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Record Information

Version

5.0

Status

Expected but not Quantified

Creation Date

2012-09-12 02:54:49 UTC

Update Date

2022-03-07 02:56:56 UTC

HMDB ID

HMDB0041243

Secondary Accession Numbers

HMDB41243

Metabolite Identification

Common Name

1,3,6-Trihydroxy-5-methoxyxanthone

Description

1,3,6-Trihydroxy-5-methoxyxanthone belongs to the class of organic compounds known as xanthones. These are polycyclic aromatic compounds containing a xanthene moiety conjugated to a ketone group at carbon 9. Xanthene is a tricyclic compound made up of two benzene rings linearly fused to each other through a pyran ring. 1,3,6-Trihydroxy-5-methoxyxanthone has been detected, but not quantified in, fruits. This could make 1,3,6-trihydroxy-5-methoxyxanthone a potential biomarker for the consumption of these foods. Based on a literature review very few articles have been published on 1,3,6-Trihydroxy-5-methoxyxanthone.

Structure

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

HMDB0041243
     RDKit          3D
1,3,6-Trihydroxy-5-methoxyxanthone
 30 32  0  0  0  0  0  0  0  0999 V2000
   -3.0784   -2.3981   -0.4996 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7808   -1.4718    0.5088 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3131   -0.1915    0.2808 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2297    0.8262    0.1328 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5921    0.5852    0.2085 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7251    2.0894   -0.0932 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3975    2.3668   -0.1742 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4816    1.3322   -0.0233 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8818    1.5881   -0.1015 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2570    2.7548   -0.3079 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7850    0.5647    0.0479 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1454    0.7956   -0.0261 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7244    2.0032   -0.2446 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.0010   -0.3034    0.1373 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4643   -1.5463    0.3607 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3710   -2.6124    0.5171 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1060   -1.7554    0.4309 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2279   -0.6849    0.2729 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0628   -0.9024    0.3428 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9506    0.0618    0.2031 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7836   -1.9831   -1.4958 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5975   -3.3879   -0.3546 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1772   -2.5938   -0.5458 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2414    1.3529    0.0957 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4264    2.9220   -0.2156 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9910    3.3540   -0.3511 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3803    2.8954   -0.3862 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.0604   -0.1191    0.0789 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.6651   -2.7776    1.4723 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7591   -2.7644    0.6100 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  4  6  1  0
  6  7  2  0
  7  8  1  0
  8  9  1  0
  9 10  2  0
  9 11  1  0
 11 12  2  0
 12 13  1  0
 12 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
 20  3  1  0
 20  8  2  0
 18 11  1  0
  1 21  1  0
  1 22  1  0
  1 23  1  0
  5 24  1  0
  6 25  1  0
  7 26  1  0
 13 27  1  0
 14 28  1  0
 16 29  1  0
 17 30  1  0
M  END


  Mrv0541 05061312302D          

 20 22  0  0  0  0            999 V2000
   -1.4289    2.4750    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 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579    0.8250    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
   -1.4289    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -0.4125    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 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
    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
    3.5724    1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434    1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -1.2375    0.0000 O   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 O   0  0  0  0  0  0  0  0  0  0  0  0
  3  2  2  0  0  0  0
  6  4  2  0  0  0  0
  6  5  1  0  0  0  0
  7  2  1  0  0  0  0
  8  3  1  0  0  0  0
  9  4  1  0  0  0  0
 10  5  2  0  0  0  0
 11  9  2  0  0  0  0
 11 10  1  0  0  0  0
 12  7  1  0  0  0  0
 12 11  1  0  0  0  0
 13  7  2  0  0  0  0
 14  8  2  0  0  0  0
 14 13  1  0  0  0  0
 15  6  1  0  0  0  0
 16  8  1  0  0  0  0
 17  9  1  0  0  0  0
 18 12  2  0  0  0  0
 19  1  1  0  0  0  0
 19 14  1  0  0  0  0
 20 10  1  0  0  0  0
 20 13  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0041243

> <DATABASE_NAME>
hmdb

> <SMILES>
COC1=C(O)C=CC2=C1OC1=CC(O)=CC(O)=C1C2=O

> <INCHI_IDENTIFIER>
InChI=1S/C14H10O6/c1-19-14-8(16)3-2-7-12(18)11-9(17)4-6(15)5-10(11)20-13(7)14/h2-5,15-17H,1H3

> <INCHI_KEY>
OIDDYVZHNYQRKQ-UHFFFAOYSA-N

> <FORMULA>
C14H10O6

> <MOLECULAR_WEIGHT>
274.2256

> <EXACT_MASS>
274.047738052

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_AVERAGE_POLARIZABILITY>
26.109188627927654

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
1,3,6-trihydroxy-5-methoxy-9H-xanthen-9-one

> <ALOGPS_LOGP>
2.52

> <JCHEM_LOGP>
2.5412729896666666

> <ALOGPS_LOGS>
-2.86

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
8.165459388873684

> <JCHEM_PKA_STRONGEST_ACIDIC>
7.464954633290247

> <JCHEM_PKA_STRONGEST_BASIC>
-4.1795051760149

> <JCHEM_POLAR_SURFACE_AREA>
96.22

> <JCHEM_REFRACTIVITY>
69.22220000000002

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
3.79e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
1,3,6-trihydroxy-5-methoxyxanthen-9-one

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0041243
     RDKit          3D
1,3,6-Trihydroxy-5-methoxyxanthone
 30 32  0  0  0  0  0  0  0  0999 V2000
   -3.0784   -2.3981   -0.4996 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7808   -1.4718    0.5088 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3131   -0.1915    0.2808 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2297    0.8262    0.1328 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5921    0.5852    0.2085 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7251    2.0894   -0.0932 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3975    2.3668   -0.1742 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4816    1.3322   -0.0233 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8818    1.5881   -0.1015 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2570    2.7548   -0.3079 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7850    0.5647    0.0479 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1454    0.7956   -0.0261 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7244    2.0032   -0.2446 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.0010   -0.3034    0.1373 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4643   -1.5463    0.3607 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3710   -2.6124    0.5171 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1060   -1.7554    0.4309 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2279   -0.6849    0.2729 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0628   -0.9024    0.3428 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9506    0.0618    0.2031 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7836   -1.9831   -1.4958 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5975   -3.3879   -0.3546 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1772   -2.5938   -0.5458 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2414    1.3529    0.0957 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4264    2.9220   -0.2156 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9910    3.3540   -0.3511 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3803    2.8954   -0.3862 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.0604   -0.1191    0.0789 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.6651   -2.7776    1.4723 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7591   -2.7644    0.6100 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  4  6  1  0
  6  7  2  0
  7  8  1  0
  8  9  1  0
  9 10  2  0
  9 11  1  0
 11 12  2  0
 12 13  1  0
 12 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
 20  3  1  0
 20  8  2  0
 18 11  1  0
  1 21  1  0
  1 22  1  0
  1 23  1  0
  5 24  1  0
  6 25  1  0
  7 26  1  0
 13 27  1  0
 14 28  1  0
 16 29  1  0
 17 30  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      -2.667   4.620   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -2.667   0.000   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       5.335   0.000   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       4.001   2.310   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       5.335   1.540   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -2.667   1.540   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       4.001  -0.770   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       2.667   0.000   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      -1.334   2.310   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0       6.668   2.310   0.000  0.00  0.00           O+0
HETATM   16  O   UNK     0      -4.001   2.310   0.000  0.00  0.00           O+0
HETATM   17  O   UNK     0       4.001  -2.310   0.000  0.00  0.00           O+0
HETATM   18  O   UNK     0       1.334  -2.310   0.000  0.00  0.00           O+0
HETATM   19  O   UNK     0      -1.334   3.850   0.000  0.00  0.00           O+0
HETATM   20  O   UNK     0       1.334   2.310   0.000  0.00  0.00           O+0
CONECT    1   19                                                            
CONECT    2    3    7                                                       
CONECT    3    2    8                                                       
CONECT    4    6    9                                                       
CONECT    5    6   10                                                       
CONECT    6    4    5   15                                                  
CONECT    7    2   12   13                                                  
CONECT    8    3   14   16                                                  
CONECT    9    4   11   17                                                  
CONECT   10    5   11   20                                                  
CONECT   11    9   10   12                                                  
CONECT   12    7   11   18                                                  
CONECT   13    7   14   20                                                  
CONECT   14    8   13   19                                                  
CONECT   15    6                                                            
CONECT   16    8                                                            
CONECT   17    9                                                            
CONECT   18   12                                                            
CONECT   19    1   14                                                       
CONECT   20   10   13                                                       
MASTER        0    0    0    0    0    0    0    0   20    0   44    0
END

COMPND    HMDB0041243
HETATM    1  C1  UNL     1      -3.078  -2.398  -0.500  1.00  0.00           C  
HETATM    2  O1  UNL     1      -2.781  -1.472   0.509  1.00  0.00           O  
HETATM    3  C2  UNL     1      -2.313  -0.192   0.281  1.00  0.00           C  
HETATM    4  C3  UNL     1      -3.230   0.826   0.133  1.00  0.00           C  
HETATM    5  O2  UNL     1      -4.592   0.585   0.208  1.00  0.00           O  
HETATM    6  C4  UNL     1      -2.725   2.089  -0.093  1.00  0.00           C  
HETATM    7  C5  UNL     1      -1.397   2.367  -0.174  1.00  0.00           C  
HETATM    8  C6  UNL     1      -0.482   1.332  -0.023  1.00  0.00           C  
HETATM    9  C7  UNL     1       0.882   1.588  -0.101  1.00  0.00           C  
HETATM   10  O3  UNL     1       1.257   2.755  -0.308  1.00  0.00           O  
HETATM   11  C8  UNL     1       1.785   0.565   0.048  1.00  0.00           C  
HETATM   12  C9  UNL     1       3.145   0.796  -0.026  1.00  0.00           C  
HETATM   13  O4  UNL     1       3.724   2.003  -0.245  1.00  0.00           O  
HETATM   14  C10 UNL     1       4.001  -0.303   0.137  1.00  0.00           C  
HETATM   15  C11 UNL     1       3.464  -1.546   0.361  1.00  0.00           C  
HETATM   16  O5  UNL     1       4.371  -2.612   0.517  1.00  0.00           O  
HETATM   17  C12 UNL     1       2.106  -1.755   0.431  1.00  0.00           C  
HETATM   18  C13 UNL     1       1.228  -0.685   0.273  1.00  0.00           C  
HETATM   19  O6  UNL     1      -0.063  -0.902   0.343  1.00  0.00           O  
HETATM   20  C14 UNL     1      -0.951   0.062   0.203  1.00  0.00           C  
HETATM   21  H1  UNL     1      -2.784  -1.983  -1.496  1.00  0.00           H  
HETATM   22  H2  UNL     1      -2.598  -3.388  -0.355  1.00  0.00           H  
HETATM   23  H3  UNL     1      -4.177  -2.594  -0.546  1.00  0.00           H  
HETATM   24  H4  UNL     1      -5.241   1.353   0.096  1.00  0.00           H  
HETATM   25  H5  UNL     1      -3.426   2.922  -0.216  1.00  0.00           H  
HETATM   26  H6  UNL     1      -0.991   3.354  -0.351  1.00  0.00           H  
HETATM   27  H7  UNL     1       3.380   2.895  -0.386  1.00  0.00           H  
HETATM   28  H8  UNL     1       5.060  -0.119   0.079  1.00  0.00           H  
HETATM   29  H9  UNL     1       4.665  -2.778   1.472  1.00  0.00           H  
HETATM   30  H10 UNL     1       1.759  -2.764   0.610  1.00  0.00           H  
CONECT    1    2   21   22   23
CONECT    2    3
CONECT    3    4    4   20
CONECT    4    5    6
CONECT    5   24
CONECT    6    7    7   25
CONECT    7    8   26
CONECT    8    9   20   20
CONECT    9   10   10   11
CONECT   11   12   12   18
CONECT   12   13   14
CONECT   13   27
CONECT   14   15   15   28
CONECT   15   16   17
CONECT   16   29
CONECT   17   18   18   30
CONECT   18   19
CONECT   19   20
END

HMDB0041243
     RDKit          3D
1,3,6-Trihydroxy-5-methoxyxanthone
 30 32  0  0  0  0  0  0  0  0999 V2000
   -3.0784   -2.3981   -0.4996 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7808   -1.4718    0.5088 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3131   -0.1915    0.2808 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2297    0.8262    0.1328 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5921    0.5852    0.2085 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7251    2.0894   -0.0932 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3975    2.3668   -0.1742 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4816    1.3322   -0.0233 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8818    1.5881   -0.1015 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2570    2.7548   -0.3079 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7850    0.5647    0.0479 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1454    0.7956   -0.0261 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7244    2.0032   -0.2446 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.0010   -0.3034    0.1373 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4643   -1.5463    0.3607 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3710   -2.6124    0.5171 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1060   -1.7554    0.4309 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2279   -0.6849    0.2729 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0628   -0.9024    0.3428 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9506    0.0618    0.2031 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7836   -1.9831   -1.4958 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5975   -3.3879   -0.3546 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1772   -2.5938   -0.5458 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2414    1.3529    0.0957 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4264    2.9220   -0.2156 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9910    3.3540   -0.3511 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3803    2.8954   -0.3862 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.0604   -0.1191    0.0789 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.6651   -2.7776    1.4723 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7591   -2.7644    0.6100 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  4  6  1  0
  6  7  2  0
  7  8  1  0
  8  9  1  0
  9 10  2  0
  9 11  1  0
 11 12  2  0
 12 13  1  0
 12 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
 20  3  1  0
 20  8  2  0
 18 11  1  0
  1 21  1  0
  1 22  1  0
  1 23  1  0
  5 24  1  0
  6 25  1  0
  7 26  1  0
 13 27  1  0
 14 28  1  0
 16 29  1  0
 17 30  1  0
M  END

View in JSmol View Stereo Labels

Synonyms

Not Available

Chemical Formula

C₁₄H₁₀O₆

Average Molecular Weight

274.2256

Monoisotopic Molecular Weight

274.047738052

IUPAC Name

1,3,6-trihydroxy-5-methoxy-9H-xanthen-9-one

Traditional Name

1,3,6-trihydroxy-5-methoxyxanthen-9-one

CAS Registry Number

41357-84-0

SMILES

COC1=C(O)C=CC2=C1OC1=CC(O)=CC(O)=C1C2=O

InChI Identifier

InChI=1S/C14H10O6/c1-19-14-8(16)3-2-7-12(18)11-9(17)4-6(15)5-10(11)20-13(7)14/h2-5,15-17H,1H3

InChI Key

OIDDYVZHNYQRKQ-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as xanthones. These are polycyclic aromatic compounds containing a xanthene moiety conjugated to a ketone group at carbon 9. Xanthene is a tricyclic compound made up of two benzene rings linearly fused to each other through a pyran ring.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Benzopyrans

Sub Class

1-benzopyrans

Direct Parent

Xanthones

Alternative Parents

Substituents

Xanthone
Chromone
Anisole
1-hydroxy-4-unsubstituted benzenoid
1-hydroxy-2-unsubstituted benzenoid
Alkyl aryl ether
Pyranone
Pyran
Benzenoid
Heteroaromatic compound
Vinylogous acid
Polyol
Ether
Oxacycle
Organic oxygen compound
Organooxygen compound
Hydrocarbon derivative
Organic oxide
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

Not Available

Ontology

Physiological effect

Not Available

Disposition

Biological location

Cellular substructure

Membrane (HMDB: HMDB0041243)
Cell membrane (HMDB: HMDB0041243)

Route of exposure

Enteral

Ingestion (HMDB: HMDB0041243)

Source

Exogenous

Exogenous (HMDB: HMDB0041243)

Food

Food (HMDB: HMDB0041243)

Fruit

Fruits (FooDB: FOOD00871)

Endogenous

Plant

Plant (HMDB: HMDB0041243)

Process

Not Available

Role

Biological role

Nutrient (HMDB: HMDB0041243)

Physical Properties

State

Solid

Experimental Molecular Properties

Property	Value	Reference
Melting Point	290 - 291 °C	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	0.38 g/L	ALOGPS
logP	2.52	ALOGPS
logP	2.54	ChemAxon
logS	-2.9	ALOGPS
pKa (Strongest Acidic)	7.46	ChemAxon
pKa (Strongest Basic)	-4.2	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	96.22 Å²	ChemAxon
Rotatable Bond Count	1	ChemAxon
Refractivity	69.22 m³·mol⁻¹	ChemAxon
Polarizability	26.11 Å³	ChemAxon
Number of Rings	3	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]+	161.69	31661259
DarkChem	[M-H]-	160.778	31661259
DeepCCS	[M+H]+	158.233	30932474
DeepCCS	[M-H]-	155.875	30932474
DeepCCS	[M-2H]-	188.761	30932474
DeepCCS	[M+Na]+	164.326	30932474
AllCCS	[M+H]+	159.5	32859911
AllCCS	[M+H-H2O]+	155.7	32859911
AllCCS	[M+NH4]+	163.1	32859911
AllCCS	[M+Na]+	164.2	32859911
AllCCS	[M-H]-	159.9	32859911
AllCCS	[M+Na-2H]-	159.1	32859911
AllCCS	[M+HCOO]-	158.4	32859911

Predicted Retention Times

Underivatized

Chromatographic Method	Retention Time	Reference
Measured using a Waters Acquity ultraperformance liquid chromatography (UPLC) ethylene-bridged hybrid (BEH) C18 column (100 mm × 2.1 mm; 1.7 μmparticle diameter). Predicted by Afia on May 17, 2022.	5.38 minutes	32390414
Predicted by Siyang on May 30, 2022	10.8937 minutes	33406817
Predicted by Siyang using ReTip algorithm on June 8, 2022	1.36 minutes	32390414
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid	1647.8 seconds	40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid	273.1 seconds	40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid	113.3 seconds	40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid	160.3 seconds	40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	217.3 seconds	40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid	508.6 seconds	40023050
BfG_NTS_RP1 =Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) with Water:ACN and 0.1% Formic Acid	471.5 seconds	40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)	344.5 seconds	40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid	726.2 seconds	40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid	349.8 seconds	40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid	1383.5 seconds	40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	267.1 seconds	40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	353.2 seconds	40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate	560.5 seconds	40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA	352.4 seconds	40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water	159.6 seconds	40023050

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
1,3,6-Trihydroxy-5-methoxyxanthone	COC1=C(O)C=CC2=C1OC1=CC(O)=CC(O)=C1C2=O	4348.3	Standard polar	33892256
1,3,6-Trihydroxy-5-methoxyxanthone	COC1=C(O)C=CC2=C1OC1=CC(O)=CC(O)=C1C2=O	2795.6	Standard non polar	33892256
1,3,6-Trihydroxy-5-methoxyxanthone	COC1=C(O)C=CC2=C1OC1=CC(O)=CC(O)=C1C2=O	2769.8	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
1,3,6-Trihydroxy-5-methoxyxanthone,1TMS,isomer #1	COC1=C(O[Si](C)(C)C)C=CC2=C1OC1=CC(O)=CC(O)=C1C2=O	2871.9	Semi standard non polar	33892256
1,3,6-Trihydroxy-5-methoxyxanthone,1TMS,isomer #2	COC1=C(O)C=CC2=C1OC1=CC(O[Si](C)(C)C)=CC(O)=C1C2=O	2872.0	Semi standard non polar	33892256
1,3,6-Trihydroxy-5-methoxyxanthone,1TMS,isomer #3	COC1=C(O)C=CC2=C1OC1=CC(O)=CC(O[Si](C)(C)C)=C1C2=O	2854.5	Semi standard non polar	33892256
1,3,6-Trihydroxy-5-methoxyxanthone,2TMS,isomer #1	COC1=C(O[Si](C)(C)C)C=CC2=C1OC1=CC(O)=CC(O[Si](C)(C)C)=C1C2=O	2802.1	Semi standard non polar	33892256
1,3,6-Trihydroxy-5-methoxyxanthone,2TMS,isomer #2	COC1=C(O[Si](C)(C)C)C=CC2=C1OC1=CC(O[Si](C)(C)C)=CC(O)=C1C2=O	2841.9	Semi standard non polar	33892256
1,3,6-Trihydroxy-5-methoxyxanthone,2TMS,isomer #3	COC1=C(O)C=CC2=C1OC1=CC(O[Si](C)(C)C)=CC(O[Si](C)(C)C)=C1C2=O	2883.5	Semi standard non polar	33892256
1,3,6-Trihydroxy-5-methoxyxanthone,3TMS,isomer #1	COC1=C(O[Si](C)(C)C)C=CC2=C1OC1=CC(O[Si](C)(C)C)=CC(O[Si](C)(C)C)=C1C2=O	2827.5	Semi standard non polar	33892256
1,3,6-Trihydroxy-5-methoxyxanthone,1TBDMS,isomer #1	COC1=C(O[Si](C)(C)C(C)(C)C)C=CC2=C1OC1=CC(O)=CC(O)=C1C2=O	3133.7	Semi standard non polar	33892256
1,3,6-Trihydroxy-5-methoxyxanthone,1TBDMS,isomer #2	COC1=C(O)C=CC2=C1OC1=CC(O[Si](C)(C)C(C)(C)C)=CC(O)=C1C2=O	3128.1	Semi standard non polar	33892256
1,3,6-Trihydroxy-5-methoxyxanthone,1TBDMS,isomer #3	COC1=C(O)C=CC2=C1OC1=CC(O)=CC(O[Si](C)(C)C(C)(C)C)=C1C2=O	3097.9	Semi standard non polar	33892256
1,3,6-Trihydroxy-5-methoxyxanthone,2TBDMS,isomer #1	COC1=C(O[Si](C)(C)C(C)(C)C)C=CC2=C1OC1=CC(O)=CC(O[Si](C)(C)C(C)(C)C)=C1C2=O	3267.8	Semi standard non polar	33892256
1,3,6-Trihydroxy-5-methoxyxanthone,2TBDMS,isomer #2	COC1=C(O[Si](C)(C)C(C)(C)C)C=CC2=C1OC1=CC(O[Si](C)(C)C(C)(C)C)=CC(O)=C1C2=O	3318.6	Semi standard non polar	33892256
1,3,6-Trihydroxy-5-methoxyxanthone,2TBDMS,isomer #3	COC1=C(O)C=CC2=C1OC1=CC(O[Si](C)(C)C(C)(C)C)=CC(O[Si](C)(C)C(C)(C)C)=C1C2=O	3344.7	Semi standard non polar	33892256
1,3,6-Trihydroxy-5-methoxyxanthone,3TBDMS,isomer #1	COC1=C(O[Si](C)(C)C(C)(C)C)C=CC2=C1OC1=CC(O[Si](C)(C)C(C)(C)C)=CC(O[Si](C)(C)C(C)(C)C)=C1C2=O	3510.9	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 - 1,3,6-Trihydroxy-5-methoxyxanthone GC-MS (Non-derivatized) - 70eV, Positive	splash10-007k-0490000000-ec90b4cee64481d0a520	2017-09-01	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 1,3,6-Trihydroxy-5-methoxyxanthone GC-MS (3 TMS) - 70eV, Positive	splash10-016r-2031900000-5edf8e9191b4bc701b40	2017-10-06	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 1,3,6-Trihydroxy-5-methoxyxanthone 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 - 1,3,6-Trihydroxy-5-methoxyxanthone 10V, Positive-QTOF	splash10-004i-0090000000-9d509f3c3eb72f2444dd	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 1,3,6-Trihydroxy-5-methoxyxanthone 20V, Positive-QTOF	splash10-004i-0090000000-721687af8141622380e8	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 1,3,6-Trihydroxy-5-methoxyxanthone 40V, Positive-QTOF	splash10-0zfr-3290000000-6601f8ec987cf42b6a10	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 1,3,6-Trihydroxy-5-methoxyxanthone 10V, Negative-QTOF	splash10-00di-0090000000-f58cbaa21ce916d45d81	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 1,3,6-Trihydroxy-5-methoxyxanthone 20V, Negative-QTOF	splash10-00di-0090000000-82e3823a7060a37c5477	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 1,3,6-Trihydroxy-5-methoxyxanthone 40V, Negative-QTOF	splash10-0ufr-0490000000-08dcba5e22a8d05f452e	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 1,3,6-Trihydroxy-5-methoxyxanthone 10V, Positive-QTOF	splash10-004i-0090000000-889d6786b5fde891f4cd	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 1,3,6-Trihydroxy-5-methoxyxanthone 20V, Positive-QTOF	splash10-004i-0090000000-889d6786b5fde891f4cd	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 1,3,6-Trihydroxy-5-methoxyxanthone 40V, Positive-QTOF	splash10-0zgi-0290000000-7a0846a8ebf406c39917	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 1,3,6-Trihydroxy-5-methoxyxanthone 10V, Negative-QTOF	splash10-00di-0090000000-52b97824b3baf812bc0a	2021-09-25	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 1,3,6-Trihydroxy-5-methoxyxanthone 20V, Negative-QTOF	splash10-00di-0090000000-a29644428860e488f6e3	2021-09-25	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 1,3,6-Trihydroxy-5-methoxyxanthone 40V, Negative-QTOF	splash10-0zfr-0190000000-b5b0732915b511f0f372	2021-09-25	Wishart Lab	View Spectrum

Biological Properties

Cellular Locations

Membrane

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

FDB021151

KNApSAcK ID

C00032586

Chemspider ID

4591590

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

5493675

PDB ID

Not Available

ChEBI ID

174597

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 1,3,6-Trihydroxy-5-methoxyxanthone (HMDB0041243)

MOL for HMDB0041243 (1,3,6-Trihydroxy-5-methoxyxanthone)

3D MOL for HMDB0041243 (1,3,6-Trihydroxy-5-methoxyxanthone)

3D SDF for HMDB0041243 (1,3,6-Trihydroxy-5-methoxyxanthone)

3D-SDF for HMDB0041243 (1,3,6-Trihydroxy-5-methoxyxanthone)

PDB for HMDB0041243 (1,3,6-Trihydroxy-5-methoxyxanthone)

3D PDB for HMDB0041243 (1,3,6-Trihydroxy-5-methoxyxanthone)

SMILES for HMDB0041243 (1,3,6-Trihydroxy-5-methoxyxanthone)

INCHI for HMDB0041243 (1,3,6-Trihydroxy-5-methoxyxanthone)

Structure for HMDB0041243 (1,3,6-Trihydroxy-5-methoxyxanthone)

3D Structure for HMDB0041243 (1,3,6-Trihydroxy-5-methoxyxanthone)

Predicted Collision Cross Sections

Predicted Retention Times

Underivatized

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra