  2  0
 15 16  1  0
 15 17  1  0
 17 18  2  0
 18 19  1  0
 19 20  1  0
  7  2  1  0
 20 10  1  0
 20  5  1  0
 18 12  1  0
  1 21  1  0
  3 22  1  0
  4 23  1  0
  7 24  1  0
  9 25  1  0
  9 26  1  0
 11 27  1  0
 13 28  1  0
 14 29  1  0
 16 30  1  0
 17 31  1  0
 20 32  1  0
M  END


  Mrv0541 05061307352D          

 20 23  0  0  0  0            999 V2000
    5.3033   -2.6629    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5275   -1.5272    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4796   -2.7100    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2608   -1.1491    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.2216   -1.2363    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1823   -2.7972    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1217   -0.6408    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.6743   -1.9260    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4883   -2.3512    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0270   -2.0203    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9548   -1.5951    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3980   -1.2834    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9156   -2.4191    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2033   -2.0674    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7507   -1.3777    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.4979   -1.8789    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2450   -2.7293    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.2284   -0.7391    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.9453   -0.5937    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6872   -2.7111    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  3  1  2  0  0  0  0
  4  2  2  0  0  0  0
  8  1  1  0  0  0  0
  8  5  2  0  0  0  0
  9  2  1  0  0  0  0
  9  6  2  0  0  0  0
 10  3  1  0  0  0  0
 11  4  1  0  0  0  0
 12  5  1  0  0  0  0
 12 10  2  0  0  0  0
 13  6  1  0  0  0  0
 13 11  2  0  0  0  0
 14 10  1  0  0  0  0
 15  7  1  0  0  0  0
 15 11  1  0  0  0  0
 15 14  1  0  0  0  0
 16  8  1  0  0  0  0
 17  9  1  0  0  0  0
 18 15  1  0  0  0  0
 19  7  1  0  0  0  0
 19 12  1  0  0  0  0
 20 13  1  0  0  0  0
 20 14  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0034105

> <DATABASE_NAME>
hmdb

> <SMILES>
OC1=CC2=C(C=C1)C1(O)COC3=C(C=CC(O)=C3)C1O2

> <INCHI_IDENTIFIER>
InChI=1S/C15H12O5/c16-8-1-3-10-12(5-8)19-7-15(18)11-4-2-9(17)6-13(11)20-14(10)15/h1-6,14,16-18H,7H2

> <INCHI_KEY>
QMXOFBXZEKTJIK-UHFFFAOYSA-N

> <FORMULA>
C15H12O5

> <MOLECULAR_WEIGHT>
272.2528

> <EXACT_MASS>
272.068473494

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_AVERAGE_POLARIZABILITY>
26.92507649611905

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
8,17-dioxatetracyclo[8.7.0.0²,⁷.0¹¹,¹⁶]heptadeca-2(7),3,5,11(16),12,14-hexaene-5,10,14-triol

> <ALOGPS_LOGP>
1.57

> <JCHEM_LOGP>
1.708148958333333

> <ALOGPS_LOGS>
-2.51

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
9.705735071945579

> <JCHEM_PKA_STRONGEST_ACIDIC>
9.104196319626872

> <JCHEM_PKA_STRONGEST_BASIC>
-4.093074864333841

> <JCHEM_POLAR_SURFACE_AREA>
79.15

> <JCHEM_REFRACTIVITY>
69.6667

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
8.45e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
glycinol (pterocarpan)

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0034105
     RDKit          3D
Glycinol
 32 35  0  0  0  0  0  0  0  0999 V2000
   -4.7213    1.1374   -1.3597 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5936    0.8035   -0.5937 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8651    1.7573    0.0842 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7580    1.4509    0.8398 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3358    0.1268    0.9391 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0555   -0.8331    0.2662 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1750   -0.5066   -0.4950 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6042   -2.1478    0.3873 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1994   -2.3494    0.3088 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5937   -1.3577    1.0714 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3758   -1.9935    2.0436 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.5240   -0.5676    0.1893 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2611   -0.8836   -0.9221 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0511    0.0585   -1.5486 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0955    1.3374   -1.0431 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8930    2.2561   -1.6897 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.3624    1.6972    0.0822 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5843    0.7313    0.6825 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7575    0.8417    1.8208 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1680   -0.2636    1.7365 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6558    1.1477   -0.9236 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1646    2.7894    0.0283 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1725    2.1778    1.3785 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7225   -1.2969   -1.0132 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0236   -3.3787    0.6558 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1248   -2.3342   -0.7720 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9060   -2.7467    1.6546 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1832   -1.9170   -1.2751 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6018   -0.2701   -2.4198 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.8758    2.4204   -1.4648 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4404    2.7159    0.4286 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4627   -0.6029    2.7444 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  2  0
  6  8  1  0
  8  9  1  0
  9 10  1  0
 10 11  1  0
 10 12  1  0
 12 13  2  0
 13 14  1  0
 14 15  2  0
 15 16  1  0
 15 17  1  0
 17 18  2  0
 18 19  1  0
 19 20  1  0
  7  2  1  0
 20 10  1  0
 20  5  1  0
 18 12  1  0
  1 21  1  0
  3 22  1  0
  4 23  1  0
  7 24  1  0
  9 25  1  0
  9 26  1  0
 11 27  1  0
 13 28  1  0
 14 29  1  0
 16 30  1  0
 17 31  1  0
 20 32  1  0
M  END

HEADER    PROTEIN                                 06-MAY-13   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   06-MAY-13         0                                  
HETATM    1  C   UNK     0       9.899  -4.971   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.985  -2.851   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       8.362  -5.059   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       2.353  -2.145   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       9.747  -2.308   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       2.207  -5.221   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       5.827  -1.196   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      10.592  -3.595   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       0.911  -4.389   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       7.517  -3.771   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       3.649  -2.978   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       8.210  -2.396   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       3.576  -4.516   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       5.979  -3.859   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       5.135  -2.572   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0      12.129  -3.507   0.000  0.00  0.00           O+0
HETATM   17  O   UNK     0      -0.457  -5.095   0.000  0.00  0.00           O+0
HETATM   18  O   UNK     0       4.160  -1.380   0.000  0.00  0.00           O+0
HETATM   19  O   UNK     0       7.365  -1.108   0.000  0.00  0.00           O+0
HETATM   20  O   UNK     0       5.016  -5.061   0.000  0.00  0.00           O+0
CONECT    1    3    8                                                       
CONECT    2    4    9                                                       
CONECT    3    1   10                                                       
CONECT    4    2   11                                                       
CONECT    5    8   12                                                       
CONECT    6    9   13                                                       
CONECT    7   15   19                                                       
CONECT    8    1    5   16                                                  
CONECT    9    2    6   17                                                  
CONECT   10    3   12   14                                                  
CONECT   11    4   13   15                                                  
CONECT   12    5   10   19                                                  
CONECT   13    6   11   20                                                  
CONECT   14   10   15   20                                                  
CONECT   15    7   11   14   18                                             
CONECT   16    8                                                            
CONECT   17    9                                                            
CONECT   18   15                                                            
CONECT   19    7   12                                                       
CONECT   20   13   14                                                       
MASTER        0    0    0    0    0    0    0    0   20    0   46    0
END

COMPND    HMDB0034105
HETATM    1  O1  UNL     1      -4.721   1.137  -1.360  1.00  0.00           O  
HETATM    2  C1  UNL     1      -3.594   0.804  -0.594  1.00  0.00           C  
HETATM    3  C2  UNL     1      -2.865   1.757   0.084  1.00  0.00           C  
HETATM    4  C3  UNL     1      -1.758   1.451   0.840  1.00  0.00           C  
HETATM    5  C4  UNL     1      -1.336   0.127   0.939  1.00  0.00           C  
HETATM    6  C5  UNL     1      -2.055  -0.833   0.266  1.00  0.00           C  
HETATM    7  C6  UNL     1      -3.175  -0.507  -0.495  1.00  0.00           C  
HETATM    8  O2  UNL     1      -1.604  -2.148   0.387  1.00  0.00           O  
HETATM    9  C7  UNL     1      -0.199  -2.349   0.309  1.00  0.00           C  
HETATM   10  C8  UNL     1       0.594  -1.358   1.071  1.00  0.00           C  
HETATM   11  O3  UNL     1       1.376  -1.994   2.044  1.00  0.00           O  
HETATM   12  C9  UNL     1       1.524  -0.568   0.189  1.00  0.00           C  
HETATM   13  C10 UNL     1       2.261  -0.884  -0.922  1.00  0.00           C  
HETATM   14  C11 UNL     1       3.051   0.059  -1.549  1.00  0.00           C  
HETATM   15  C12 UNL     1       3.095   1.337  -1.043  1.00  0.00           C  
HETATM   16  O4  UNL     1       3.893   2.256  -1.690  1.00  0.00           O  
HETATM   17  C13 UNL     1       2.362   1.697   0.082  1.00  0.00           C  
HETATM   18  C14 UNL     1       1.584   0.731   0.682  1.00  0.00           C  
HETATM   19  O5  UNL     1       0.758   0.842   1.821  1.00  0.00           O  
HETATM   20  C15 UNL     1      -0.168  -0.264   1.736  1.00  0.00           C  
HETATM   21  H1  UNL     1      -5.656   1.148  -0.924  1.00  0.00           H  
HETATM   22  H2  UNL     1      -3.165   2.789   0.028  1.00  0.00           H  
HETATM   23  H3  UNL     1      -1.172   2.178   1.378  1.00  0.00           H  
HETATM   24  H4  UNL     1      -3.723  -1.297  -1.013  1.00  0.00           H  
HETATM   25  H5  UNL     1       0.024  -3.379   0.656  1.00  0.00           H  
HETATM   26  H6  UNL     1       0.125  -2.334  -0.772  1.00  0.00           H  
HETATM   27  H7  UNL     1       1.906  -2.747   1.655  1.00  0.00           H  
HETATM   28  H8  UNL     1       2.183  -1.917  -1.275  1.00  0.00           H  
HETATM   29  H9  UNL     1       3.602  -0.270  -2.420  1.00  0.00           H  
HETATM   30  H10 UNL     1       4.876   2.420  -1.465  1.00  0.00           H  
HETATM   31  H11 UNL     1       2.440   2.716   0.429  1.00  0.00           H  
HETATM   32  H12 UNL     1      -0.463  -0.603   2.744  1.00  0.00           H  
CONECT    1    2   21
CONECT    2    3    3    7
CONECT    3    4   22
CONECT    4    5    5   23
CONECT    5    6   20
CONECT    6    7    7    8
CONECT    7   24
CONECT    8    9
CONECT    9   10   25   26
CONECT   10   11   12   20
CONECT   11   27
CONECT   12   13   13   18
CONECT   13   14   28
CONECT   14   15   15   29
CONECT   15   16   17
CONECT   16   30
CONECT   17   18   18   31
CONECT   18   19
CONECT   19   20
CONECT   20   32
END

HMDB0034105
     RDKit          3D
Glycinol
 32 35  0  0  0  0  0  0  0  0999 V2000
   -4.7213    1.1374   -1.3597 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5936    0.8035   -0.5937 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8651    1.7573    0.0842 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7580    1.4509    0.8398 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3358    0.1268    0.9391 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0555   -0.8331    0.2662 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1750   -0.5066   -0.4950 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6042   -2.1478    0.3873 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1994   -2.3494    0.3088 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5937   -1.3577    1.0714 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3758   -1.9935    2.0436 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.5240   -0.5676    0.1893 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2611   -0.8836   -0.9221 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0511    0.0585   -1.5486 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0955    1.3374   -1.0431 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8930    2.2561   -1.6897 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.3624    1.6972    0.0822 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5843    0.7313    0.6825 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7575    0.8417    1.8208 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1680   -0.2636    1.7365 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6558    1.1477   -0.9236 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1646    2.7894    0.0283 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1725    2.1778    1.3785 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7225   -1.2969   -1.0132 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0236   -3.3787    0.6558 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1248   -2.3342   -0.7720 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9060   -2.7467    1.6546 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1832   -1.9170   -1.2751 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6018   -0.2701   -2.4198 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.8758    2.4204   -1.4648 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4404    2.7159    0.4286 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4627   -0.6029    2.7444 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  2  0
  6  8  1  0
  8  9  1  0
  9 10  1  0
 10 11  1  0
 10 12  1  0
 12 13  2  0
 13 14  1  0
 14 15  2  0
 15 16  1  0
 15 17  1  0
 17 18  2  0
 18 19  1  0
 19 20  1  0
  7  2  1  0
 20 10  1  0
 20  5  1  0
 18 12  1  0
  1 21  1  0
  3 22  1  0
  4 23  1  0
  7 24  1  0
  9 25  1  0
  9 26  1  0
 11 27  1  0
 13 28  1  0
 14 29  1  0
 16 30  1  0
 17 31  1  0
 20 32  1  0
M  END

View in JSmol View Stereo Labels

Synonyms

Value	Source
(-)-Glycinol	HMDB
(6AlphaS,11alphas)-3,6alpha,9-trihydroxypterocarpan	HMDB
(6AS,11as)-3,6a,9-trihydroxypterocarpan	HMDB
3,6,9-Trihydroxypterocarpan	HMDB
6AS11as-36a9-trihydroxypterocarpan	HMDB
6H-benzofuro[3,2-c][1]Benzopyran-3,6a,9(11ah)-triol, 9ci	HMDB

Chemical Formula

C₁₅H₁₂O₅

Average Molecular Weight

272.2528

Monoisotopic Molecular Weight

272.068473494

IUPAC Name

8,17-dioxatetracyclo[8.7.0.0²,⁷.0¹¹,¹⁶]heptadeca-2(7),3,5,11(16),12,14-hexaene-5,10,14-triol

Traditional Name

glycinol (pterocarpan)

CAS Registry Number

69393-95-9

SMILES

OC1=CC2=C(C=C1)C1(O)COC3=C(C=CC(O)=C3)C1O2

InChI Identifier

InChI=1S/C15H12O5/c16-8-1-3-10-12(5-8)19-7-15(18)11-4-2-9(17)6-13(11)20-14(10)15/h1-6,14,16-18H,7H2

InChI Key

QMXOFBXZEKTJIK-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as pterocarpans. These are benzo-pyrano-furano-benzene compounds, containing the 6H-[1]benzofuro[3,2-c]chromene skeleton. They are derivatives of isoflavonoids.

Kingdom

Organic compounds

Super Class

Phenylpropanoids and polyketides

Class

Isoflavonoids

Sub Class

Furanoisoflavonoids

Direct Parent

Pterocarpans

Alternative Parents

Substituents

Pterocarpan
Isoflavanol
Isoflavan
Chromane
Benzopyran
1-benzopyran
Coumaran
Benzofuran
1-hydroxy-2-unsubstituted benzenoid
Alkyl aryl ether
Benzenoid
Tertiary alcohol
Oxacycle
Organoheterocyclic compound
Ether
Polyol
Alcohol
Organic oxygen compound
Hydrocarbon derivative
Organooxygen compound
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

a small molecule (6AS11AS-36A9-TRIHYDROXYPTEROCARPAN )

Ontology

Physiological effect

Not Available

Disposition

Biological location

Cellular substructure

Extracellular (HMDB: HMDB0034105)
Cytoplasm (HMDB: HMDB0034105)

Cytoplasm (HMDB: HMDB0034105)
Extracellular (HMDB: HMDB0034105)

Route of exposure

Enteral

Ingestion (HMDB: HMDB0034105)

Source

Exogenous

Food

Food (HMDB: HMDB0034105)

Pulse

Bean

Gram bean (FooDB: FOOD00199)
Scarlet bean (FooDB: FOOD00132)

Pulses (FooDB: FOOD00867)

Soy

Soy bean (FooDB: FOOD00085)

Not Available

Physical Properties

State

Not Available

Experimental Molecular Properties

Property	Value	Reference
Melting Point	Not Available	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	Not Available	Not Available
LogP	Not Available	Not Available

Experimental Chromatographic Properties

Not Available

Predicted Molecular Properties

Property	Value	Source
Water Solubility	0.84 g/L	ALOGPS
logP	1.57	ALOGPS
logP	1.71	ChemAxon
logS	-2.5	ALOGPS
pKa (Strongest Acidic)	9.1	ChemAxon
pKa (Strongest Basic)	-4.1	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	79.15 Å²	ChemAxon
Rotatable Bond Count	0	ChemAxon
Refractivity	69.67 m³·mol⁻¹	ChemAxon
Polarizability	26.93 Å³	ChemAxon
Number of Rings	4	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Predicted Chromatographic Properties

Predicted Collision Cross Sections

Predictor	Adduct Type	CCS Value (Å²)	Reference
DarkChem	[M+H]+	162.97	31661259
DarkChem	[M-H]-	163.17	31661259
DeepCCS	[M+H]+	162.339	30932474
DeepCCS	[M-H]-	159.982	30932474
DeepCCS	[M-2H]-	193.882	30932474
DeepCCS	[M+Na]+	168.99	30932474
AllCCS	[M+H]+	162.8	32859911
AllCCS	[M+H-H2O]+	159.0	32859911
AllCCS	[M+NH4]+	166.3	32859911
AllCCS	[M+Na]+	167.3	32859911
AllCCS	[M-H]-	165.0	32859911
AllCCS	[M+Na-2H]-	164.2	32859911
AllCCS	[M+HCOO]-	163.5	32859911

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
Glycinol	OC1=CC2=C(C=C1)C1(O)COC3=C(C=CC(O)=C3)C1O2	3973.9	Standard polar	33892256
Glycinol	OC1=CC2=C(C=C1)C1(O)COC3=C(C=CC(O)=C3)C1O2	2615.3	Standard non polar	33892256
Glycinol	OC1=CC2=C(C=C1)C1(O)COC3=C(C=CC(O)=C3)C1O2	2819.8	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
Glycinol,1TMS,isomer #1	C[Si](C)(C)OC1=CC=C2C(=C1)OC1C3=CC=C(O)C=C3OCC21O	2617.6	Semi standard non polar	33892256
Glycinol,1TMS,isomer #2	C[Si](C)(C)OC12COC3=CC(O)=CC=C3C1OC1=CC(O)=CC=C12	2666.1	Semi standard non polar	33892256
Glycinol,1TMS,isomer #3	C[Si](C)(C)OC1=CC=C2C(=C1)OCC1(O)C3=CC=C(O)C=C3OC21	2627.8	Semi standard non polar	33892256
Glycinol,2TMS,isomer #1	C[Si](C)(C)OC1=CC=C2C(=C1)OCC1(O)C3=CC=C(O[Si](C)(C)C)C=C3OC21	2685.4	Semi standard non polar	33892256
Glycinol,2TMS,isomer #2	C[Si](C)(C)OC1=CC=C2C(=C1)OC1C3=CC=C(O)C=C3OCC21O[Si](C)(C)C	2616.1	Semi standard non polar	33892256
Glycinol,2TMS,isomer #3	C[Si](C)(C)OC1=CC=C2C(=C1)OCC1(O[Si](C)(C)C)C3=CC=C(O)C=C3OC21	2626.0	Semi standard non polar	33892256
Glycinol,3TMS,isomer #1	C[Si](C)(C)OC1=CC=C2C(=C1)OCC1(O[Si](C)(C)C)C3=CC=C(O[Si](C)(C)C)C=C3OC21	2695.3	Semi standard non polar	33892256
Glycinol,1TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC1=CC=C2C(=C1)OC1C3=CC=C(O)C=C3OCC21O	2886.8	Semi standard non polar	33892256
Glycinol,1TBDMS,isomer #2	CC(C)(C)[Si](C)(C)OC12COC3=CC(O)=CC=C3C1OC1=CC(O)=CC=C12	2940.2	Semi standard non polar	33892256
Glycinol,1TBDMS,isomer #3	CC(C)(C)[Si](C)(C)OC1=CC=C2C(=C1)OCC1(O)C3=CC=C(O)C=C3OC21	2906.7	Semi standard non polar	33892256
Glycinol,2TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC1=CC=C2C(=C1)OCC1(O)C3=CC=C(O[Si](C)(C)C(C)(C)C)C=C3OC21	3172.5	Semi standard non polar	33892256
Glycinol,2TBDMS,isomer #2	CC(C)(C)[Si](C)(C)OC1=CC=C2C(=C1)OC1C3=CC=C(O)C=C3OCC21O[Si](C)(C)C(C)(C)C	3125.8	Semi standard non polar	33892256
Glycinol,2TBDMS,isomer #3	CC(C)(C)[Si](C)(C)OC1=CC=C2C(=C1)OCC1(O[Si](C)(C)C(C)(C)C)C3=CC=C(O)C=C3OC21	3136.1	Semi standard non polar	33892256
Glycinol,3TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC1=CC=C2C(=C1)OCC1(O[Si](C)(C)C(C)(C)C)C3=CC=C(O[Si](C)(C)C(C)(C)C)C=C3OC21	3388.6	Semi standard non polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted GC-MS	Predicted GC-MS Spectrum - Glycinol GC-MS (Non-derivatized) - 70eV, Positive	splash10-006x-1390000000-03247c0439f7f23ecb93	2017-09-01	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Glycinol GC-MS (3 TMS) - 70eV, Positive	splash10-00di-6301900000-e98ae9d9b1e6e06dad24	2017-10-06	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Glycinol GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum

MS/MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Glycinol 10V, Positive-QTOF	splash10-00di-0090000000-89076b1424a2b5347c64	2015-05-27	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Glycinol 20V, Positive-QTOF	splash10-00di-0090000000-4f713deccce1e2eeb99b	2015-05-27	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Glycinol 40V, Positive-QTOF	splash10-0296-9210000000-c3a13ba93565382ef587	2015-05-27	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Glycinol 10V, Negative-QTOF	splash10-00di-0090000000-2c169a573920349692a4	2015-05-27	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Glycinol 20V, Negative-QTOF	splash10-00di-0090000000-db6c37567de37e26f11d	2015-05-27	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Glycinol 40V, Negative-QTOF	splash10-052o-5690000000-14e38b0224023759d399	2015-05-27	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Glycinol 10V, Negative-QTOF	splash10-00di-0090000000-d6b6f6391b4e9f4522f4	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Glycinol 20V, Negative-QTOF	splash10-00di-0390000000-1440e0965dfc5aac238c	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Glycinol 40V, Negative-QTOF	splash10-05tf-4390000000-77e65a54952a48719b72	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Glycinol 10V, Positive-QTOF	splash10-00di-0090000000-031a5312b116bdf1aa4a	2021-09-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Glycinol 20V, Positive-QTOF	splash10-00di-0090000000-cdb65eb7f4ab7a17bce6	2021-09-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Glycinol 40V, Positive-QTOF	splash10-03k9-5940000000-798b4a64e574722b56c4	2021-09-24	Wishart Lab	View Spectrum

Biological Properties

Cellular Locations

Cytoplasm
Extracellular

Biospecimen Locations

Not Available

Tissue Locations

Not Available

Pathways

Not Available

Name	SMPDB/PathBank	KEGG

Normal Concentrations

Not Available

Abnormal Concentrations

Not Available

Associated Disorders and Diseases

Disease References

None

Associated OMIM IDs

None

External Links

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

KNApSAcK ID

Chemspider ID

KEGG Compound ID

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Glycinol

METLIN ID

Not Available

PubChem Compound

4629012

PDB ID

Not Available

ChEBI ID

15649

Food Biomarker Ontology

Not Available

VMH ID

Not Available

MarkerDB ID

Not Available

Good Scents ID

Not Available

References

Synthesis Reference

Not Available

Material Safety Data Sheet (MSDS)

Not Available

General References

(). Yannai, Shmuel. (2004) Dictionary of food compounds with CD-ROM: Additives, flavors, and ingredients. Boca Raton: Chapman & Hall/CRC.. .

Showing metabocard for Glycinol (HMDB0034105)

MOL for HMDB0034105 (Glycinol)

3D MOL for HMDB0034105 (Glycinol)

3D SDF for HMDB0034105 (Glycinol)

3D-SDF for HMDB0034105 (Glycinol)

PDB for HMDB0034105 (Glycinol)

3D PDB for HMDB0034105 (Glycinol)

SMILES for HMDB0034105 (Glycinol)

INCHI for HMDB0034105 (Glycinol)

Structure for HMDB0034105 (Glycinol)

3D Structure for HMDB0034105 (Glycinol)

Predicted Collision Cross Sections

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra