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Record Information

Version

5.0

Status

Detected but not Quantified

Creation Date

2021-09-10 23:46:34 UTC

Update Date

2021-09-26 22:56:03 UTC

HMDB ID

HMDB0246762

Secondary Accession Numbers

None

Metabolite Identification

Common Name

5-Carboxyfluorescein

Description

5-Carboxyfluorescein, also known as 5-FAM, 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 5-Carboxyfluorescein. This compound has been identified in human blood as reported by (PMID: 31557052 ). 5-carboxyfluorescein is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically 5-Carboxyfluorescein 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 05041403422D          

 28 32  0  0  0  0            999 V2000
    0.1623   -0.2004    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8543   -1.3527    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3232    1.1661    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9692   -0.3722    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1901   -0.5991    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5027    1.0801    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4598    1.1972    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1596   -1.9342    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4721   -0.2551    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0925    0.5843    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3391   -2.0202    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.8079    0.4985    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2667    1.0254    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5214    0.2407    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0106   -0.5131    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1669    0.3265    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4953   -1.1807    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6516   -0.3411    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8994    0.7560    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9343    1.5102    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3464    0.2405    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0033   -2.7738    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.6284    0.5845    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4516    0.1431    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1541    1.5407    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9345    2.3352    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.3159   -1.0947    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6016    1.0250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  4  1  2  0  0  0  0
  5  2  2  0  0  0  0
  6  3  2  0  0  0  0
 10  1  1  0  0  0  0
 10  7  2  0  0  0  0
 11  2  1  0  0  0  0
 11  8  2  0  0  0  0
 12  3  1  0  0  0  0
 12  9  2  0  0  0  0
 13  7  1  0  0  0  0
 14  4  1  0  0  0  0
 14 13  2  0  0  0  0
 15  5  1  0  0  0  0
 16  6  1  0  0  0  0
 17  8  1  0  0  0  0
 17 15  2  0  0  0  0
 18  9  1  0  0  0  0
 18 16  2  0  0  0  0
 19 10  1  0  0  0  0
 20 13  1  0  0  0  0
 21 14  1  0  0  0  0
 21 15  1  0  0  0  0
 21 16  1  0  0  0  0
 22 11  1  0  0  0  0
 23 12  1  0  0  0  0
 24 19  2  0  0  0  0
 25 19  1  0  0  0  0
 26 20  2  0  0  0  0
 27 17  1  0  0  0  0
 27 18  1  0  0  0  0
 28 20  1  0  0  0  0
 28 21  1  0  0  0  0
M  END

HMDB0246762
     RDKit          3D
5-Carboxyfluorescein
 40 44  0  0  0  0  0  0  0  0999 V2000
    5.6168   -0.4660    1.4835 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.0891   -0.2898    0.3767 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.9564   -0.1633   -0.7215 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.6550   -0.2104    0.1704 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7932   -0.3319    1.2330 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4110   -0.2592    1.0605 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8913   -0.0615   -0.1984 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7409    0.0616   -1.2688 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1138   -0.0098   -1.1036 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9411    0.2600   -2.4642 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4558    0.4062   -3.6153 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3927    0.2565   -2.1138 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5059    0.0636   -0.7344 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1700    1.2636   -0.1520 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6022    2.5028   -0.4054 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1204    3.6702    0.0740 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2653    3.6048    0.8475 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8728    4.7369    1.3840 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8582    2.3891    1.1205 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3044    1.2123    0.6159 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9074   -0.0124    0.8948 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3546   -1.1638    0.3935 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0260   -2.3504    0.7231 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5328   -3.5414    0.2583 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1829   -4.7332    0.5729 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3919   -3.5631   -0.5219 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7607   -2.3963   -0.8263 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2277   -1.1572   -0.3741 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.4048    0.7405   -0.8143 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1957   -0.4883    2.2305 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7780   -0.3616    1.9332 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8107    0.0798   -1.9022 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3107    2.5816   -1.0192 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6759    4.6440   -0.1239 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5523    5.0172    2.3105 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7636    2.3447    1.7330 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9195   -2.3388    1.3336 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9166   -5.0666   -0.0629 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9959   -4.4897   -0.8919 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1354   -2.3805   -1.4355 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
  8 10  1  0
 10 11  2  0
 10 12  1  0
 12 13  1  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
 20 21  1  0
 21 22  1  0
 22 23  2  0
 23 24  1  0
 24 25  1  0
 24 26  2  0
 26 27  1  0
 27 28  2  0
  9  4  1  0
 28 13  1  0
 13  7  1  0
 20 14  1  0
 28 22  1  0
  3 29  1  0
  5 30  1  0
  6 31  1  0
  9 32  1  0
 15 33  1  0
 16 34  1  0
 18 35  1  0
 19 36  1  0
 23 37  1  0
 25 38  1  0
 26 39  1  0
 27 40  1  0
M  END


  Mrv0541 05041403422D          

 28 32  0  0  0  0            999 V2000
    0.1623   -0.2004    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8543   -1.3527    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3232    1.1661    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9692   -0.3722    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1901   -0.5991    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5027    1.0801    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4598    1.1972    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1596   -1.9342    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4721   -0.2551    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0925    0.5843    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3391   -2.0202    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.8079    0.4985    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2667    1.0254    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5214    0.2407    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0106   -0.5131    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1669    0.3265    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4953   -1.1807    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6516   -0.3411    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8994    0.7560    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9343    1.5102    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3464    0.2405    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0033   -2.7738    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.6284    0.5845    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4516    0.1431    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1541    1.5407    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9345    2.3352    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.3159   -1.0947    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6016    1.0250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  4  1  2  0  0  0  0
  5  2  2  0  0  0  0
  6  3  2  0  0  0  0
 10  1  1  0  0  0  0
 10  7  2  0  0  0  0
 11  2  1  0  0  0  0
 11  8  2  0  0  0  0
 12  3  1  0  0  0  0
 12  9  2  0  0  0  0
 13  7  1  0  0  0  0
 14  4  1  0  0  0  0
 14 13  2  0  0  0  0
 15  5  1  0  0  0  0
 16  6  1  0  0  0  0
 17  8  1  0  0  0  0
 17 15  2  0  0  0  0
 18  9  1  0  0  0  0
 18 16  2  0  0  0  0
 19 10  1  0  0  0  0
 20 13  1  0  0  0  0
 21 14  1  0  0  0  0
 21 15  1  0  0  0  0
 21 16  1  0  0  0  0
 22 11  1  0  0  0  0
 23 12  1  0  0  0  0
 24 19  2  0  0  0  0
 25 19  1  0  0  0  0
 26 20  2  0  0  0  0
 27 17  1  0  0  0  0
 27 18  1  0  0  0  0
 28 20  1  0  0  0  0
 28 21  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0246762

> <DATABASE_NAME>
hmdb

> <SMILES>
OC(=O)C1=CC2=C(C=C1)C1(OC2=O)C2=C(OC3=C1C=CC(O)=C3)C=C(O)C=C2

> <INCHI_IDENTIFIER>
InChI=1S/C21H12O7/c22-11-2-5-15-17(8-11)27-18-9-12(23)3-6-16(18)21(15)14-4-1-10(19(24)25)7-13(14)20(26)28-21/h1-9,22-23H,(H,24,25)

> <INCHI_KEY>
NJYVEMPWNAYQQN-UHFFFAOYSA-N

> <FORMULA>
C21H12O7

> <MOLECULAR_WEIGHT>
376.3158

> <EXACT_MASS>
376.058302738

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_AVERAGE_POLARIZABILITY>
36.46845666870573

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
3',6'-dihydroxy-3-oxo-3H-spiro[2-benzofuran-1,9'-xanthene]-5-carboxylic acid

> <ALOGPS_LOGP>
3.23

> <JCHEM_LOGP>
3.537925731333333

> <ALOGPS_LOGS>
-4.47

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
8.719017281665057

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.832686464033405

> <JCHEM_PKA_STRONGEST_BASIC>
-6.021395709788817

> <JCHEM_POLAR_SURFACE_AREA>
113.29000000000002

> <JCHEM_REFRACTIVITY>
98.47629999999998

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.27e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
5-carboxyfluorescein

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0246762
     RDKit          3D
5-Carboxyfluorescein
 40 44  0  0  0  0  0  0  0  0999 V2000
    5.6168   -0.4660    1.4835 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.0891   -0.2898    0.3767 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.9564   -0.1633   -0.7215 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.6550   -0.2104    0.1704 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7932   -0.3319    1.2330 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4110   -0.2592    1.0605 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8913   -0.0615   -0.1984 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7409    0.0616   -1.2688 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1138   -0.0098   -1.1036 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9411    0.2600   -2.4642 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4558    0.4062   -3.6153 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3927    0.2565   -2.1138 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5059    0.0636   -0.7344 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1700    1.2636   -0.1520 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6022    2.5028   -0.4054 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1204    3.6702    0.0740 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2653    3.6048    0.8475 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8728    4.7369    1.3840 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8582    2.3891    1.1205 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3044    1.2123    0.6159 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9074   -0.0124    0.8948 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3546   -1.1638    0.3935 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0260   -2.3504    0.7231 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5328   -3.5414    0.2583 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1829   -4.7332    0.5729 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3919   -3.5631   -0.5219 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7607   -2.3963   -0.8263 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2277   -1.1572   -0.3741 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.4048    0.7405   -0.8143 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1957   -0.4883    2.2305 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7780   -0.3616    1.9332 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8107    0.0798   -1.9022 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3107    2.5816   -1.0192 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6759    4.6440   -0.1239 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5523    5.0172    2.3105 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7636    2.3447    1.7330 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9195   -2.3388    1.3336 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9166   -5.0666   -0.0629 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9959   -4.4897   -0.8919 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1354   -2.3805   -1.4355 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
  8 10  1  0
 10 11  2  0
 10 12  1  0
 12 13  1  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
 20 21  1  0
 21 22  1  0
 22 23  2  0
 23 24  1  0
 24 25  1  0
 24 26  2  0
 26 27  1  0
 27 28  2  0
  9  4  1  0
 28 13  1  0
 13  7  1  0
 20 14  1  0
 28 22  1  0
  3 29  1  0
  5 30  1  0
  6 31  1  0
  9 32  1  0
 15 33  1  0
 16 34  1  0
 18 35  1  0
 19 36  1  0
 23 37  1  0
 25 38  1  0
 26 39  1  0
 27 40  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  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+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
HETATM   26  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   27  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   28  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
CONECT    1    4   10                                                       
CONECT    2    5   11                                                       
CONECT    3    6   12                                                       
CONECT    4    1   14                                                       
CONECT    5    2   15                                                       
CONECT    6    3   16                                                       
CONECT    7   10   13                                                       
CONECT    8   11   17                                                       
CONECT    9   12   18                                                       
CONECT   10    1    7   19                                                  
CONECT   11    2    8   22                                                  
CONECT   12    3    9   23                                                  
CONECT   13    7   14   20                                                  
CONECT   14    4   13   21                                                  
CONECT   15    5   17   21                                                  
CONECT   16    6   18   21                                                  
CONECT   17    8   15   27                                                  
CONECT   18    9   16   27                                                  
CONECT   19   10   24   25                                                  
CONECT   20   13   26   28                                                  
CONECT   21   14   15   16   28                                             
CONECT   22   11                                                            
CONECT   23   12                                                            
CONECT   24   19                                                            
CONECT   25   19                                                            
CONECT   26   20                                                            
CONECT   27   17   18                                                       
CONECT   28   20   21                                                       
MASTER        0    0    0    0    0    0    0    0   28    0   64    0
END

COMPND    HMDB0246762
HETATM    1  O1  UNL     1       5.617  -0.466   1.483  1.00  0.00           O  
HETATM    2  C1  UNL     1       5.089  -0.290   0.377  1.00  0.00           C  
HETATM    3  O2  UNL     1       5.956  -0.163  -0.721  1.00  0.00           O  
HETATM    4  C2  UNL     1       3.655  -0.210   0.170  1.00  0.00           C  
HETATM    5  C3  UNL     1       2.793  -0.332   1.233  1.00  0.00           C  
HETATM    6  C4  UNL     1       1.411  -0.259   1.060  1.00  0.00           C  
HETATM    7  C5  UNL     1       0.891  -0.062  -0.198  1.00  0.00           C  
HETATM    8  C6  UNL     1       1.741   0.062  -1.269  1.00  0.00           C  
HETATM    9  C7  UNL     1       3.114  -0.010  -1.104  1.00  0.00           C  
HETATM   10  C8  UNL     1       0.941   0.260  -2.464  1.00  0.00           C  
HETATM   11  O3  UNL     1       1.456   0.406  -3.615  1.00  0.00           O  
HETATM   12  O4  UNL     1      -0.393   0.256  -2.114  1.00  0.00           O  
HETATM   13  C9  UNL     1      -0.506   0.064  -0.734  1.00  0.00           C  
HETATM   14  C10 UNL     1      -1.170   1.264  -0.152  1.00  0.00           C  
HETATM   15  C11 UNL     1      -0.602   2.503  -0.405  1.00  0.00           C  
HETATM   16  C12 UNL     1      -1.120   3.670   0.074  1.00  0.00           C  
HETATM   17  C13 UNL     1      -2.265   3.605   0.848  1.00  0.00           C  
HETATM   18  O5  UNL     1      -2.873   4.737   1.384  1.00  0.00           O  
HETATM   19  C14 UNL     1      -2.858   2.389   1.121  1.00  0.00           C  
HETATM   20  C15 UNL     1      -2.304   1.212   0.616  1.00  0.00           C  
HETATM   21  O6  UNL     1      -2.907  -0.012   0.895  1.00  0.00           O  
HETATM   22  C16 UNL     1      -2.355  -1.164   0.394  1.00  0.00           C  
HETATM   23  C17 UNL     1      -3.026  -2.350   0.723  1.00  0.00           C  
HETATM   24  C18 UNL     1      -2.533  -3.541   0.258  1.00  0.00           C  
HETATM   25  O7  UNL     1      -3.183  -4.733   0.573  1.00  0.00           O  
HETATM   26  C19 UNL     1      -1.392  -3.563  -0.522  1.00  0.00           C  
HETATM   27  C20 UNL     1      -0.761  -2.396  -0.826  1.00  0.00           C  
HETATM   28  C21 UNL     1      -1.228  -1.157  -0.374  1.00  0.00           C  
HETATM   29  H1  UNL     1       6.405   0.741  -0.814  1.00  0.00           H  
HETATM   30  H2  UNL     1       3.196  -0.488   2.231  1.00  0.00           H  
HETATM   31  H3  UNL     1       0.778  -0.362   1.933  1.00  0.00           H  
HETATM   32  H4  UNL     1       3.811   0.080  -1.902  1.00  0.00           H  
HETATM   33  H5  UNL     1       0.311   2.582  -1.019  1.00  0.00           H  
HETATM   34  H6  UNL     1      -0.676   4.644  -0.124  1.00  0.00           H  
HETATM   35  H7  UNL     1      -2.552   5.017   2.310  1.00  0.00           H  
HETATM   36  H8  UNL     1      -3.764   2.345   1.733  1.00  0.00           H  
HETATM   37  H9  UNL     1      -3.919  -2.339   1.334  1.00  0.00           H  
HETATM   38  H10 UNL     1      -3.917  -5.067  -0.063  1.00  0.00           H  
HETATM   39  H11 UNL     1      -0.996  -4.490  -0.892  1.00  0.00           H  
HETATM   40  H12 UNL     1       0.135  -2.381  -1.435  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3    4
CONECT    3   29
CONECT    4    5    5    9
CONECT    5    6   30
CONECT    6    7    7   31
CONECT    7    8   13
CONECT    8    9    9   10
CONECT    9   32
CONECT   10   11   11   12
CONECT   12   13
CONECT   13   14   28
CONECT   14   15   15   20
CONECT   15   16   33
CONECT   16   17   17   34
CONECT   17   18   19
CONECT   18   35
CONECT   19   20   20   36
CONECT   20   21
CONECT   21   22
CONECT   22   23   23   28
CONECT   23   24   37
CONECT   24   25   26   26
CONECT   25   38
CONECT   26   27   39
CONECT   27   28   28   40
END

HMDB0246762
     RDKit          3D
5-Carboxyfluorescein
 40 44  0  0  0  0  0  0  0  0999 V2000
    5.6168   -0.4660    1.4835 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.0891   -0.2898    0.3767 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.9564   -0.1633   -0.7215 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.6550   -0.2104    0.1704 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7932   -0.3319    1.2330 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4110   -0.2592    1.0605 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8913   -0.0615   -0.1984 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7409    0.0616   -1.2688 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1138   -0.0098   -1.1036 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9411    0.2600   -2.4642 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4558    0.4062   -3.6153 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3927    0.2565   -2.1138 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5059    0.0636   -0.7344 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1700    1.2636   -0.1520 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6022    2.5028   -0.4054 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1204    3.6702    0.0740 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2653    3.6048    0.8475 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8728    4.7369    1.3840 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8582    2.3891    1.1205 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3044    1.2123    0.6159 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9074   -0.0124    0.8948 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3546   -1.1638    0.3935 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0260   -2.3504    0.7231 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5328   -3.5414    0.2583 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1829   -4.7332    0.5729 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3919   -3.5631   -0.5219 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7607   -2.3963   -0.8263 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2277   -1.1572   -0.3741 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.4048    0.7405   -0.8143 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1957   -0.4883    2.2305 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7780   -0.3616    1.9332 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8107    0.0798   -1.9022 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3107    2.5816   -1.0192 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6759    4.6440   -0.1239 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5523    5.0172    2.3105 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7636    2.3447    1.7330 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9195   -2.3388    1.3336 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9166   -5.0666   -0.0629 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9959   -4.4897   -0.8919 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1354   -2.3805   -1.4355 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
  8 10  1  0
 10 11  2  0
 10 12  1  0
 12 13  1  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
 20 21  1  0
 21 22  1  0
 22 23  2  0
 23 24  1  0
 24 25  1  0
 24 26  2  0
 26 27  1  0
 27 28  2  0
  9  4  1  0
 28 13  1  0
 13  7  1  0
 20 14  1  0
 28 22  1  0
  3 29  1  0
  5 30  1  0
  6 31  1  0
  9 32  1  0
 15 33  1  0
 16 34  1  0
 18 35  1  0
 19 36  1  0
 23 37  1  0
 25 38  1  0
 26 39  1  0
 27 40  1  0
M  END

View in JSmol View Stereo Labels

Synonyms

Value	Source
4(5)-Carboxyfluorescein	ChEBI
4-Carboxyfluorescein	ChEBI
5-FAM	ChEBI

Chemical Formula

C₂₁H₁₂O₇

Average Molecular Weight

376.3158

Monoisotopic Molecular Weight

376.058302738

IUPAC Name

3',6'-dihydroxy-3-oxo-3H-spiro[2-benzofuran-1,9'-xanthene]-5-carboxylic acid

Traditional Name

5-carboxyfluorescein

CAS Registry Number

Not Available

SMILES

OC(=O)C1=CC2=C(C=C1)C1(OC2=O)C2=C(OC3=C1C=CC(O)=C3)C=C(O)C=C2

InChI Identifier

InChI=1S/C21H12O7/c22-11-2-5-15-17(8-11)27-18-9-12(23)3-6-16(18)21(15)14-4-1-10(19(24)25)7-13(14)20(26)28-21/h1-9,22-23H,(H,24,25)

InChI Key

NJYVEMPWNAYQQN-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
Meta_phthalic_acid
Diaryl ether
Benzofuranone
Phthalide
Isobenzofuranone
Isobenzofuran
Isocoumaran
1-hydroxy-2-unsubstituted benzenoid
Benzenoid
Dicarboxylic acid or derivatives
Lactone
Carboxylic acid ester
Oxacycle
Ether
Carboxylic acid
Carboxylic acid derivative
Hydrocarbon derivative
Organic oxide
Organooxygen compound
Organic oxygen compound
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

monocarboxylic acid (CHEBI:51617 )

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	3.23	ALOGPS
logP	3.54	ChemAxon
logS	-4.5	ALOGPS
pKa (Strongest Acidic)	3.83	ChemAxon
pKa (Strongest Basic)	-6	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	113.29 Å²	ChemAxon
Rotatable Bond Count	1	ChemAxon
Refractivity	98.48 m³·mol⁻¹	ChemAxon
Polarizability	36.47 Å³	ChemAxon
Number of Rings	5	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]+	185.162	30932474
DeepCCS	[M-H]-	182.804	30932474
DeepCCS	[M-2H]-	216.427	30932474
DeepCCS	[M+Na]+	191.582	30932474
AllCCS	[M+H]+	186.4	32859911
AllCCS	[M+H-H2O]+	183.4	32859911
AllCCS	[M+NH4]+	189.1	32859911
AllCCS	[M+Na]+	189.9	32859911
AllCCS	[M-H]-	185.8	32859911
AllCCS	[M+Na-2H]-	184.6	32859911
AllCCS	[M+HCOO]-	183.6	32859911

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
5-Carboxyfluorescein	OC(=O)C1=CC2=C(C=C1)C1(OC2=O)C2=C(OC3=C1C=CC(O)=C3)C=C(O)C=C2	5560.7	Standard polar	33892256
5-Carboxyfluorescein	OC(=O)C1=CC2=C(C=C1)C1(OC2=O)C2=C(OC3=C1C=CC(O)=C3)C=C(O)C=C2	3325.2	Standard non polar	33892256
5-Carboxyfluorescein	OC(=O)C1=CC2=C(C=C1)C1(OC2=O)C2=C(OC3=C1C=CC(O)=C3)C=C(O)C=C2	3939.1	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 - 5-Carboxyfluorescein GC-MS (Non-derivatized) - 70eV, Positive	splash10-004i-1189000000-c54d8b10309a2e7516db	2021-09-23	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 5-Carboxyfluorescein GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 5-Carboxyfluorescein GC-MS (TMS_1_1) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 5-Carboxyfluorescein GC-MS (TMS_1_2) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 5-Carboxyfluorescein GC-MS (TMS_2_1) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 5-Carboxyfluorescein GC-MS (TMS_2_2) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 5-Carboxyfluorescein GC-MS (TMS_3_1) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 5-Carboxyfluorescein GC-MS (TBDMS_1_1) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 5-Carboxyfluorescein GC-MS (TBDMS_1_2) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 5-Carboxyfluorescein GC-MS (TBDMS_2_1) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 5-Carboxyfluorescein GC-MS (TBDMS_2_2) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 5-Carboxyfluorescein GC-MS (TBDMS_3_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 - 5-Carboxyfluorescein 10V, Positive-QTOF	splash10-004i-0009000000-ab059c0ca933ae4bbc53	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5-Carboxyfluorescein 20V, Positive-QTOF	splash10-0059-0009000000-35637289809d1bd84348	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5-Carboxyfluorescein 40V, Positive-QTOF	splash10-0a4i-0009000000-6aac2e13d838d5cecc28	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5-Carboxyfluorescein 10V, Negative-QTOF	splash10-004i-0009000000-40fdbb038bc4cd627365	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5-Carboxyfluorescein 20V, Negative-QTOF	splash10-001i-0009000000-65ca3a33a444f1c08b53	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5-Carboxyfluorescein 40V, Negative-QTOF	splash10-004i-1119000000-4d87d6c9564c03556170	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

110316

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

6-Carboxyfluorescein

METLIN ID

Not Available

PubChem Compound

123755

PDB ID

Not Available

ChEBI ID

51617

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 5-Carboxyfluorescein (HMDB0246762)

MOL for HMDB0246762 (5-Carboxyfluorescein)

3D MOL for HMDB0246762 (5-Carboxyfluorescein)

3D SDF for HMDB0246762 (5-Carboxyfluorescein)

3D-SDF for HMDB0246762 (5-Carboxyfluorescein)

PDB for HMDB0246762 (5-Carboxyfluorescein)

3D PDB for HMDB0246762 (5-Carboxyfluorescein)

SMILES for HMDB0246762 (5-Carboxyfluorescein)

INCHI for HMDB0246762 (5-Carboxyfluorescein)

Structure for HMDB0246762 (5-Carboxyfluorescein)

3D Structure for HMDB0246762 (5-Carboxyfluorescein)

Predicted Collision Cross Sections

Predicted Kovats Retention Indices

Underivatized

GC-MS Spectra

MS/MS Spectra