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Record Information

Version

5.0

Status

Detected but not Quantified

Creation Date

2021-09-10 22:03:25 UTC

Update Date

2021-09-26 22:53:03 UTC

HMDB ID

HMDB0244936

Secondary Accession Numbers

None

Metabolite Identification

Common Name

2-(6-Hydroxy-3-oxo-3H-xanthen-9-yl)benzoic acid

Description

fluorescein (acid form) 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 a significant number of articles have been published on fluorescein (acid form). This compound has been identified in human blood as reported by (PMID: 31557052 ). 2-(6-hydroxy-3-oxo-3h-xanthen-9-yl)benzoic acid is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically 2-(6-Hydroxy-3-oxo-3H-xanthen-9-yl)benzoic acid 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

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


  Mrv0541 05041404002D          

 25 28  0  0  0  0            999 V2000
    2.1434   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -1.6500    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
    3.5724   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    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
    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
    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
    2.8579    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -0.4125    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
    4.2868    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7158    2.4750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    2.4750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.7717    0.6674    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.0013   -0.4125    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
  7  5  2  0  0  0  0
  8  6  2  0  0  0  0
 11  5  1  0  0  0  0
 11  9  2  0  0  0  0
 12  6  1  0  0  0  0
 12 10  1  0  0  0  0
 13  3  2  0  0  0  0
 14  4  2  0  0  0  0
 14 13  1  0  0  0  0
 15  7  1  0  0  0  0
 16  8  1  0  0  0  0
 17  9  1  0  0  0  0
 17 15  2  0  0  0  0
 18 10  2  0  0  0  0
 18 16  1  0  0  0  0
 19 13  1  0  0  0  0
 19 15  1  0  0  0  0
 19 16  2  0  0  0  0
 20 14  1  0  0  0  0
 21 11  1  0  0  0  0
 22 12  2  0  0  0  0
 23 20  2  0  0  0  0
 24 20  1  0  0  0  0
 25 17  1  0  0  0  0
 25 18  1  0  0  0  0
M  END

HMDB0244936
     RDKit          3D
2-(6-Hydroxy-3-oxo-3H-xanthen-9-yl)benzoic acid
 37 40  0  0  0  0  0  0  0  0999 V2000
   -0.5547   -0.3006    2.1620 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7453    0.0338    1.9648 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6010    0.0865    3.0531 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1765    0.3477    0.6291 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5077    0.7218    0.4067 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9638    1.0315   -0.8593 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0575    0.9555   -1.8800 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7466    0.5889   -1.6728 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3031    0.2827   -0.4085 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0984   -0.0966   -0.2704 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4902   -1.4165   -0.3764 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4148   -2.4334   -0.6159 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0137   -3.7569   -0.7175 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3518   -4.0980   -0.5831 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6891   -5.3145   -0.6840 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.3118   -3.1258   -0.3418 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8881   -1.8219   -0.2418 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7477   -0.8640   -0.0153 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.3940    0.4084    0.0901 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3564    1.3664    0.3301 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0524    2.7094    0.4503 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0723    3.6248    0.6927 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7480    3.1436    0.3314 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7789    2.1960    0.0918 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0883    0.8366   -0.0297 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5053   -0.3549    3.0760 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1901    0.7699    1.2348 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9856    1.3210   -1.0455 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3992    1.1945   -2.8744 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0981    0.5564   -2.5467 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4623   -2.1890   -0.7238 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7054   -4.5214   -0.9026 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3460   -3.4266   -0.2423 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.3858    1.0196    0.4234 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2878    3.8167    1.6675 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5473    4.2026    0.4314 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2309    2.5059   -0.0034 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  2  4  1  0
  4  5  2  0
  5  6  1  0
  6  7  2  0
  7  8  1  0
  8  9  2  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
 14 16  1  0
 16 17  2  0
 17 18  1  0
 18 19  1  0
 19 20  2  0
 20 21  1  0
 21 22  1  0
 21 23  2  0
 23 24  1  0
 24 25  2  0
  9  4  1  0
 25 10  1  0
 17 11  1  0
 25 19  1  0
  3 26  1  0
  5 27  1  0
  6 28  1  0
  7 29  1  0
  8 30  1  0
 12 31  1  0
 13 32  1  0
 16 33  1  0
 20 34  1  0
 22 35  1  0
 23 36  1  0
 24 37  1  0
M  END


  Mrv0541 05041404002D          

 25 28  0  0  0  0            999 V2000
    2.1434   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -1.6500    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
    3.5724   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    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
    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
    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
    2.8579    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -0.4125    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
    4.2868    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7158    2.4750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    2.4750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.7717    0.6674    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.0013   -0.4125    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
  7  5  2  0  0  0  0
  8  6  2  0  0  0  0
 11  5  1  0  0  0  0
 11  9  2  0  0  0  0
 12  6  1  0  0  0  0
 12 10  1  0  0  0  0
 13  3  2  0  0  0  0
 14  4  2  0  0  0  0
 14 13  1  0  0  0  0
 15  7  1  0  0  0  0
 16  8  1  0  0  0  0
 17  9  1  0  0  0  0
 17 15  2  0  0  0  0
 18 10  2  0  0  0  0
 18 16  1  0  0  0  0
 19 13  1  0  0  0  0
 19 15  1  0  0  0  0
 19 16  2  0  0  0  0
 20 14  1  0  0  0  0
 21 11  1  0  0  0  0
 22 12  2  0  0  0  0
 23 20  2  0  0  0  0
 24 20  1  0  0  0  0
 25 17  1  0  0  0  0
 25 18  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0244936

> <DATABASE_NAME>
hmdb

> <SMILES>
OC(=O)C1=CC=CC=C1C1=C2C=CC(=O)C=C2OC2=C1C=CC(O)=C2

> <INCHI_IDENTIFIER>
InChI=1S/C20H12O5/c21-11-5-7-15-17(9-11)25-18-10-12(22)6-8-16(18)19(15)13-3-1-2-4-14(13)20(23)24/h1-10,21H,(H,23,24)

> <INCHI_KEY>
YKGGGCXBWXHKIZ-UHFFFAOYSA-N

> <FORMULA>
C20H12O5

> <MOLECULAR_WEIGHT>
332.3063

> <EXACT_MASS>
332.068473494

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_AVERAGE_POLARIZABILITY>
33.224828708127696

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
2-(6-hydroxy-3-oxo-3H-xanthen-9-yl)benzoic acid

> <ALOGPS_LOGP>
3.41

> <JCHEM_LOGP>
2.649186265272868

> <ALOGPS_LOGS>
-4.71

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
6.444405988287619

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.6977110930058164

> <JCHEM_PKA_STRONGEST_BASIC>
2.852834707480935

> <JCHEM_POLAR_SURFACE_AREA>
83.83

> <JCHEM_REFRACTIVITY>
103.41259999999997

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
6.46e-03 g/l

> <JCHEM_TRADITIONAL_IUPAC>
2-(3-hydroxy-6-oxoxanthen-9-yl)benzoic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0244936
     RDKit          3D
2-(6-Hydroxy-3-oxo-3H-xanthen-9-yl)benzoic acid
 37 40  0  0  0  0  0  0  0  0999 V2000
   -0.5547   -0.3006    2.1620 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7453    0.0338    1.9648 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6010    0.0865    3.0531 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1765    0.3477    0.6291 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5077    0.7218    0.4067 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9638    1.0315   -0.8593 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0575    0.9555   -1.8800 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7466    0.5889   -1.6728 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3031    0.2827   -0.4085 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0984   -0.0966   -0.2704 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4902   -1.4165   -0.3764 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4148   -2.4334   -0.6159 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0137   -3.7569   -0.7175 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3518   -4.0980   -0.5831 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6891   -5.3145   -0.6840 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.3118   -3.1258   -0.3418 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8881   -1.8219   -0.2418 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7477   -0.8640   -0.0153 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.3940    0.4084    0.0901 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3564    1.3664    0.3301 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0524    2.7094    0.4503 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0723    3.6248    0.6927 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7480    3.1436    0.3314 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7789    2.1960    0.0918 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0883    0.8366   -0.0297 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5053   -0.3549    3.0760 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1901    0.7699    1.2348 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9856    1.3210   -1.0455 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3992    1.1945   -2.8744 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0981    0.5564   -2.5467 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4623   -2.1890   -0.7238 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7054   -4.5214   -0.9026 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3460   -3.4266   -0.2423 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.3858    1.0196    0.4234 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2878    3.8167    1.6675 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5473    4.2026    0.4314 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2309    2.5059   -0.0034 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  2  4  1  0
  4  5  2  0
  5  6  1  0
  6  7  2  0
  7  8  1  0
  8  9  2  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
 14 16  1  0
 16 17  2  0
 17 18  1  0
 18 19  1  0
 19 20  2  0
 20 21  1  0
 21 22  1  0
 21 23  2  0
 23 24  1  0
 24 25  2  0
  9  4  1  0
 25 10  1  0
 17 11  1  0
 25 19  1  0
  3 26  1  0
  5 27  1  0
  6 28  1  0
  7 29  1  0
  8 30  1  0
 12 31  1  0
 13 32  1  0
 16 33  1  0
 20 34  1  0
 22 35  1  0
 23 36  1  0
 24 37  1  0
M  END

HEADER    PROTEIN                                 04-MAY-14   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   04-MAY-14         0                                  
HETATM    1  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       0.000   0.000   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       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       0.000   0.000   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       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   21  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   22  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   23  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   24  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   25  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
CONECT    1    2    3                                                       
CONECT    2    1    4                                                       
CONECT    3    1   13                                                       
CONECT    4    2   14                                                       
CONECT    5    7   11                                                       
CONECT    6    8   12                                                       
CONECT    7    5   15                                                       
CONECT    8    6   16                                                       
CONECT    9   11   17                                                       
CONECT   10   12   18                                                       
CONECT   11    5    9   21                                                  
CONECT   12    6   10   22                                                  
CONECT   13    3   14   19                                                  
CONECT   14    4   13   20                                                  
CONECT   15    7   17   19                                                  
CONECT   16    8   18   19                                                  
CONECT   17    9   15   25                                                  
CONECT   18   10   16   25                                                  
CONECT   19   13   15   16                                                  
CONECT   20   14   23   24                                                  
CONECT   21   11                                                            
CONECT   22   12                                                            
CONECT   23   20                                                            
CONECT   24   20                                                            
CONECT   25   17   18                                                       
MASTER        0    0    0    0    0    0    0    0   25    0   56    0
END

COMPND    HMDB0244936
HETATM    1  O1  UNL     1      -0.555  -0.301   2.162  1.00  0.00           O  
HETATM    2  C1  UNL     1      -1.745   0.034   1.965  1.00  0.00           C  
HETATM    3  O2  UNL     1      -2.601   0.086   3.053  1.00  0.00           O  
HETATM    4  C2  UNL     1      -2.176   0.348   0.629  1.00  0.00           C  
HETATM    5  C3  UNL     1      -3.508   0.722   0.407  1.00  0.00           C  
HETATM    6  C4  UNL     1      -3.964   1.031  -0.859  1.00  0.00           C  
HETATM    7  C5  UNL     1      -3.058   0.956  -1.880  1.00  0.00           C  
HETATM    8  C6  UNL     1      -1.747   0.589  -1.673  1.00  0.00           C  
HETATM    9  C7  UNL     1      -1.303   0.283  -0.408  1.00  0.00           C  
HETATM   10  C8  UNL     1       0.098  -0.097  -0.270  1.00  0.00           C  
HETATM   11  C9  UNL     1       0.490  -1.416  -0.376  1.00  0.00           C  
HETATM   12  C10 UNL     1      -0.415  -2.433  -0.616  1.00  0.00           C  
HETATM   13  C11 UNL     1       0.014  -3.757  -0.718  1.00  0.00           C  
HETATM   14  C12 UNL     1       1.352  -4.098  -0.583  1.00  0.00           C  
HETATM   15  O3  UNL     1       1.689  -5.315  -0.684  1.00  0.00           O  
HETATM   16  C13 UNL     1       2.312  -3.126  -0.342  1.00  0.00           C  
HETATM   17  C14 UNL     1       1.888  -1.822  -0.242  1.00  0.00           C  
HETATM   18  O4  UNL     1       2.748  -0.864  -0.015  1.00  0.00           O  
HETATM   19  C15 UNL     1       2.394   0.408   0.090  1.00  0.00           C  
HETATM   20  C16 UNL     1       3.356   1.366   0.330  1.00  0.00           C  
HETATM   21  C17 UNL     1       3.052   2.709   0.450  1.00  0.00           C  
HETATM   22  O5  UNL     1       4.072   3.625   0.693  1.00  0.00           O  
HETATM   23  C18 UNL     1       1.748   3.144   0.331  1.00  0.00           C  
HETATM   24  C19 UNL     1       0.779   2.196   0.092  1.00  0.00           C  
HETATM   25  C20 UNL     1       1.088   0.837  -0.030  1.00  0.00           C  
HETATM   26  H1  UNL     1      -3.505  -0.355   3.076  1.00  0.00           H  
HETATM   27  H2  UNL     1      -4.190   0.770   1.235  1.00  0.00           H  
HETATM   28  H3  UNL     1      -4.986   1.321  -1.046  1.00  0.00           H  
HETATM   29  H4  UNL     1      -3.399   1.194  -2.874  1.00  0.00           H  
HETATM   30  H5  UNL     1      -1.098   0.556  -2.547  1.00  0.00           H  
HETATM   31  H6  UNL     1      -1.462  -2.189  -0.724  1.00  0.00           H  
HETATM   32  H7  UNL     1      -0.705  -4.521  -0.903  1.00  0.00           H  
HETATM   33  H8  UNL     1       3.346  -3.427  -0.242  1.00  0.00           H  
HETATM   34  H9  UNL     1       4.386   1.020   0.423  1.00  0.00           H  
HETATM   35  H10 UNL     1       4.288   3.817   1.667  1.00  0.00           H  
HETATM   36  H11 UNL     1       1.547   4.203   0.431  1.00  0.00           H  
HETATM   37  H12 UNL     1      -0.231   2.506  -0.003  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3    4
CONECT    3   26
CONECT    4    5    5    9
CONECT    5    6   27
CONECT    6    7    7   28
CONECT    7    8   29
CONECT    8    9    9   30
CONECT    9   10
CONECT   10   11   11   25
CONECT   11   12   17
CONECT   12   13   13   31
CONECT   13   14   32
CONECT   14   15   15   16
CONECT   16   17   17   33
CONECT   17   18
CONECT   18   19
CONECT   19   20   20   25
CONECT   20   21   34
CONECT   21   22   23   23
CONECT   22   35
CONECT   23   24   36
CONECT   24   25   25   37
END

HMDB0244936
     RDKit          3D
2-(6-Hydroxy-3-oxo-3H-xanthen-9-yl)benzoic acid
 37 40  0  0  0  0  0  0  0  0999 V2000
   -0.5547   -0.3006    2.1620 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7453    0.0338    1.9648 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6010    0.0865    3.0531 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1765    0.3477    0.6291 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5077    0.7218    0.4067 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9638    1.0315   -0.8593 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0575    0.9555   -1.8800 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7466    0.5889   -1.6728 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3031    0.2827   -0.4085 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0984   -0.0966   -0.2704 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4902   -1.4165   -0.3764 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4148   -2.4334   -0.6159 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0137   -3.7569   -0.7175 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3518   -4.0980   -0.5831 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6891   -5.3145   -0.6840 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.3118   -3.1258   -0.3418 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8881   -1.8219   -0.2418 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7477   -0.8640   -0.0153 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.3940    0.4084    0.0901 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3564    1.3664    0.3301 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0524    2.7094    0.4503 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0723    3.6248    0.6927 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7480    3.1436    0.3314 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7789    2.1960    0.0918 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0883    0.8366   -0.0297 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5053   -0.3549    3.0760 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1901    0.7699    1.2348 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9856    1.3210   -1.0455 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3992    1.1945   -2.8744 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0981    0.5564   -2.5467 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4623   -2.1890   -0.7238 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7054   -4.5214   -0.9026 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3460   -3.4266   -0.2423 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.3858    1.0196    0.4234 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2878    3.8167    1.6675 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5473    4.2026    0.4314 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2309    2.5059   -0.0034 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  2  4  1  0
  4  5  2  0
  5  6  1  0
  6  7  2  0
  7  8  1  0
  8  9  2  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
 14 16  1  0
 16 17  2  0
 17 18  1  0
 18 19  1  0
 19 20  2  0
 20 21  1  0
 21 22  1  0
 21 23  2  0
 23 24  1  0
 24 25  2  0
  9  4  1  0
 25 10  1  0
 17 11  1  0
 25 19  1  0
  3 26  1  0
  5 27  1  0
  6 28  1  0
  7 29  1  0
  8 30  1  0
 12 31  1  0
 13 32  1  0
 16 33  1  0
 20 34  1  0
 22 35  1  0
 23 36  1  0
 24 37  1  0
M  END

View in JSmol View Stereo Labels

Synonyms

Value	Source
2-(3-Hydroxy-6-oxo-xanthen-9-yl)benzoic acid	ChEBI
2-(3-Hydroxy-6-oxoxanthen-9-yl)benzoic acid	ChEBI
Fluorescein (free acid)	ChEBI
Fluorescein acid	ChEBI
2-(3-Hydroxy-6-oxo-xanthen-9-yl)benzoate	Generator
2-(3-Hydroxy-6-oxoxanthen-9-yl)benzoate	Generator
Funduscein-25fluorescein	ChEMBL
Fluorescite	ChEMBL, MeSH
2-(6-Hydroxy-3-oxo-3H-xanthen-9-yl)benzoate	Generator
Disodium salt, fluorescein	MeSH
Fluor I strip a.t.	MeSH
Ful-glo	MeSH
Minims fluoresceine	MeSH
Fluorescein, disodium	MeSH
Disodium fluorescein	MeSH
Fluorescein monosodium salt	MeSH
Fluoresceine, minims	MeSH
Uranine	MeSH
Fluorescein, sodium	MeSH
Sodium fluorescein	MeSH
Fluorescéine sodique faure	MeSH
Diofluor	MeSH
Dipotassium salt, fluorescein	MeSH
D And C yellow no. 7	MeSH
Fluorescein dipotassium salt	MeSH
Fluorescein sodium	MeSH
Fluoresceina, colircusi	MeSH
Monosodium salt, fluorescein	MeSH
Fluor-I-strip a.t.	MeSH
Ful glo	MeSH
Fluorescein	MeSH
Fluorescein disodium salt	MeSH
Fluorescein sodium, minims	MeSH
Colircusi fluoresceina	MeSH
Minims fluorescein sodium	MeSH
Optifluor diba	MeSH
Sodium, fluorescein	MeSH
Minims stains	MeSH
D And C yellow no. 8	MeSH
Fluorets	MeSH
Funduscein	MeSH

Chemical Formula

C₂₀H₁₂O₅

Average Molecular Weight

332.3063

Monoisotopic Molecular Weight

332.068473494

IUPAC Name

2-(6-hydroxy-3-oxo-3H-xanthen-9-yl)benzoic acid

Traditional Name

2-(3-hydroxy-6-oxoxanthen-9-yl)benzoic acid

CAS Registry Number

Not Available

SMILES

OC(=O)C1=CC=CC=C1C1=C2C=CC(=O)C=C2OC2=C1C=CC(O)=C2

InChI Identifier

InChI=1S/C20H12O5/c21-11-5-7-15-17(9-11)25-18-10-12(22)6-8-16(18)19(15)13-3-1-2-4-14(13)20(23)24/h1-10,21H,(H,23,24)

InChI Key

YKGGGCXBWXHKIZ-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.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Benzopyrans

Sub Class

1-benzopyrans

Direct Parent

Xanthenes

Alternative Parents

Substituents

Xanthene
Benzoic acid or derivatives
Benzoic acid
Benzoyl
1-hydroxy-2-unsubstituted benzenoid
Benzenoid
Monocyclic benzene moiety
Heteroaromatic compound
Cyclic ketone
Oxacycle
Monocarboxylic acid or derivatives
Carboxylic acid
Carboxylic acid derivative
Organic oxide
Organooxygen compound
Organic oxygen compound
Hydrocarbon derivative
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

Not Available

Ontology

Physiological effect

Not Available

Disposition

Biological location

Non-excretory biofluid

Biofluid or Excreta

Blood (PMID: 31557052)

Process

Not Available

Role

Not Available

Physical Properties

State

Not Available

Experimental Molecular Properties

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

Experimental Chromatographic Properties

Not Available

Predicted Molecular Properties

Property	Value	Source
logP	3.41	ALOGPS
logP	2.65	ChemAxon
logS	-4.7	ALOGPS
pKa (Strongest Acidic)	3.7	ChemAxon
pKa (Strongest Basic)	2.85	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	83.83 Å²	ChemAxon
Rotatable Bond Count	1	ChemAxon
Refractivity	103.41 m³·mol⁻¹	ChemAxon
Polarizability	33.22 Å³	ChemAxon
Number of Rings	4	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Predicted Chromatographic Properties

Predicted Collision Cross Sections

Predictor	Adduct Type	CCS Value (Å²)	Reference
DeepCCS	[M+H]+	171.276	30932474
DeepCCS	[M-H]-	168.918	30932474
DeepCCS	[M-2H]-	202.842	30932474
DeepCCS	[M+Na]+	178.07	30932474

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
2-(6-Hydroxy-3-oxo-3H-xanthen-9-yl)benzoic acid	OC(=O)C1=CC=CC=C1C1=C2C=CC(=O)C=C2OC2=C1C=CC(O)=C2	4811.3	Standard polar	33892256
2-(6-Hydroxy-3-oxo-3H-xanthen-9-yl)benzoic acid	OC(=O)C1=CC=CC=C1C1=C2C=CC(=O)C=C2OC2=C1C=CC(O)=C2	2879.3	Standard non polar	33892256
2-(6-Hydroxy-3-oxo-3H-xanthen-9-yl)benzoic acid	OC(=O)C1=CC=CC=C1C1=C2C=CC(=O)C=C2OC2=C1C=CC(O)=C2	3304.7	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 - 2-(6-Hydroxy-3-oxo-3H-xanthen-9-yl)benzoic acid GC-MS (Non-derivatized) - 70eV, Positive	splash10-0w39-0059000000-29112bab97263ebf541b	2021-09-24	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 2-(6-Hydroxy-3-oxo-3H-xanthen-9-yl)benzoic acid GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 2-(6-Hydroxy-3-oxo-3H-xanthen-9-yl)benzoic acid GC-MS (TMS_1_1) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 2-(6-Hydroxy-3-oxo-3H-xanthen-9-yl)benzoic acid GC-MS (TMS_1_2) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 2-(6-Hydroxy-3-oxo-3H-xanthen-9-yl)benzoic acid GC-MS (TMS_2_1) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 2-(6-Hydroxy-3-oxo-3H-xanthen-9-yl)benzoic acid GC-MS (TBDMS_1_1) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 2-(6-Hydroxy-3-oxo-3H-xanthen-9-yl)benzoic acid GC-MS (TBDMS_1_2) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 2-(6-Hydroxy-3-oxo-3H-xanthen-9-yl)benzoic acid GC-MS (TBDMS_2_1) - 70eV, Positive	Not Available	2021-11-03	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 - 2-(6-Hydroxy-3-oxo-3H-xanthen-9-yl)benzoic acid 10V, Positive-QTOF	splash10-00lr-0009000000-d50860ce3685897ed62d	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2-(6-Hydroxy-3-oxo-3H-xanthen-9-yl)benzoic acid 20V, Positive-QTOF	splash10-014i-0009000000-a4b261a049cdd05f1abf	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2-(6-Hydroxy-3-oxo-3H-xanthen-9-yl)benzoic acid 40V, Positive-QTOF	splash10-014r-0079000000-b736232db146395a9be6	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2-(6-Hydroxy-3-oxo-3H-xanthen-9-yl)benzoic acid 10V, Negative-QTOF	splash10-000i-0093000000-8df36253060fd34fda4c	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2-(6-Hydroxy-3-oxo-3H-xanthen-9-yl)benzoic acid 20V, Negative-QTOF	splash10-000i-0090000000-ad76c01409fa18536a26	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2-(6-Hydroxy-3-oxo-3H-xanthen-9-yl)benzoic acid 40V, Negative-QTOF	splash10-06s9-0090000000-ca243d1895397beb36a8	2021-10-12	Wishart Lab	View Spectrum

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Blood

Tissue Locations

Not Available

Pathways

Not Available

Name	SMPDB/PathBank	KEGG

Normal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Blood	Detected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	31557052	details

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

Not Available

KNApSAcK ID

Not Available

Chemspider ID

3266

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Fluorescein

METLIN ID

Not Available

PubChem Compound

Not Available

PDB ID

Not Available

ChEBI ID

172923

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

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 ]

Showing metabocard for 2-(6-Hydroxy-3-oxo-3H-xanthen-9-yl)benzoic acid (HMDB0244936)

MOL for HMDB0244936 (2-(6-Hydroxy-3-oxo-3H-xanthen-9-yl)benzoic acid)

3D MOL for HMDB0244936 (2-(6-Hydroxy-3-oxo-3H-xanthen-9-yl)benzoic acid)

3D SDF for HMDB0244936 (2-(6-Hydroxy-3-oxo-3H-xanthen-9-yl)benzoic acid)

3D-SDF for HMDB0244936 (2-(6-Hydroxy-3-oxo-3H-xanthen-9-yl)benzoic acid)

PDB for HMDB0244936 (2-(6-Hydroxy-3-oxo-3H-xanthen-9-yl)benzoic acid)

3D PDB for HMDB0244936 (2-(6-Hydroxy-3-oxo-3H-xanthen-9-yl)benzoic acid)

SMILES for HMDB0244936 (2-(6-Hydroxy-3-oxo-3H-xanthen-9-yl)benzoic acid)

INCHI for HMDB0244936 (2-(6-Hydroxy-3-oxo-3H-xanthen-9-yl)benzoic acid)

Structure for HMDB0244936 (2-(6-Hydroxy-3-oxo-3H-xanthen-9-yl)benzoic acid)

3D Structure for HMDB0244936 (2-(6-Hydroxy-3-oxo-3H-xanthen-9-yl)benzoic acid)

Predicted Collision Cross Sections

Predicted Kovats Retention Indices

Underivatized

GC-MS Spectra

MS/MS Spectra