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Showing metabocard for 9-Hydroxyxanthene (HMDB0247601)

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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2021-09-11 00:36:16 UTC
Update Date2021-09-26 22:57:22 UTC
HMDB IDHMDB0247601
Secondary Accession NumbersNone
Metabolite Identification
Common Name9-Hydroxyxanthene
Description9-Hydroxyxanthene, also known as xanthen-9-ol or xanthydrol, belongs to the class of organic compounds known as xanthenes. These are polycyclic aromatic compounds containing a xanthene moiety, which consists of two benzene rings joined to each other by a pyran ring. Based on a literature review very few articles have been published on 9-Hydroxyxanthene. This compound has been identified in human blood as reported by (PMID: 31557052 ). 9-hydroxyxanthene is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically 9-Hydroxyxanthene is part of the human exposome. The exposome can be defined as the collection of all the exposures of an individual in a lifetime and how those exposures relate to health. An individual's exposure begins before birth and includes insults from environmental and occupational sources.
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0247601 (9-Hydroxyxanthene)

  Mrv1652306031606242D          

 15 17  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
    0.7145    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
    0.7145    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
    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 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
    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
    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
  3  1  2  0  0  0  0
  4  2  2  0  0  0  0
  5  1  1  0  0  0  0
  6  2  1  0  0  0  0
  7  3  1  0  0  0  0
  8  4  1  0  0  0  0
  9  5  2  0  0  0  0
 10  6  2  0  0  0  0
 11  7  2  0  0  0  0
 11  9  1  0  0  0  0
 12  8  2  0  0  0  0
 12 10  1  0  0  0  0
 13  9  1  0  0  0  0
 13 10  1  0  0  0  0
 14 13  1  0  0  0  0
 15 11  1  0  0  0  0
 15 12  1  0  0  0  0
M  END
Download

3D MOL for HMDB0247601 (9-Hydroxyxanthene)

HMDB0247601
     RDKit          3D
9-Hydroxyxanthene
 25 27  0  0  0  0  0  0  0  0999 V2000
   -0.0564   -1.7754   -1.4647 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0055   -1.1893   -0.1816 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2043   -0.3935   -0.0019 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4571   -1.0163   -0.1120 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6382   -0.3289    0.0451 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5333    1.0194    0.3197 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3129    1.6509    0.4321 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1170    0.9519    0.2724 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0919    1.6099    0.3904 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2645    0.8908    0.2269 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4870    1.5727    0.3496 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6769    0.9039    0.1962 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6542   -0.4412   -0.0789 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4729   -1.1309   -0.2038 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2557   -0.4536   -0.0482 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9235   -2.1560   -1.6665 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0211   -2.0180    0.5624 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5094   -2.0852   -0.3302 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5661   -0.8709   -0.0530 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4541    1.5875    0.4487 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2192    2.7129    0.6483 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4873    2.6438    0.5688 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.5980    1.4761    0.3006 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.5929   -0.9660   -0.1995 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4255   -2.1947   -0.4209 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  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
 14 15  2  0
 15  2  1  0
  8  3  1  0
 15 10  1  0
  1 16  1  0
  2 17  1  0
  4 18  1  0
  5 19  1  0
  6 20  1  0
  7 21  1  0
 11 22  1  0
 12 23  1  0
 13 24  1  0
 14 25  1  0
M  END
Download

3D SDF for HMDB0247601 (9-Hydroxyxanthene)

  Mrv1652306031606242D          

 15 17  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
    0.7145    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
    0.7145    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
    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 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
    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
    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
  3  1  2  0  0  0  0
  4  2  2  0  0  0  0
  5  1  1  0  0  0  0
  6  2  1  0  0  0  0
  7  3  1  0  0  0  0
  8  4  1  0  0  0  0
  9  5  2  0  0  0  0
 10  6  2  0  0  0  0
 11  7  2  0  0  0  0
 11  9  1  0  0  0  0
 12  8  2  0  0  0  0
 12 10  1  0  0  0  0
 13  9  1  0  0  0  0
 13 10  1  0  0  0  0
 14 13  1  0  0  0  0
 15 11  1  0  0  0  0
 15 12  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0247601

> <DATABASE_NAME>
hmdb

> <SMILES>
OC1C2=CC=CC=C2OC2=CC=CC=C12

> <INCHI_IDENTIFIER>
InChI=1S/C13H10O2/c14-13-9-5-1-3-7-11(9)15-12-8-4-2-6-10(12)13/h1-8,13-14H

> <INCHI_KEY>
JFRMYMMIJXLMBB-UHFFFAOYSA-N

> <FORMULA>
C13H10O2

> <MOLECULAR_WEIGHT>
198.221

> <EXACT_MASS>
198.068079562

> <JCHEM_ACCEPTOR_COUNT>
1

> <JCHEM_ATOM_COUNT>
25

> <JCHEM_AVERAGE_POLARIZABILITY>
20.962361304451637

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
9H-xanthen-9-ol

> <ALOGPS_LOGP>
2.68

> <JCHEM_LOGP>
2.5171776029999995

> <ALOGPS_LOGS>
-2.14

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
13.211561792022316

> <JCHEM_PKA_STRONGEST_BASIC>
-3.58106287216944

> <JCHEM_POLAR_SURFACE_AREA>
29.46

> <JCHEM_REFRACTIVITY>
57.33950000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.42e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
xanthydrol

> <JCHEM_VEBER_RULE>
1

$$$$
Download

3D-SDF for HMDB0247601 (9-Hydroxyxanthene)

HMDB0247601
     RDKit          3D
9-Hydroxyxanthene
 25 27  0  0  0  0  0  0  0  0999 V2000
   -0.0564   -1.7754   -1.4647 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0055   -1.1893   -0.1816 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2043   -0.3935   -0.0019 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4571   -1.0163   -0.1120 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6382   -0.3289    0.0451 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5333    1.0194    0.3197 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3129    1.6509    0.4321 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1170    0.9519    0.2724 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0919    1.6099    0.3904 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2645    0.8908    0.2269 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4870    1.5727    0.3496 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6769    0.9039    0.1962 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6542   -0.4412   -0.0789 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4729   -1.1309   -0.2038 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2557   -0.4536   -0.0482 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9235   -2.1560   -1.6665 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0211   -2.0180    0.5624 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5094   -2.0852   -0.3302 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5661   -0.8709   -0.0530 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4541    1.5875    0.4487 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2192    2.7129    0.6483 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4873    2.6438    0.5688 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.5980    1.4761    0.3006 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.5929   -0.9660   -0.1995 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4255   -2.1947   -0.4209 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  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
 14 15  2  0
 15  2  1  0
  8  3  1  0
 15 10  1  0
  1 16  1  0
  2 17  1  0
  4 18  1  0
  5 19  1  0
  6 20  1  0
  7 21  1  0
 11 22  1  0
 12 23  1  0
 13 24  1  0
 14 25  1  0
M  END
Download

PDB for HMDB0247601 (9-Hydroxyxanthene)

HEADER    PROTEIN                                 03-JUN-16   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   03-JUN-16         0                                  
HETATM    1  C   UNK     0       9.336   2.310   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       9.336   3.850   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       1.334   3.850   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       8.002   1.540   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       8.002   4.620   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       2.667   4.620   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       5.335   0.000   0.000  0.00  0.00           O+0
HETATM   15  O   UNK     0       5.335   4.620   0.000  0.00  0.00           O+0
CONECT    1    3    5                                                       
CONECT    2    4    6                                                       
CONECT    3    1    7                                                       
CONECT    4    2    8                                                       
CONECT    5    1    9                                                       
CONECT    6    2   10                                                       
CONECT    7    3   11                                                       
CONECT    8    4   12                                                       
CONECT    9    5   11   13                                                  
CONECT   10    6   12   13                                                  
CONECT   11    7    9   15                                                  
CONECT   12    8   10   15                                                  
CONECT   13    9   10   14                                                  
CONECT   14   13                                                            
CONECT   15   11   12                                                       
MASTER        0    0    0    0    0    0    0    0   15    0   34    0
END
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3D PDB for HMDB0247601 (9-Hydroxyxanthene)

COMPND    HMDB0247601
HETATM    1  O1  UNL     1      -0.056  -1.775  -1.465  1.00  0.00           O  
HETATM    2  C1  UNL     1       0.006  -1.189  -0.182  1.00  0.00           C  
HETATM    3  C2  UNL     1      -1.204  -0.394  -0.002  1.00  0.00           C  
HETATM    4  C3  UNL     1      -2.457  -1.016  -0.112  1.00  0.00           C  
HETATM    5  C4  UNL     1      -3.638  -0.329   0.045  1.00  0.00           C  
HETATM    6  C5  UNL     1      -3.533   1.019   0.320  1.00  0.00           C  
HETATM    7  C6  UNL     1      -2.313   1.651   0.432  1.00  0.00           C  
HETATM    8  C7  UNL     1      -1.117   0.952   0.272  1.00  0.00           C  
HETATM    9  O2  UNL     1       0.092   1.610   0.390  1.00  0.00           O  
HETATM   10  C8  UNL     1       1.265   0.891   0.227  1.00  0.00           C  
HETATM   11  C9  UNL     1       2.487   1.573   0.350  1.00  0.00           C  
HETATM   12  C10 UNL     1       3.677   0.904   0.196  1.00  0.00           C  
HETATM   13  C11 UNL     1       3.654  -0.441  -0.079  1.00  0.00           C  
HETATM   14  C12 UNL     1       2.473  -1.131  -0.204  1.00  0.00           C  
HETATM   15  C13 UNL     1       1.256  -0.454  -0.048  1.00  0.00           C  
HETATM   16  H1  UNL     1      -0.923  -2.156  -1.667  1.00  0.00           H  
HETATM   17  H2  UNL     1      -0.021  -2.018   0.562  1.00  0.00           H  
HETATM   18  H3  UNL     1      -2.509  -2.085  -0.330  1.00  0.00           H  
HETATM   19  H4  UNL     1      -4.566  -0.871  -0.053  1.00  0.00           H  
HETATM   20  H5  UNL     1      -4.454   1.588   0.449  1.00  0.00           H  
HETATM   21  H6  UNL     1      -2.219   2.713   0.648  1.00  0.00           H  
HETATM   22  H7  UNL     1       2.487   2.644   0.569  1.00  0.00           H  
HETATM   23  H8  UNL     1       4.598   1.476   0.301  1.00  0.00           H  
HETATM   24  H9  UNL     1       4.593  -0.966  -0.199  1.00  0.00           H  
HETATM   25  H10 UNL     1       2.425  -2.195  -0.421  1.00  0.00           H  
CONECT    1    2   16
CONECT    2    3   15   17
CONECT    3    4    4    8
CONECT    4    5   18
CONECT    5    6    6   19
CONECT    6    7   20
CONECT    7    8    8   21
CONECT    8    9
CONECT    9   10
CONECT   10   11   11   15
CONECT   11   12   22
CONECT   12   13   13   23
CONECT   13   14   24
CONECT   14   15   15   25
END
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SMILES for HMDB0247601 (9-Hydroxyxanthene)

OC1C2=CC=CC=C2OC2=CC=CC=C12
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INCHI for HMDB0247601 (9-Hydroxyxanthene)

InChI=1S/C13H10O2/c14-13-9-5-1-3-7-11(9)15-12-8-4-2-6-10(12)13/h1-8,13-14H
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View in JSmolView Stereo Labels
Synonyms
ValueSource
Xanthen-9-olHMDB
XanthydrolHMDB
Chemical FormulaC13H10O2
Average Molecular Weight198.221
Monoisotopic Molecular Weight198.068079562
IUPAC Name9H-xanthen-9-ol
Traditional Namexanthydrol
CAS Registry NumberNot Available
SMILES
OC1C2=CC=CC=C2OC2=CC=CC=C12
InChI Identifier
InChI=1S/C13H10O2/c14-13-9-5-1-3-7-11(9)15-12-8-4-2-6-10(12)13/h1-8,13-14H
InChI KeyJFRMYMMIJXLMBB-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as xanthenes. These are polycyclic aromatic compounds containing a xanthene moiety, which consists of two benzene rings joined to each other by a pyran ring.
KingdomOrganic compounds
Super ClassOrganoheterocyclic compounds
ClassBenzopyrans
Sub Class1-benzopyrans
Direct ParentXanthenes
Alternative Parents
Substituents
  • Xanthene
  • Diaryl ether
  • Benzenoid
  • Secondary alcohol
  • Oxacycle
  • Ether
  • Organic oxygen compound
  • Hydrocarbon derivative
  • Organooxygen compound
  • Alcohol
  • Aromatic heteropolycyclic compound
Molecular FrameworkAromatic heteropolycyclic compounds
External DescriptorsNot Available
Ontology
Physiological effectNot Available
Disposition
Biological locationSource
ProcessNot Available
RoleNot Available
Physical Properties
StateNot Available
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot 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 LocationsNot Available
Biospecimen Locations
  • Blood
Tissue LocationsNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodDetected but not QuantifiedNot QuantifiedNot SpecifiedNot SpecifiedNormal details
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDNot Available
KNApSAcK IDNot Available
Chemspider ID65693
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound72861
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. Barupal DK, Fiehn O: Generating the Blood Exposome Database Using a Comprehensive Text Mining and Database Fusion Approach. Environ Health Perspect. 2019 Sep;127(9):97008. doi: 10.1289/EHP4713. Epub 2019 Sep 26. [PubMed:31557052 ]