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Showing metabocard for 2-Hydroxyxanthone (HMDB0032997)

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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2012-09-11 17:53:09 UTC
Update Date2022-03-07 02:53:33 UTC
HMDB IDHMDB0032997
Secondary Accession Numbers
  • HMDB32997
Metabolite Identification
Common Name2-Hydroxyxanthone
Description2-Hydroxyxanthone 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. 2-Hydroxyxanthone exists as a solid and is considered to be practically insoluble (in water) and relatively neutral. Within the cell, 2-hydroxyxanthone is primarily located in the membrane (predicted from logP). Outside of the human body, 2-hydroxyxanthone can be found in fruits, herbs and spices, and mammee apple. This makes 2-hydroxyxanthone a potential biomarker for the consumption of these food products.
Structure
Data?1563862336
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0032997 (2-Hydroxyxanthone)

  Mrv0541 05061306512D          

 16 18  0  0  0  0            999 V2000
    5.0013    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0013    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868    2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    2.0625    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
    1.4289    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 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
    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
    0.0000    0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579    2.4750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  2  0  0  0  0
  3  1  1  0  0  0  0
  4  2  1  0  0  0  0
  6  5  2  0  0  0  0
  8  5  1  0  0  0  0
  8  7  2  0  0  0  0
  9  3  2  0  0  0  0
 10  7  1  0  0  0  0
 11  4  2  0  0  0  0
 11  9  1  0  0  0  0
 12  6  1  0  0  0  0
 12 10  2  0  0  0  0
 13  9  1  0  0  0  0
 13 10  1  0  0  0  0
 14  8  1  0  0  0  0
 15 13  2  0  0  0  0
 16 11  1  0  0  0  0
 16 12  1  0  0  0  0
M  END
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3D MOL for HMDB0032997 (2-Hydroxyxanthone)

HMDB0032997
     RDKit          3D
2-Hydroxyxanthone
 24 26  0  0  0  0  0  0  0  0999 V2000
    0.1078    2.4681    0.4573 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1853    1.2255    0.2797 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3934    0.5861    0.1268 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5828    1.3065    0.1648 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7974    0.6648    0.0113 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8131   -0.7043   -0.1807 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6222   -1.4261   -0.2189 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4104   -0.7844   -0.0655 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2857   -1.4535   -0.0998 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9012   -0.8970    0.0403 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0606   -1.6554   -0.0046 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2922   -1.0556    0.1440 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3495    0.3068    0.3373 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5887    0.9097    0.4867 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2083    1.0723    0.3842 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9685    0.4618    0.2337 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5415    2.3760    0.3164 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.7304    1.2374    0.0422 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.7754   -1.1810   -0.2980 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6408   -2.4999   -0.3699 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9694   -2.7216   -0.1583 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2219   -1.6436    0.1107 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0732    1.2458   -0.3401 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2529    2.1616    0.5387 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  5  6  2  0
  6  7  1  0
  7  8  2  0
  8  9  1  0
  9 10  1  0
 10 11  2  0
 11 12  1  0
 12 13  2  0
 13 14  1  0
 13 15  1  0
 15 16  2  0
 16  2  1  0
  8  3  1  0
 16 10  1  0
  4 17  1  0
  5 18  1  0
  6 19  1  0
  7 20  1  0
 11 21  1  0
 12 22  1  0
 14 23  1  0
 15 24  1  0
M  END
Download

3D SDF for HMDB0032997 (2-Hydroxyxanthone)

  Mrv0541 05061306512D          

 16 18  0  0  0  0            999 V2000
    5.0013    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0013    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868    2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    2.0625    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
    1.4289    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 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
    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
    0.0000    0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579    2.4750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  2  0  0  0  0
  3  1  1  0  0  0  0
  4  2  1  0  0  0  0
  6  5  2  0  0  0  0
  8  5  1  0  0  0  0
  8  7  2  0  0  0  0
  9  3  2  0  0  0  0
 10  7  1  0  0  0  0
 11  4  2  0  0  0  0
 11  9  1  0  0  0  0
 12  6  1  0  0  0  0
 12 10  2  0  0  0  0
 13  9  1  0  0  0  0
 13 10  1  0  0  0  0
 14  8  1  0  0  0  0
 15 13  2  0  0  0  0
 16 11  1  0  0  0  0
 16 12  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0032997

> <DATABASE_NAME>
hmdb

> <SMILES>
OC1=CC2=C(OC3=CC=CC=C3C2=O)C=C1

> <INCHI_IDENTIFIER>
InChI=1S/C13H8O3/c14-8-5-6-12-10(7-8)13(15)9-3-1-2-4-11(9)16-12/h1-7,14H

> <INCHI_KEY>
WSACHQJPCNOREV-UHFFFAOYSA-N

> <FORMULA>
C13H8O3

> <MOLECULAR_WEIGHT>
212.2008

> <EXACT_MASS>
212.047344122

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_AVERAGE_POLARIZABILITY>
21.34822063535274

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
2-hydroxy-9H-xanthen-9-one

> <ALOGPS_LOGP>
3.03

> <JCHEM_LOGP>
2.6560748986666667

> <ALOGPS_LOGS>
-3.00

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
9.111797945639948

> <JCHEM_PKA_STRONGEST_BASIC>
-5.9420641139282795

> <JCHEM_POLAR_SURFACE_AREA>
46.53

> <JCHEM_REFRACTIVITY>
58.79720000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.12e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
2-hydroxyxanthen-9-one

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for HMDB0032997 (2-Hydroxyxanthone)

HMDB0032997
     RDKit          3D
2-Hydroxyxanthone
 24 26  0  0  0  0  0  0  0  0999 V2000
    0.1078    2.4681    0.4573 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1853    1.2255    0.2797 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3934    0.5861    0.1268 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5828    1.3065    0.1648 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7974    0.6648    0.0113 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8131   -0.7043   -0.1807 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6222   -1.4261   -0.2189 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4104   -0.7844   -0.0655 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2857   -1.4535   -0.0998 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9012   -0.8970    0.0403 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0606   -1.6554   -0.0046 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2922   -1.0556    0.1440 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3495    0.3068    0.3373 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5887    0.9097    0.4867 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2083    1.0723    0.3842 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9685    0.4618    0.2337 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5415    2.3760    0.3164 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.7304    1.2374    0.0422 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.7754   -1.1810   -0.2980 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6408   -2.4999   -0.3699 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9694   -2.7216   -0.1583 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2219   -1.6436    0.1107 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0732    1.2458   -0.3401 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2529    2.1616    0.5387 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  5  6  2  0
  6  7  1  0
  7  8  2  0
  8  9  1  0
  9 10  1  0
 10 11  2  0
 11 12  1  0
 12 13  2  0
 13 14  1  0
 13 15  1  0
 15 16  2  0
 16  2  1  0
  8  3  1  0
 16 10  1  0
  4 17  1  0
  5 18  1  0
  6 19  1  0
  7 20  1  0
 11 21  1  0
 12 22  1  0
 14 23  1  0
 15 24  1  0
M  END
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PDB for HMDB0032997 (2-Hydroxyxanthone)

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       9.336   2.310   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       9.336   3.850   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       8.002   1.540   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       8.002   4.620   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       1.334   3.850   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       2.667   4.620   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       6.668   2.310   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       4.001   2.310   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       6.668   3.850   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       4.001   3.850   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       5.335   1.540   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0       0.000   1.540   0.000  0.00  0.00           O+0
HETATM   15  O   UNK     0       5.335   0.000   0.000  0.00  0.00           O+0
HETATM   16  O   UNK     0       5.335   4.620   0.000  0.00  0.00           O+0
CONECT    1    2    3                                                       
CONECT    2    1    4                                                       
CONECT    3    1    9                                                       
CONECT    4    2   11                                                       
CONECT    5    6    8                                                       
CONECT    6    5   12                                                       
CONECT    7    8   10                                                       
CONECT    8    5    7   14                                                  
CONECT    9    3   11   13                                                  
CONECT   10    7   12   13                                                  
CONECT   11    4    9   16                                                  
CONECT   12    6   10   16                                                  
CONECT   13    9   10   15                                                  
CONECT   14    8                                                            
CONECT   15   13                                                            
CONECT   16   11   12                                                       
MASTER        0    0    0    0    0    0    0    0   16    0   36    0
END
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3D PDB for HMDB0032997 (2-Hydroxyxanthone)

COMPND    HMDB0032997
HETATM    1  O1  UNL     1       0.108   2.468   0.457  1.00  0.00           O  
HETATM    2  C1  UNL     1       0.185   1.226   0.280  1.00  0.00           C  
HETATM    3  C2  UNL     1       1.393   0.586   0.127  1.00  0.00           C  
HETATM    4  C3  UNL     1       2.583   1.306   0.165  1.00  0.00           C  
HETATM    5  C4  UNL     1       3.797   0.665   0.011  1.00  0.00           C  
HETATM    6  C5  UNL     1       3.813  -0.704  -0.181  1.00  0.00           C  
HETATM    7  C6  UNL     1       2.622  -1.426  -0.219  1.00  0.00           C  
HETATM    8  C7  UNL     1       1.410  -0.784  -0.066  1.00  0.00           C  
HETATM    9  O2  UNL     1       0.286  -1.454  -0.100  1.00  0.00           O  
HETATM   10  C8  UNL     1      -0.901  -0.897   0.040  1.00  0.00           C  
HETATM   11  C9  UNL     1      -2.061  -1.655  -0.005  1.00  0.00           C  
HETATM   12  C10 UNL     1      -3.292  -1.056   0.144  1.00  0.00           C  
HETATM   13  C11 UNL     1      -3.350   0.307   0.337  1.00  0.00           C  
HETATM   14  O3  UNL     1      -4.589   0.910   0.487  1.00  0.00           O  
HETATM   15  C12 UNL     1      -2.208   1.072   0.384  1.00  0.00           C  
HETATM   16  C13 UNL     1      -0.968   0.462   0.234  1.00  0.00           C  
HETATM   17  H1  UNL     1       2.541   2.376   0.316  1.00  0.00           H  
HETATM   18  H2  UNL     1       4.730   1.237   0.042  1.00  0.00           H  
HETATM   19  H3  UNL     1       4.775  -1.181  -0.298  1.00  0.00           H  
HETATM   20  H4  UNL     1       2.641  -2.500  -0.370  1.00  0.00           H  
HETATM   21  H5  UNL     1      -1.969  -2.722  -0.158  1.00  0.00           H  
HETATM   22  H6  UNL     1      -4.222  -1.644   0.111  1.00  0.00           H  
HETATM   23  H7  UNL     1      -5.073   1.246  -0.340  1.00  0.00           H  
HETATM   24  H8  UNL     1      -2.253   2.162   0.539  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3   16
CONECT    3    4    4    8
CONECT    4    5   17
CONECT    5    6    6   18
CONECT    6    7   19
CONECT    7    8    8   20
CONECT    8    9
CONECT    9   10
CONECT   10   11   11   16
CONECT   11   12   21
CONECT   12   13   13   22
CONECT   13   14   15
CONECT   14   23
CONECT   15   16   16   24
END
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SMILES for HMDB0032997 (2-Hydroxyxanthone)

OC1=CC2=C(OC3=CC=CC=C3C2=O)C=C1
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INCHI for HMDB0032997 (2-Hydroxyxanthone)

InChI=1S/C13H8O3/c14-8-5-6-12-10(7-8)13(15)9-3-1-2-4-11(9)16-12/h1-7,14H
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View in JSmolView Stereo Labels
Synonyms
ValueSource
2-Hydroxy-9H-xanthen-9-oneHMDB
2-Hydroxy-9H-xanthen-9-one, 9ciHMDB
2-Hydroxy-xanthen-9-oneHMDB
Chemical FormulaC13H8O3
Average Molecular Weight212.2008
Monoisotopic Molecular Weight212.047344122
IUPAC Name2-hydroxy-9H-xanthen-9-one
Traditional Name2-hydroxyxanthen-9-one
CAS Registry Number1915-98-6
SMILES
OC1=CC2=C(OC3=CC=CC=C3C2=O)C=C1
InChI Identifier
InChI=1S/C13H8O3/c14-8-5-6-12-10(7-8)13(15)9-3-1-2-4-11(9)16-12/h1-7,14H
InChI KeyWSACHQJPCNOREV-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.
KingdomOrganic compounds
Super ClassOrganoheterocyclic compounds
ClassBenzopyrans
Sub Class1-benzopyrans
Direct ParentXanthones
Alternative Parents
Substituents
  • Xanthone
  • Chromone
  • 1-hydroxy-2-unsubstituted benzenoid
  • Pyranone
  • Benzenoid
  • Pyran
  • Heteroaromatic compound
  • Oxacycle
  • Organic oxygen compound
  • Organic oxide
  • Hydrocarbon derivative
  • Organooxygen compound
  • Aromatic heteropolycyclic compound
Molecular FrameworkAromatic heteropolycyclic compounds
External DescriptorsNot Available
Ontology
Physiological effectNot Available
Disposition
Biological locationRoute of exposureSource
ProcessNot Available
Role
Biological role
Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting Point241 - 241.5 °CNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
Predicted Chromatographic Properties
Spectra
Biological Properties
Cellular Locations
  • Membrane
Biospecimen LocationsNot Available
Tissue LocationsNot Available
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB010986
KNApSAcK IDC00035014
Chemspider ID67281
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound74708
PDB IDNot Available
ChEBI IDNot Available
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General References
  1. (). Yannai, Shmuel. (2004) Dictionary of food compounds with CD-ROM: Additives, flavors, and ingredients. Boca Raton: Chapman & Hall/CRC.. .