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Record Information

Version

5.0

Status

Expected but not Quantified

Creation Date

2012-09-11 22:51:12 UTC

Update Date

2022-03-07 02:55:25 UTC

HMDB ID

HMDB0037600

Secondary Accession Numbers

HMDB37600

Metabolite Identification

Common Name

Xanthomicrol

Description

Xanthomicrol belongs to the class of organic compounds known as 8-o-methylated flavonoids. These are flavonoids with methoxy groups attached to the C8 atom of the flavonoid backbone. Thus, xanthomicrol is considered to be a flavonoid. Xanthomicrol is found, on average, in the highest concentration within sweet basils (Ocimum basilicum). Xanthomicrol has also been detected, but not quantified in, several different foods, such as citrus, herbs and spices, peppermints (Mentha X piperita), and winter savories (Satureja montana). This could make xanthomicrol a potential biomarker for the consumption of these foods. Xanthomicrol is a secondary metabolite. Secondary metabolites are metabolically or physiologically non-essential metabolites that may serve a role as defense or signalling molecules. In some cases they are simply molecules that arise from the incomplete metabolism of other secondary metabolites. Based on a literature review a small amount of articles have been published on Xanthomicrol.

Structure

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

HMDB0037600
     RDKit          3D
Xanthomicrol
 41 43  0  0  0  0  0  0  0  0999 V2000
    4.2903    2.1978   -0.4114 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6615    1.3422    0.5025 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.7309    0.3925    0.2203 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0808   -0.8955   -0.0815 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4094   -1.2353   -0.0990 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.1308   -1.7096    1.0019 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1242   -1.8958   -0.3775 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5381   -3.1447   -0.6663 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7887   -1.5637   -0.3622 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2065   -2.4596   -0.6343 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0433   -3.6435   -0.9153 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5167   -2.0397   -0.5960 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8450   -0.7390   -0.2900 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2197   -0.2608   -0.2405 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3006   -1.0588   -0.4926 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6045   -0.5441   -0.4305 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7941    0.7637   -0.1158 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.0594    1.2887   -0.0491 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7093    1.6045    0.1472 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4400    1.0691    0.0782 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8326    0.0691   -0.0389 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.4302   -0.2693   -0.0593 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3959    0.7094    0.2318 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0095    1.9921    0.5304 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8570    2.9785   -0.4655 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4531    3.1701    0.1126 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.2976    1.7855   -0.6476 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6887    2.4079   -1.3083 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.6497   -1.3626    1.9181 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.1842   -1.3722    0.8950 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.1117   -2.8184    0.9651 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1693   -3.9975   -0.8963 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3189   -2.7498   -0.8123 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1877   -2.0996   -0.7450 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.4228   -1.2330   -0.6424 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.5467    1.2600    0.8332 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9003    2.6427    0.3950 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5722    1.7069    0.2799 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2923    2.6209   -1.4279 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3615    3.8858   -0.1209 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2217    3.2051   -0.6483 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
  5  6  1  0
  4  7  1  0
  7  8  1  0
  7  9  2  0
  9 10  1  0
 10 11  2  0
 10 12  1  0
 12 13  2  0
 13 14  1  0
 14 15  2  0
 15 16  1  0
 16 17  2  0
 17 18  1  0
 17 19  1  0
 19 20  2  0
 13 21  1  0
 21 22  1  0
 22 23  2  0
 23 24  1  0
 24 25  1  0
 23  3  1  0
 22  9  1  0
 20 14  1  0
  1 26  1  0
  1 27  1  0
  1 28  1  0
  6 29  1  0
  6 30  1  0
  6 31  1  0
  8 32  1  0
 12 33  1  0
 15 34  1  0
 16 35  1  0
 18 36  1  0
 19 37  1  0
 20 38  1  0
 25 39  1  0
 25 40  1  0
 25 41  1  0
M  END


  Mrv0541 05061309532D          

 25 27  0  0  0  0            999 V2000
    2.8579    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434    2.0625    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
   -2.8579    2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5724    1.2375    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
   -2.1434    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5724    2.0625    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    0.8250    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
    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
    1.4289    0.0000    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
    1.4289    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2868    2.4750    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   -1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -0.4125    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
    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
  6  4  1  0  0  0  0
  7  5  2  0  0  0  0
  9  4  2  0  0  0  0
  9  5  1  0  0  0  0
 10  6  2  0  0  0  0
 10  7  1  0  0  0  0
 11  8  1  0  0  0  0
 12  8  2  0  0  0  0
 12  9  1  0  0  0  0
 13 11  1  0  0  0  0
 14 13  2  0  0  0  0
 15 13  1  0  0  0  0
 16 14  1  0  0  0  0
 17 15  2  0  0  0  0
 18 16  2  0  0  0  0
 18 17  1  0  0  0  0
 19 10  1  0  0  0  0
 20 11  2  0  0  0  0
 21 14  1  0  0  0  0
 22  1  1  0  0  0  0
 22 16  1  0  0  0  0
 23  2  1  0  0  0  0
 23 17  1  0  0  0  0
 24  3  1  0  0  0  0
 24 18  1  0  0  0  0
 25 12  1  0  0  0  0
 25 15  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0037600

> <DATABASE_NAME>
hmdb

> <SMILES>
COC1=C(OC)C(OC)=C2OC(=CC(=O)C2=C1O)C1=CC=C(O)C=C1

> <INCHI_IDENTIFIER>
InChI=1S/C18H16O7/c1-22-16-14(21)13-11(20)8-12(9-4-6-10(19)7-5-9)25-15(13)17(23-2)18(16)24-3/h4-8,19,21H,1-3H3

> <INCHI_KEY>
SAMBWAJRKKEEOR-UHFFFAOYSA-N

> <FORMULA>
C18H16O7

> <MOLECULAR_WEIGHT>
344.3154

> <EXACT_MASS>
344.089602866

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_AVERAGE_POLARIZABILITY>
34.64078963877199

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
5-hydroxy-2-(4-hydroxyphenyl)-6,7,8-trimethoxy-4H-chromen-4-one

> <ALOGPS_LOGP>
2.89

> <JCHEM_LOGP>
2.5372406583333333

> <ALOGPS_LOGS>
-3.91

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
9.71204236478852

> <JCHEM_PKA_STRONGEST_ACIDIC>
8.67398531709772

> <JCHEM_PKA_STRONGEST_BASIC>
-4.2915477595730005

> <JCHEM_POLAR_SURFACE_AREA>
94.45000000000002

> <JCHEM_REFRACTIVITY>
90.3226

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
4.21e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
xanthomicrol

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0037600
     RDKit          3D
Xanthomicrol
 41 43  0  0  0  0  0  0  0  0999 V2000
    4.2903    2.1978   -0.4114 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6615    1.3422    0.5025 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.7309    0.3925    0.2203 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0808   -0.8955   -0.0815 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4094   -1.2353   -0.0990 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.1308   -1.7096    1.0019 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1242   -1.8958   -0.3775 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5381   -3.1447   -0.6663 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7887   -1.5637   -0.3622 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2065   -2.4596   -0.6343 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0433   -3.6435   -0.9153 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5167   -2.0397   -0.5960 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8450   -0.7390   -0.2900 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2197   -0.2608   -0.2405 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3006   -1.0588   -0.4926 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6045   -0.5441   -0.4305 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7941    0.7637   -0.1158 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.0594    1.2887   -0.0491 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7093    1.6045    0.1472 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4400    1.0691    0.0782 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8326    0.0691   -0.0389 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.4302   -0.2693   -0.0593 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3959    0.7094    0.2318 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0095    1.9921    0.5304 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8570    2.9785   -0.4655 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4531    3.1701    0.1126 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.2976    1.7855   -0.6476 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6887    2.4079   -1.3083 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.6497   -1.3626    1.9181 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.1842   -1.3722    0.8950 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.1117   -2.8184    0.9651 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1693   -3.9975   -0.8963 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3189   -2.7498   -0.8123 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1877   -2.0996   -0.7450 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.4228   -1.2330   -0.6424 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.5467    1.2600    0.8332 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9003    2.6427    0.3950 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5722    1.7069    0.2799 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2923    2.6209   -1.4279 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3615    3.8858   -0.1209 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2217    3.2051   -0.6483 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
  5  6  1  0
  4  7  1  0
  7  8  1  0
  7  9  2  0
  9 10  1  0
 10 11  2  0
 10 12  1  0
 12 13  2  0
 13 14  1  0
 14 15  2  0
 15 16  1  0
 16 17  2  0
 17 18  1  0
 17 19  1  0
 19 20  2  0
 13 21  1  0
 21 22  1  0
 22 23  2  0
 23 24  1  0
 24 25  1  0
 23  3  1  0
 22  9  1  0
 20 14  1  0
  1 26  1  0
  1 27  1  0
  1 28  1  0
  6 29  1  0
  6 30  1  0
  6 31  1  0
  8 32  1  0
 12 33  1  0
 15 34  1  0
 16 35  1  0
 18 36  1  0
 19 37  1  0
 20 38  1  0
 25 39  1  0
 25 40  1  0
 25 41  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       5.335   0.000   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       2.667   4.620   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       4.001   3.850   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -4.001   3.850   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -5.335   1.540   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -5.335   4.620   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -6.668   2.310   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -2.667   0.000   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -4.001   2.310   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -6.668   3.850   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      -1.334  -0.770   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      -2.667   1.540   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       2.667   0.000   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
HETATM   19  O   UNK     0      -8.002   4.620   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
HETATM   21  O   UNK     0       1.334  -2.310   0.000  0.00  0.00           O+0
HETATM   22  O   UNK     0       4.001  -0.770   0.000  0.00  0.00           O+0
HETATM   23  O   UNK     0       1.334   3.850   0.000  0.00  0.00           O+0
HETATM   24  O   UNK     0       4.001   2.310   0.000  0.00  0.00           O+0
HETATM   25  O   UNK     0      -1.334   2.310   0.000  0.00  0.00           O+0
CONECT    1   22                                                            
CONECT    2   23                                                            
CONECT    3   24                                                            
CONECT    4    6    9                                                       
CONECT    5    7    9                                                       
CONECT    6    4   10                                                       
CONECT    7    5   10                                                       
CONECT    8   11   12                                                       
CONECT    9    4    5   12                                                  
CONECT   10    6    7   19                                                  
CONECT   11    8   13   20                                                  
CONECT   12    8    9   25                                                  
CONECT   13   11   14   15                                                  
CONECT   14   13   16   21                                                  
CONECT   15   13   17   25                                                  
CONECT   16   14   18   22                                                  
CONECT   17   15   18   23                                                  
CONECT   18   16   17   24                                                  
CONECT   19   10                                                            
CONECT   20   11                                                            
CONECT   21   14                                                            
CONECT   22    1   16                                                       
CONECT   23    2   17                                                       
CONECT   24    3   18                                                       
CONECT   25   12   15                                                       
MASTER        0    0    0    0    0    0    0    0   25    0   54    0
END

COMPND    HMDB0037600
HETATM    1  C1  UNL     1       4.290   2.198  -0.411  1.00  0.00           C  
HETATM    2  O1  UNL     1       3.662   1.342   0.502  1.00  0.00           O  
HETATM    3  C2  UNL     1       2.731   0.392   0.220  1.00  0.00           C  
HETATM    4  C3  UNL     1       3.081  -0.896  -0.081  1.00  0.00           C  
HETATM    5  O2  UNL     1       4.409  -1.235  -0.099  1.00  0.00           O  
HETATM    6  C4  UNL     1       5.131  -1.710   1.002  1.00  0.00           C  
HETATM    7  C5  UNL     1       2.124  -1.896  -0.377  1.00  0.00           C  
HETATM    8  O3  UNL     1       2.538  -3.145  -0.666  1.00  0.00           O  
HETATM    9  C6  UNL     1       0.789  -1.564  -0.362  1.00  0.00           C  
HETATM   10  C7  UNL     1      -0.207  -2.460  -0.634  1.00  0.00           C  
HETATM   11  O4  UNL     1       0.043  -3.644  -0.915  1.00  0.00           O  
HETATM   12  C8  UNL     1      -1.517  -2.040  -0.596  1.00  0.00           C  
HETATM   13  C9  UNL     1      -1.845  -0.739  -0.290  1.00  0.00           C  
HETATM   14  C10 UNL     1      -3.220  -0.261  -0.240  1.00  0.00           C  
HETATM   15  C11 UNL     1      -4.301  -1.059  -0.493  1.00  0.00           C  
HETATM   16  C12 UNL     1      -5.604  -0.544  -0.431  1.00  0.00           C  
HETATM   17  C13 UNL     1      -5.794   0.764  -0.116  1.00  0.00           C  
HETATM   18  O5  UNL     1      -7.059   1.289  -0.049  1.00  0.00           O  
HETATM   19  C14 UNL     1      -4.709   1.604   0.147  1.00  0.00           C  
HETATM   20  C15 UNL     1      -3.440   1.069   0.078  1.00  0.00           C  
HETATM   21  O6  UNL     1      -0.833   0.069  -0.039  1.00  0.00           O  
HETATM   22  C16 UNL     1       0.430  -0.269  -0.059  1.00  0.00           C  
HETATM   23  C17 UNL     1       1.396   0.709   0.232  1.00  0.00           C  
HETATM   24  O7  UNL     1       1.009   1.992   0.530  1.00  0.00           O  
HETATM   25  C18 UNL     1       0.857   2.979  -0.466  1.00  0.00           C  
HETATM   26  H1  UNL     1       4.453   3.170   0.113  1.00  0.00           H  
HETATM   27  H2  UNL     1       5.298   1.786  -0.648  1.00  0.00           H  
HETATM   28  H3  UNL     1       3.689   2.408  -1.308  1.00  0.00           H  
HETATM   29  H4  UNL     1       4.650  -1.363   1.918  1.00  0.00           H  
HETATM   30  H5  UNL     1       6.184  -1.372   0.895  1.00  0.00           H  
HETATM   31  H6  UNL     1       5.112  -2.818   0.965  1.00  0.00           H  
HETATM   32  H7  UNL     1       2.169  -3.998  -0.896  1.00  0.00           H  
HETATM   33  H8  UNL     1      -2.319  -2.750  -0.812  1.00  0.00           H  
HETATM   34  H9  UNL     1      -4.188  -2.100  -0.745  1.00  0.00           H  
HETATM   35  H10 UNL     1      -6.423  -1.233  -0.642  1.00  0.00           H  
HETATM   36  H11 UNL     1      -7.547   1.260   0.833  1.00  0.00           H  
HETATM   37  H12 UNL     1      -4.900   2.643   0.395  1.00  0.00           H  
HETATM   38  H13 UNL     1      -2.572   1.707   0.280  1.00  0.00           H  
HETATM   39  H14 UNL     1       1.292   2.621  -1.428  1.00  0.00           H  
HETATM   40  H15 UNL     1       1.362   3.886  -0.121  1.00  0.00           H  
HETATM   41  H16 UNL     1      -0.222   3.205  -0.648  1.00  0.00           H  
CONECT    1    2   26   27   28
CONECT    2    3
CONECT    3    4    4   23
CONECT    4    5    7
CONECT    5    6
CONECT    6   29   30   31
CONECT    7    8    9    9
CONECT    8   32
CONECT    9   10   22
CONECT   10   11   11   12
CONECT   12   13   13   33
CONECT   13   14   21
CONECT   14   15   15   20
CONECT   15   16   34
CONECT   16   17   17   35
CONECT   17   18   19
CONECT   18   36
CONECT   19   20   20   37
CONECT   20   38
CONECT   21   22
CONECT   22   23   23
CONECT   23   24
CONECT   24   25
CONECT   25   39   40   41
END

HMDB0037600
     RDKit          3D
Xanthomicrol
 41 43  0  0  0  0  0  0  0  0999 V2000
    4.2903    2.1978   -0.4114 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6615    1.3422    0.5025 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.7309    0.3925    0.2203 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0808   -0.8955   -0.0815 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4094   -1.2353   -0.0990 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.1308   -1.7096    1.0019 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1242   -1.8958   -0.3775 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5381   -3.1447   -0.6663 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7887   -1.5637   -0.3622 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2065   -2.4596   -0.6343 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0433   -3.6435   -0.9153 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5167   -2.0397   -0.5960 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8450   -0.7390   -0.2900 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2197   -0.2608   -0.2405 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3006   -1.0588   -0.4926 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6045   -0.5441   -0.4305 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7941    0.7637   -0.1158 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.0594    1.2887   -0.0491 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7093    1.6045    0.1472 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4400    1.0691    0.0782 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8326    0.0691   -0.0389 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.4302   -0.2693   -0.0593 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3959    0.7094    0.2318 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0095    1.9921    0.5304 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8570    2.9785   -0.4655 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4531    3.1701    0.1126 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.2976    1.7855   -0.6476 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6887    2.4079   -1.3083 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.6497   -1.3626    1.9181 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.1842   -1.3722    0.8950 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.1117   -2.8184    0.9651 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1693   -3.9975   -0.8963 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3189   -2.7498   -0.8123 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1877   -2.0996   -0.7450 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.4228   -1.2330   -0.6424 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.5467    1.2600    0.8332 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9003    2.6427    0.3950 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5722    1.7069    0.2799 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2923    2.6209   -1.4279 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3615    3.8858   -0.1209 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2217    3.2051   -0.6483 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
  5  6  1  0
  4  7  1  0
  7  8  1  0
  7  9  2  0
  9 10  1  0
 10 11  2  0
 10 12  1  0
 12 13  2  0
 13 14  1  0
 14 15  2  0
 15 16  1  0
 16 17  2  0
 17 18  1  0
 17 19  1  0
 19 20  2  0
 13 21  1  0
 21 22  1  0
 22 23  2  0
 23 24  1  0
 24 25  1  0
 23  3  1  0
 22  9  1  0
 20 14  1  0
  1 26  1  0
  1 27  1  0
  1 28  1  0
  6 29  1  0
  6 30  1  0
  6 31  1  0
  8 32  1  0
 12 33  1  0
 15 34  1  0
 16 35  1  0
 18 36  1  0
 19 37  1  0
 20 38  1  0
 25 39  1  0
 25 40  1  0
 25 41  1  0
M  END

View in JSmol View Stereo Labels

Synonyms

Value	Source
4',5-Dihydroxy-6,7,8-trimethoxyflavone	ChEBI
5-Hydroxy-2-(4-hydroxyphenyl)-6,7,8-trimethoxy-4H-1-benzopyran-4-one	HMDB

Chemical Formula

C₁₈H₁₆O₇

Average Molecular Weight

344.3154

Monoisotopic Molecular Weight

344.089602866

IUPAC Name

5-hydroxy-2-(4-hydroxyphenyl)-6,7,8-trimethoxy-4H-chromen-4-one

Traditional Name

xanthomicrol

CAS Registry Number

16545-23-6

SMILES

COC1=C(OC)C(OC)=C2OC(=CC(=O)C2=C1O)C1=CC=C(O)C=C1

InChI Identifier

InChI=1S/C18H16O7/c1-22-16-14(21)13-11(20)8-12(9-4-6-10(19)7-5-9)25-15(13)17(23-2)18(16)24-3/h4-8,19,21H,1-3H3

InChI Key

SAMBWAJRKKEEOR-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as 8-o-methylated flavonoids. These are flavonoids with methoxy groups attached to the C8 atom of the flavonoid backbone.

Kingdom

Organic compounds

Super Class

Phenylpropanoids and polyketides

Class

Flavonoids

Sub Class

O-methylated flavonoids

Direct Parent

8-O-methylated flavonoids

Alternative Parents

Substituents

6-methoxyflavonoid-skeleton
8-methoxyflavonoid-skeleton
7-methoxyflavonoid-skeleton
4'-hydroxyflavonoid
5-hydroxyflavonoid
Flavone
Hydroxyflavonoid
Chromone
Benzopyran
1-benzopyran
Anisole
Alkyl aryl ether
1-hydroxy-2-unsubstituted benzenoid
Phenol
Pyranone
Benzenoid
Pyran
Monocyclic benzene moiety
Vinylogous acid
Heteroaromatic compound
Ether
Organoheterocyclic compound
Oxacycle
Organic oxygen compound
Organooxygen compound
Hydrocarbon derivative
Organic oxide
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

dihydroxyflavone (CHEBI:35047 )
trimethoxyflavone (CHEBI:35047 )
Flavones and Flavonols (C14476 )
Flavones and Flavonols (LMPK12111447 )

Ontology

Physiological effect

Not Available

Disposition

Biological location

Cellular substructure

Membrane (HMDB: HMDB0037600)
Cell membrane (HMDB: HMDB0037600)

Route of exposure

Enteral

Ingestion (HMDB: HMDB0037600)

Source

Exogenous

Exogenous (HMDB: HMDB0037600)

Food

Food (HMDB: HMDB0037600)

Herb and spice

Herb

Herbs and Spices (FooDB: FOOD00866)

Fruit

Citrus

Citrus (FooDB: FOOD00859)

Endogenous

Plant

Plant (HMDB: HMDB0037600)

Not Available

EC 1.1.1.21 (aldehyde reductase) inhibitor (HMDB: HMDB0037600)

Physical Properties

State

Solid

Experimental Molecular Properties

Property	Value	Reference
Melting Point	227 - 230 °C	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	159.7 mg/L @ 25 °C (est)	The Good Scents Company Information System
LogP	Not Available	Not Available

Experimental Chromatographic Properties

Not Available

Predicted Molecular Properties

Property	Value	Source
Water Solubility	0.042 g/L	ALOGPS
logP	2.89	ALOGPS
logP	2.54	ChemAxon
logS	-3.9	ALOGPS
pKa (Strongest Acidic)	8.67	ChemAxon
pKa (Strongest Basic)	-4.3	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	7	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	94.45 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	90.32 m³·mol⁻¹	ChemAxon
Polarizability	34.64 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]+	180.418	31661259
DarkChem	[M-H]-	181.97	31661259
DeepCCS	[M+H]+	182.75	30932474
DeepCCS	[M-H]-	180.34	30932474
DeepCCS	[M-2H]-	214.684	30932474
DeepCCS	[M+Na]+	190.223	30932474
AllCCS	[M+H]+	179.7	32859911
AllCCS	[M+H-H2O]+	176.4	32859911
AllCCS	[M+NH4]+	182.8	32859911
AllCCS	[M+Na]+	183.7	32859911
AllCCS	[M-H]-	181.7	32859911
AllCCS	[M+Na-2H]-	181.4	32859911
AllCCS	[M+HCOO]-	181.1	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. Predicted by Afia on May 17, 2022.	6.84 minutes	32390414
Predicted by Siyang on May 30, 2022	13.2233 minutes	33406817
Predicted by Siyang using ReTip algorithm on June 8, 2022	1.18 minutes	32390414
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid	2490.6 seconds	40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid	264.0 seconds	40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid	169.4 seconds	40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid	171.8 seconds	40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	392.5 seconds	40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid	564.8 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	700.3 seconds	40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)	123.2 seconds	40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid	1117.3 seconds	40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid	479.0 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	1494.6 seconds	40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	372.6 seconds	40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	448.2 seconds	40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate	396.5 seconds	40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA	203.1 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	66.7 seconds	40023050

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
Xanthomicrol	COC1=C(OC)C(OC)=C2OC(=CC(=O)C2=C1O)C1=CC=C(O)C=C1	4818.1	Standard polar	33892256
Xanthomicrol	COC1=C(OC)C(OC)=C2OC(=CC(=O)C2=C1O)C1=CC=C(O)C=C1	3229.9	Standard non polar	33892256
Xanthomicrol	COC1=C(OC)C(OC)=C2OC(=CC(=O)C2=C1O)C1=CC=C(O)C=C1	3252.2	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
Xanthomicrol,1TMS,isomer #1	COC1=C(OC)C(O[Si](C)(C)C)=C2C(=O)C=C(C3=CC=C(O)C=C3)OC2=C1OC	3164.5	Semi standard non polar	33892256
Xanthomicrol,1TMS,isomer #2	COC1=C(OC)C(O)=C2C(=O)C=C(C3=CC=C(O[Si](C)(C)C)C=C3)OC2=C1OC	3228.7	Semi standard non polar	33892256
Xanthomicrol,2TMS,isomer #1	COC1=C(OC)C(O[Si](C)(C)C)=C2C(=O)C=C(C3=CC=C(O[Si](C)(C)C)C=C3)OC2=C1OC	3203.9	Semi standard non polar	33892256
Xanthomicrol,1TBDMS,isomer #1	COC1=C(OC)C(O[Si](C)(C)C(C)(C)C)=C2C(=O)C=C(C3=CC=C(O)C=C3)OC2=C1OC	3412.2	Semi standard non polar	33892256
Xanthomicrol,1TBDMS,isomer #2	COC1=C(OC)C(O)=C2C(=O)C=C(C3=CC=C(O[Si](C)(C)C(C)(C)C)C=C3)OC2=C1OC	3434.8	Semi standard non polar	33892256
Xanthomicrol,2TBDMS,isomer #1	COC1=C(OC)C(O[Si](C)(C)C(C)(C)C)=C2C(=O)C=C(C3=CC=C(O[Si](C)(C)C(C)(C)C)C=C3)OC2=C1OC	3644.9	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 - Xanthomicrol GC-MS (Non-derivatized) - 70eV, Positive	splash10-02vi-0119000000-0c0e3709b7f79d4ca206	2017-09-01	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Xanthomicrol GC-MS (2 TMS) - 70eV, Positive	splash10-00di-1111900000-21e3d411a6a5821413b0	2017-10-06	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Xanthomicrol 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 - Xanthomicrol 10V, Positive-QTOF	splash10-0002-0009000000-444df5d8e4a6a98b29e2	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Xanthomicrol 20V, Positive-QTOF	splash10-0002-0009000000-17bd95784ea2af1d207b	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Xanthomicrol 40V, Positive-QTOF	splash10-00mk-2393000000-dde4b83302a1581e7635	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Xanthomicrol 10V, Negative-QTOF	splash10-0006-0009000000-7123f771ed6080c1a185	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Xanthomicrol 20V, Negative-QTOF	splash10-0006-0019000000-7d461a8e7316b5241de2	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Xanthomicrol 40V, Negative-QTOF	splash10-05r4-1491000000-f7bf40ad7c31df0b7fea	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Xanthomicrol 10V, Negative-QTOF	splash10-0006-0009000000-72fbd0eb75bc9ea05c55	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Xanthomicrol 20V, Negative-QTOF	splash10-0f96-0009000000-a822a609c08dacb282e4	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Xanthomicrol 10V, Positive-QTOF	splash10-0002-0009000000-5dc8eb0c39637af07086	2021-09-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Xanthomicrol 20V, Positive-QTOF	splash10-0002-0009000000-5dc6fda56294b4fda1a7	2021-09-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Xanthomicrol 40V, Positive-QTOF	splash10-0uk9-0249000000-6e1101312f640edf1533	2021-09-24	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

KNApSAcK ID

Chemspider ID

KEGG Compound ID

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

73207

PDB ID

Not Available

ChEBI ID

35047

Food Biomarker Ontology

Not Available

VMH ID

Not Available

MarkerDB ID

Not Available

Good Scents ID

rw1862661

References

Synthesis Reference

Not Available

Material Safety Data Sheet (MSDS)

Not Available

General References

Abbaszadeh H, Ebrahimi SA, Akhavan MM: Antiangiogenic activity of xanthomicrol and calycopterin, two polymethoxylated hydroxyflavones in both in vitro and ex vivo models. Phytother Res. 2014 Nov;28(11):1661-70. doi: 10.1002/ptr.5179. Epub 2014 Jun 3. [PubMed:24895220 ]

Showing metabocard for Xanthomicrol (HMDB0037600)

MOL for HMDB0037600 (Xanthomicrol)

3D MOL for HMDB0037600 (Xanthomicrol)

3D SDF for HMDB0037600 (Xanthomicrol)

3D-SDF for HMDB0037600 (Xanthomicrol)

PDB for HMDB0037600 (Xanthomicrol)

3D PDB for HMDB0037600 (Xanthomicrol)

SMILES for HMDB0037600 (Xanthomicrol)

INCHI for HMDB0037600 (Xanthomicrol)

Structure for HMDB0037600 (Xanthomicrol)

3D Structure for HMDB0037600 (Xanthomicrol)

Predicted Collision Cross Sections

Predicted Retention Times

Underivatized

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra