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Record Information

Version

5.0

Status

Detected but not Quantified

Creation Date

2021-09-10 21:49:24 UTC

Update Date

2021-09-26 22:52:35 UTC

HMDB ID

HMDB0244679

Secondary Accession Numbers

None

Metabolite Identification

Common Name

6-CFDA N-succinimidyl ester

Description

6-CFDA N-succinimidyl ester, also known as cfda-se or CFSE, 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 6-CFDA N-succinimidyl ester. This compound has been identified in human blood as reported by (PMID: 31557052 ). 6-cfda n-succinimidyl ester is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically 6-CFDA N-succinimidyl ester 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

  Mrv1652309102123492D          

 41 46  0  0  0  0            999 V2000
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    5.6284    0.2405    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.8079    0.3265    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4721    1.0801    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6516    1.1661    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1669    0.4985    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5027   -0.2551    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3232   -0.3411    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3464    0.5845    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0106    1.3381    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4953    2.0057    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3159    1.9197    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1596    2.7592    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3391    2.8452    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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 39 41  1  0  0  0  0
 11 41  1  0  0  0  0
M  END

HMDB0244679
     RDKit          3D
6-CFDA N-succinimidyl ester
 60 65  0  0  0  0  0  0  0  0999 V2000
   -3.8573   -7.4165    1.1260 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5270   -6.0930    0.5387 C   0  0  0  0  0  0  0  0  0  0  0  0
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M  END

  Mrv1652309102123492D          

 41 46  0  0  0  0            999 V2000
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 27 29  1  0  0  0  0
 29 30  2  0  0  0  0
 29 31  1  0  0  0  0
 31 32  1  0  0  0  0
 32 33  1  0  0  0  0
 33 34  2  0  0  0  0
 33 35  1  0  0  0  0
 35 36  1  0  0  0  0
 36 37  1  0  0  0  0
 32 37  1  0  0  0  0
 37 38  2  0  0  0  0
 24 39  1  0  0  0  0
 39 40  2  0  0  0  0
 39 41  1  0  0  0  0
 11 41  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0244679

> <DATABASE_NAME>
hmdb

> <SMILES>
CC(=O)OC1=CC2=C(C=C1)C1(OC(=O)C3=C1C=C(C=C3)C(=O)ON1C(=O)CCC1=O)C1=C(O2)C=C(OC(C)=O)C=C1

> <INCHI_IDENTIFIER>
InChI=1S/C29H19NO11/c1-14(31)37-17-4-7-20-23(12-17)39-24-13-18(38-15(2)32)5-8-21(24)29(20)22-11-16(3-6-19(22)28(36)40-29)27(35)41-30-25(33)9-10-26(30)34/h3-8,11-13H,9-10H2,1-2H3

> <INCHI_KEY>
JGPOSNWWINVNFV-UHFFFAOYSA-N

> <FORMULA>
C29H19NO11

> <MOLECULAR_WEIGHT>
557.467

> <EXACT_MASS>
557.095810436

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
60

> <JCHEM_AVERAGE_POLARIZABILITY>
54.63026536123982

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2,5-dioxopyrrolidin-1-yl 3',6'-bis(acetyloxy)-3-oxo-3H-spiro[2-benzofuran-1,9'-xanthene]-6-carboxylate

> <ALOGPS_LOGP>
3.16

> <JCHEM_LOGP>
2.929163712

> <ALOGPS_LOGS>
-5.41

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
6

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
17.697288180773068

> <JCHEM_PKA_STRONGEST_BASIC>
-3.7368742982302794

> <JCHEM_POLAR_SURFACE_AREA>
151.80999999999997

> <JCHEM_REFRACTIVITY>
137.3331

> <JCHEM_ROTATABLE_BOND_COUNT>
7

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
2.17e-03 g/l

> <JCHEM_TRADITIONAL_IUPAC>
2,5-dioxopyrrolidin-1-yl 3',6'-bis(acetyloxy)-3-oxospiro[2-benzofuran-1,9'-xanthene]-6-carboxylate

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0244679
     RDKit          3D
6-CFDA N-succinimidyl ester
 60 65  0  0  0  0  0  0  0  0999 V2000
   -3.8573   -7.4165    1.1260 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5270   -6.0930    0.5387 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2222   -5.6108   -0.4033 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4580   -5.3262    0.9820 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1962   -4.0913    0.3936 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3465   -3.9560   -0.6850 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0961   -2.7155   -1.2596 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7034   -1.5899   -0.7499 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5561   -1.7027    0.3285 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7925   -2.9488    0.8866 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1910   -0.5847    0.8779 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9965    0.6751    0.3726 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6372    1.7939    0.9285 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4474    3.0617    0.4312 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0970    4.1444    1.0034 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6922    4.7043    2.2098 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3660    5.8624    2.8501 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6823    4.1438    2.7391 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5923    3.2009   -0.6500 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9606    2.0999   -1.1996 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1535    0.8371   -0.7006 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4349   -0.2930   -1.3727 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9299   -0.4029   -2.7226 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8836   -0.1603   -3.5950 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0024   -0.1705   -4.8632 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3470    0.1044   -2.8663 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6332    0.3878   -3.2716 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6227    0.5877   -2.3322 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3135    0.5011   -0.9765 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3991    0.7154   -0.0022 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1313    0.6327    1.2135 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.6795    1.0004   -0.3972 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.7478    1.2107    0.4299 N   0  0  0  0  0  0  0  0  0  0  0  0
    7.0961    1.1301   -0.0629 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.4747    0.8736   -1.2512 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.0615    1.3914    1.0254 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.2380    1.1444    2.2713 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.8587    1.5209    1.7930 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9338    2.0321    2.4754 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.0272    0.2189   -0.6178 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0109    0.0132   -1.5283 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9303   -8.0395    1.2633 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3238   -7.2716    2.1215 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5024   -7.9489    0.4158 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8801   -4.8755   -1.0606 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4175   -2.7107   -2.0985 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4697   -2.9891    1.7307 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2960    1.6400    1.7700 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7037    6.2878    3.6114 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3305    5.5525    3.3437 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5974    6.6443    2.0672 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4566    4.2063   -1.0235 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2864    2.2366   -2.0587 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8326    0.4453   -4.3409 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6372    0.8119   -2.6200 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.4075    2.4307    0.9497 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.9196    0.6823    0.9591 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.5608    1.7534    3.1321 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.2669    0.0593    2.4851 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8170    0.1592    0.4566 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  0
  2  4  1  0
  4  5  1  0
  5  6  2  0
  6  7  1  0
  7  8  2  0
  8  9  1  0
  9 10  2  0
  9 11  1  0
 11 12  1  0
 12 13  2  0
 13 14  1  0
 14 15  1  0
 15 16  1  0
 16 17  1  0
 16 18  2  0
 14 19  2  0
 19 20  1  0
 20 21  2  0
 21 22  1  0
 22 23  1  0
 23 24  1  0
 24 25  2  0
 24 26  1  0
 26 27  2  0
 27 28  1  0
 28 29  2  0
 29 30  1  0
 30 31  2  0
 30 32  1  0
 32 33  1  0
 33 34  1  0
 34 35  2  0
 34 36  1  0
 36 37  1  0
 37 38  1  0
 38 39  2  0
 29 40  1  0
 40 41  2  0
 10  5  1  0
 21 12  1  0
 41 22  1  0
 22  8  1  0
 41 26  1  0
 38 33  1  0
  1 42  1  0
  1 43  1  0
  1 44  1  0
  6 45  1  0
  7 46  1  0
 10 47  1  0
 13 48  1  0
 17 49  1  0
 17 50  1  0
 17 51  1  0
 19 52  1  0
 20 53  1  0
 27 54  1  0
 28 55  1  0
 36 56  1  0
 36 57  1  0
 37 58  1  0
 37 59  1  0
 40 60  1  0
M  END

HEADER    PROTEIN                                 10-SEP-21   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   10-SEP-21         0                                  
HETATM    1  C   UNK     0      12.665  -1.118   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      11.133  -0.958   0.000  0.00  0.00           C+0
HETATM    3  O   UNK     0      10.228  -2.204   0.000  0.00  0.00           O+0
HETATM    4  O   UNK     0      10.506   0.449   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0       8.975   0.609   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       8.348   2.016   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       6.816   2.177   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       5.912   0.931   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       6.538  -0.476   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       8.070  -0.637   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       4.380   1.091   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       3.753   2.498   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       4.658   3.744   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0       6.190   3.583   0.000  0.00  0.00           O+0
HETATM   15  C   UNK     0       4.031   5.151   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       2.500   5.311   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       1.595   4.065   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       2.222   2.658   0.000  0.00  0.00           C+0
HETATM   19  O   UNK     0       1.873   6.718   0.000  0.00  0.00           O+0
HETATM   20  C   UNK     0       0.341   6.878   0.000  0.00  0.00           C+0
HETATM   21  O   UNK     0      -0.564   5.632   0.000  0.00  0.00           O+0
HETATM   22  C   UNK     0      -0.286   8.285   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       2.840   1.091   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       2.364  -0.374   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       0.858  -0.695   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0      -0.173   0.449   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0       0.303   1.914   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0       1.809   2.235   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0      -0.728   3.058   0.000  0.00  0.00           C+0
HETATM   30  O   UNK     0      -0.252   4.523   0.000  0.00  0.00           O+0
HETATM   31  O   UNK     0      -2.234   2.738   0.000  0.00  0.00           O+0
HETATM   32  N   UNK     0      -3.265   3.882   0.000  0.00  0.00           N+0
HETATM   33  C   UNK     0      -4.796   3.720   0.000  0.00  0.00           C+0
HETATM   34  O   UNK     0      -5.566   2.387   0.000  0.00  0.00           O+0
HETATM   35  C   UNK     0      -5.423   5.127   0.000  0.00  0.00           C+0
HETATM   36  C   UNK     0      -4.279   6.158   0.000  0.00  0.00           C+0
HETATM   37  C   UNK     0      -2.945   5.388   0.000  0.00  0.00           C+0
HETATM   38  O   UNK     0      -1.539   6.015   0.000  0.00  0.00           O+0
HETATM   39  C   UNK     0       3.611  -1.279   0.000  0.00  0.00           C+0
HETATM   40  O   UNK     0       3.611  -2.819   0.000  0.00  0.00           O+0
HETATM   41  O   UNK     0       4.856  -0.373   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    4                                                  
CONECT    3    2                                                            
CONECT    4    2    5                                                       
CONECT    5    4    6   10                                                  
CONECT    6    5    7                                                       
CONECT    7    6    8   14                                                  
CONECT    8    7    9   11                                                  
CONECT    9    8   10                                                       
CONECT   10    9    5                                                       
CONECT   11    8   12   23   41                                             
CONECT   12   11   13   18                                                  
CONECT   13   12   14   15                                                  
CONECT   14   13    7                                                       
CONECT   15   13   16                                                       
CONECT   16   15   17   19                                                  
CONECT   17   16   18                                                       
CONECT   18   17   12                                                       
CONECT   19   16   20                                                       
CONECT   20   19   21   22                                                  
CONECT   21   20                                                            
CONECT   22   20                                                            
CONECT   23   11   24   28                                                  
CONECT   24   23   25   39                                                  
CONECT   25   24   26                                                       
CONECT   26   25   27                                                       
CONECT   27   26   28   29                                                  
CONECT   28   27   23                                                       
CONECT   29   27   30   31                                                  
CONECT   30   29                                                            
CONECT   31   29   32                                                       
CONECT   32   31   33   37                                                  
CONECT   33   32   34   35                                                  
CONECT   34   33                                                            
CONECT   35   33   36                                                       
CONECT   36   35   37                                                       
CONECT   37   36   32   38                                                  
CONECT   38   37                                                            
CONECT   39   24   40   41                                                  
CONECT   40   39                                                            
CONECT   41   39   11                                                       
MASTER        0    0    0    0    0    0    0    0   41    0   92    0
END

COMPND    HMDB0244679
HETATM    1  C1  UNL     1      -3.857  -7.417   1.126  1.00  0.00           C  
HETATM    2  C2  UNL     1      -3.527  -6.093   0.539  1.00  0.00           C  
HETATM    3  O1  UNL     1      -4.222  -5.611  -0.403  1.00  0.00           O  
HETATM    4  O2  UNL     1      -2.458  -5.326   0.982  1.00  0.00           O  
HETATM    5  C3  UNL     1      -2.196  -4.091   0.394  1.00  0.00           C  
HETATM    6  C4  UNL     1      -1.347  -3.956  -0.685  1.00  0.00           C  
HETATM    7  C5  UNL     1      -1.096  -2.715  -1.260  1.00  0.00           C  
HETATM    8  C6  UNL     1      -1.703  -1.590  -0.750  1.00  0.00           C  
HETATM    9  C7  UNL     1      -2.556  -1.703   0.328  1.00  0.00           C  
HETATM   10  C8  UNL     1      -2.792  -2.949   0.887  1.00  0.00           C  
HETATM   11  O3  UNL     1      -3.191  -0.585   0.878  1.00  0.00           O  
HETATM   12  C9  UNL     1      -2.997   0.675   0.373  1.00  0.00           C  
HETATM   13  C10 UNL     1      -3.637   1.794   0.928  1.00  0.00           C  
HETATM   14  C11 UNL     1      -3.447   3.062   0.431  1.00  0.00           C  
HETATM   15  O4  UNL     1      -4.097   4.144   1.003  1.00  0.00           O  
HETATM   16  C12 UNL     1      -3.692   4.704   2.210  1.00  0.00           C  
HETATM   17  C13 UNL     1      -4.366   5.862   2.850  1.00  0.00           C  
HETATM   18  O5  UNL     1      -2.682   4.144   2.739  1.00  0.00           O  
HETATM   19  C14 UNL     1      -2.592   3.201  -0.650  1.00  0.00           C  
HETATM   20  C15 UNL     1      -1.961   2.100  -1.200  1.00  0.00           C  
HETATM   21  C16 UNL     1      -2.153   0.837  -0.701  1.00  0.00           C  
HETATM   22  C17 UNL     1      -1.435  -0.293  -1.373  1.00  0.00           C  
HETATM   23  O6  UNL     1      -1.930  -0.403  -2.723  1.00  0.00           O  
HETATM   24  C18 UNL     1      -0.884  -0.160  -3.595  1.00  0.00           C  
HETATM   25  O7  UNL     1      -1.002  -0.171  -4.863  1.00  0.00           O  
HETATM   26  C19 UNL     1       0.347   0.104  -2.866  1.00  0.00           C  
HETATM   27  C20 UNL     1       1.633   0.388  -3.272  1.00  0.00           C  
HETATM   28  C21 UNL     1       2.623   0.588  -2.332  1.00  0.00           C  
HETATM   29  C22 UNL     1       2.313   0.501  -0.977  1.00  0.00           C  
HETATM   30  C23 UNL     1       3.399   0.715  -0.002  1.00  0.00           C  
HETATM   31  O8  UNL     1       3.131   0.633   1.214  1.00  0.00           O  
HETATM   32  O9  UNL     1       4.680   1.000  -0.397  1.00  0.00           O  
HETATM   33  N1  UNL     1       5.748   1.211   0.430  1.00  0.00           N  
HETATM   34  C24 UNL     1       7.096   1.130  -0.063  1.00  0.00           C  
HETATM   35  O10 UNL     1       7.475   0.874  -1.251  1.00  0.00           O  
HETATM   36  C25 UNL     1       8.061   1.391   1.025  1.00  0.00           C  
HETATM   37  C26 UNL     1       7.238   1.144   2.271  1.00  0.00           C  
HETATM   38  C27 UNL     1       5.859   1.521   1.793  1.00  0.00           C  
HETATM   39  O11 UNL     1       4.934   2.032   2.475  1.00  0.00           O  
HETATM   40  C28 UNL     1       1.027   0.219  -0.618  1.00  0.00           C  
HETATM   41  C29 UNL     1       0.011   0.013  -1.528  1.00  0.00           C  
HETATM   42  H1  UNL     1      -2.930  -8.040   1.263  1.00  0.00           H  
HETATM   43  H2  UNL     1      -4.324  -7.272   2.122  1.00  0.00           H  
HETATM   44  H3  UNL     1      -4.502  -7.949   0.416  1.00  0.00           H  
HETATM   45  H4  UNL     1      -0.880  -4.876  -1.061  1.00  0.00           H  
HETATM   46  H5  UNL     1      -0.418  -2.711  -2.098  1.00  0.00           H  
HETATM   47  H6  UNL     1      -3.470  -2.989   1.731  1.00  0.00           H  
HETATM   48  H7  UNL     1      -4.296   1.640   1.770  1.00  0.00           H  
HETATM   49  H8  UNL     1      -3.704   6.288   3.611  1.00  0.00           H  
HETATM   50  H9  UNL     1      -5.331   5.553   3.344  1.00  0.00           H  
HETATM   51  H10 UNL     1      -4.597   6.644   2.067  1.00  0.00           H  
HETATM   52  H11 UNL     1      -2.457   4.206  -1.024  1.00  0.00           H  
HETATM   53  H12 UNL     1      -1.286   2.237  -2.059  1.00  0.00           H  
HETATM   54  H13 UNL     1       1.833   0.445  -4.341  1.00  0.00           H  
HETATM   55  H14 UNL     1       3.637   0.812  -2.620  1.00  0.00           H  
HETATM   56  H15 UNL     1       8.407   2.431   0.950  1.00  0.00           H  
HETATM   57  H16 UNL     1       8.920   0.682   0.959  1.00  0.00           H  
HETATM   58  H17 UNL     1       7.561   1.753   3.132  1.00  0.00           H  
HETATM   59  H18 UNL     1       7.267   0.059   2.485  1.00  0.00           H  
HETATM   60  H19 UNL     1       0.817   0.159   0.457  1.00  0.00           H  
CONECT    1    2   42   43   44
CONECT    2    3    3    4
CONECT    4    5
CONECT    5    6    6   10
CONECT    6    7   45
CONECT    7    8    8   46
CONECT    8    9   22
CONECT    9   10   10   11
CONECT   10   47
CONECT   11   12
CONECT   12   13   13   21
CONECT   13   14   48
CONECT   14   15   19   19
CONECT   15   16
CONECT   16   17   18   18
CONECT   17   49   50   51
CONECT   19   20   52
CONECT   20   21   21   53
CONECT   21   22
CONECT   22   23   41
CONECT   23   24
CONECT   24   25   25   26
CONECT   26   27   27   41
CONECT   27   28   54
CONECT   28   29   29   55
CONECT   29   30   40
CONECT   30   31   31   32
CONECT   32   33
CONECT   33   34   38
CONECT   34   35   35   36
CONECT   36   37   56   57
CONECT   37   38   58   59
CONECT   38   39   39
CONECT   40   41   41   60
END

HMDB0244679
     RDKit          3D
6-CFDA N-succinimidyl ester
 60 65  0  0  0  0  0  0  0  0999 V2000
   -3.8573   -7.4165    1.1260 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5270   -6.0930    0.5387 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2222   -5.6108   -0.4033 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4580   -5.3262    0.9820 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1962   -4.0913    0.3936 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3465   -3.9560   -0.6850 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0961   -2.7155   -1.2596 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7034   -1.5899   -0.7499 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5561   -1.7027    0.3285 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7925   -2.9488    0.8866 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1910   -0.5847    0.8779 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9965    0.6751    0.3726 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6372    1.7939    0.9285 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4474    3.0617    0.4312 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0970    4.1444    1.0034 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6922    4.7043    2.2098 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3660    5.8624    2.8501 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6823    4.1438    2.7391 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5923    3.2009   -0.6500 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9606    2.0999   -1.1996 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1535    0.8371   -0.7006 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4349   -0.2930   -1.3727 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9299   -0.4029   -2.7226 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8836   -0.1603   -3.5950 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0024   -0.1705   -4.8632 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3470    0.1044   -2.8663 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6332    0.3878   -3.2716 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6227    0.5877   -2.3322 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3135    0.5011   -0.9765 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3991    0.7154   -0.0022 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1313    0.6327    1.2135 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.6795    1.0004   -0.3972 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.7478    1.2107    0.4299 N   0  0  0  0  0  0  0  0  0  0  0  0
    7.0961    1.1301   -0.0629 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.4747    0.8736   -1.2512 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.0615    1.3914    1.0254 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.2380    1.1444    2.2713 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.8587    1.5209    1.7930 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9338    2.0321    2.4754 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.0272    0.2189   -0.6178 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0109    0.0132   -1.5283 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9303   -8.0395    1.2633 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3238   -7.2716    2.1215 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5024   -7.9489    0.4158 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8801   -4.8755   -1.0606 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4175   -2.7107   -2.0985 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4697   -2.9891    1.7307 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2960    1.6400    1.7700 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7037    6.2878    3.6114 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3305    5.5525    3.3437 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5974    6.6443    2.0672 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4566    4.2063   -1.0235 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2864    2.2366   -2.0587 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8326    0.4453   -4.3409 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6372    0.8119   -2.6200 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.4075    2.4307    0.9497 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.9196    0.6823    0.9591 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.5608    1.7534    3.1321 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.2669    0.0593    2.4851 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8170    0.1592    0.4566 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  0
  2  4  1  0
  4  5  1  0
  5  6  2  0
  6  7  1  0
  7  8  2  0
  8  9  1  0
  9 10  2  0
  9 11  1  0
 11 12  1  0
 12 13  2  0
 13 14  1  0
 14 15  1  0
 15 16  1  0
 16 17  1  0
 16 18  2  0
 14 19  2  0
 19 20  1  0
 20 21  2  0
 21 22  1  0
 22 23  1  0
 23 24  1  0
 24 25  2  0
 24 26  1  0
 26 27  2  0
 27 28  1  0
 28 29  2  0
 29 30  1  0
 30 31  2  0
 30 32  1  0
 32 33  1  0
 33 34  1  0
 34 35  2  0
 34 36  1  0
 36 37  1  0
 37 38  1  0
 38 39  2  0
 29 40  1  0
 40 41  2  0
 10  5  1  0
 21 12  1  0
 41 22  1  0
 22  8  1  0
 41 26  1  0
 38 33  1  0
  1 42  1  0
  1 43  1  0
  1 44  1  0
  6 45  1  0
  7 46  1  0
 10 47  1  0
 13 48  1  0
 17 49  1  0
 17 50  1  0
 17 51  1  0
 19 52  1  0
 20 53  1  0
 27 54  1  0
 28 55  1  0
 36 56  1  0
 36 57  1  0
 37 58  1  0
 37 59  1  0
 40 60  1  0
M  END

View in JSmol View Stereo Labels

Synonyms

Value	Source
2,5-Dioxopyrrolidin-1-yl 3',6'-bis(acetyloxy)-3-oxo-3H-spiro[2-benzofuran-1,9'-xanthene]-6-carboxylic acid	HMDB
5-(6)-Carboxyfluorescein diacetate succinimidyl ester	HMDB
5-Carboxyfluorescein diacetate succinimidyl ester and 6-carboxyfluorescein diacetate succinimidyl ester	HMDB
CFDA-se	HMDB
CFDASE	HMDB
CFSE	HMDB
Carboxyfluorescein diacetate succinimidyl ester	HMDB

Chemical Formula

C₂₉H₁₉NO₁₁

Average Molecular Weight

557.467

Monoisotopic Molecular Weight

557.095810436

IUPAC Name

2,5-dioxopyrrolidin-1-yl 3',6'-bis(acetyloxy)-3-oxo-3H-spiro[2-benzofuran-1,9'-xanthene]-6-carboxylate

Traditional Name

2,5-dioxopyrrolidin-1-yl 3',6'-bis(acetyloxy)-3-oxospiro[2-benzofuran-1,9'-xanthene]-6-carboxylate

CAS Registry Number

Not Available

SMILES

CC(=O)OC1=CC2=C(C=C1)C1(OC(=O)C3=C1C=C(C=C3)C(=O)ON1C(=O)CCC1=O)C1=C(O2)C=C(OC(C)=O)C=C1

InChI Identifier

InChI=1S/C29H19NO11/c1-14(31)37-17-4-7-20-23(12-17)39-24-13-18(38-15(2)32)5-8-21(24)29(20)22-11-16(3-6-19(22)28(36)40-29)27(35)41-30-25(33)9-10-26(30)34/h3-8,11-13H,9-10H2,1-2H3

InChI Key

JGPOSNWWINVNFV-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
Tetracarboxylic acid or derivatives
Para_phthalic_acid
Diaryl ether
Benzofuranone
Phthalide
Isobenzofuranone
Isocoumaran
Isobenzofuran
Benzenoid
2-pyrrolidone
Pyrrolidone
Pyrrolidine
Dicarboximide
Lactone
Carboxylic acid ester
Carboxylic acid salt
Lactam
Carboxylic acid derivative
Ether
Oxacycle
Azacycle
Carbonyl group
Organic nitrogen compound
Hydrocarbon derivative
Organic oxide
Organopnictogen compound
Organic oxygen compound
Organonitrogen compound
Organooxygen compound
Organic salt
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)

Source

Exogenous

Exogenous (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	3.16	ALOGPS
logP	2.93	ChemAxon
logS	-5.4	ALOGPS
pKa (Strongest Acidic)	17.7	ChemAxon
pKa (Strongest Basic)	-3.7	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	6	ChemAxon
Hydrogen Donor Count	0	ChemAxon
Polar Surface Area	151.81 Å²	ChemAxon
Rotatable Bond Count	7	ChemAxon
Refractivity	137.33 m³·mol⁻¹	ChemAxon
Polarizability	54.63 Å³	ChemAxon
Number of Rings	6	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	Yes	ChemAxon

Predicted Chromatographic Properties

Predicted Collision Cross Sections

Predictor	Adduct Type	CCS Value (Å²)	Reference
DeepCCS	[M+H]+	224.636	30932474
DeepCCS	[M-H]-	222.741	30932474
DeepCCS	[M-2H]-	255.98	30932474
DeepCCS	[M+Na]+	230.366	30932474
AllCCS	[M+H]+	223.9	32859911
AllCCS	[M+H-H2O]+	222.3	32859911
AllCCS	[M+NH4]+	225.4	32859911
AllCCS	[M+Na]+	225.8	32859911
AllCCS	[M-H]-	219.8	32859911
AllCCS	[M+Na-2H]-	220.4	32859911
AllCCS	[M+HCOO]-	221.3	32859911

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
6-CFDA N-succinimidyl ester	CC(=O)OC1=CC2=C(C=C1)C1(OC(=O)C3=C1C=C(C=C3)C(=O)ON1C(=O)CCC1=O)C1=C(O2)C=C(OC(C)=O)C=C1	6826.6	Standard polar	33892256
6-CFDA N-succinimidyl ester	CC(=O)OC1=CC2=C(C=C1)C1(OC(=O)C3=C1C=C(C=C3)C(=O)ON1C(=O)CCC1=O)C1=C(O2)C=C(OC(C)=O)C=C1	4500.0	Standard non polar	33892256
6-CFDA N-succinimidyl ester	CC(=O)OC1=CC2=C(C=C1)C1(OC(=O)C3=C1C=C(C=C3)C(=O)ON1C(=O)CCC1=O)C1=C(O2)C=C(OC(C)=O)C=C1	4604.0	Semi standard non polar	33892256

Spectra

MS/MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 6-CFDA N-succinimidyl ester 10V, Positive-QTOF	splash10-0a4i-0000090000-dc29573caf30f336de89	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 6-CFDA N-succinimidyl ester 20V, Positive-QTOF	splash10-0aou-0000970000-c5e9b3a90a8079090b6a	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 6-CFDA N-succinimidyl ester 40V, Positive-QTOF	splash10-0g4i-0000900000-b5b34c5b17a33184c6c2	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 6-CFDA N-succinimidyl ester 10V, Negative-QTOF	splash10-00di-0000940000-80e1cc47a4a7868a0407	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 6-CFDA N-succinimidyl ester 20V, Negative-QTOF	splash10-076r-1000980000-a1eedd7c92997c0b3bed	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 6-CFDA N-succinimidyl ester 40V, Negative-QTOF	splash10-014i-3001910000-76404c5bff6d9aaf3552	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

4226037

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

5048409

PDB ID

Not Available

ChEBI ID

Not Available

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 6-CFDA N-succinimidyl ester (HMDB0244679)

MOL for HMDB0244679 (6-CFDA N-succinimidyl ester)

3D MOL for HMDB0244679 (6-CFDA N-succinimidyl ester)

3D SDF for HMDB0244679 (6-CFDA N-succinimidyl ester)

3D-SDF for HMDB0244679 (6-CFDA N-succinimidyl ester)

PDB for HMDB0244679 (6-CFDA N-succinimidyl ester)

3D PDB for HMDB0244679 (6-CFDA N-succinimidyl ester)

SMILES for HMDB0244679 (6-CFDA N-succinimidyl ester)

INCHI for HMDB0244679 (6-CFDA N-succinimidyl ester)

Structure for HMDB0244679 (6-CFDA N-succinimidyl ester)

3D Structure for HMDB0244679 (6-CFDA N-succinimidyl ester)

Predicted Collision Cross Sections

Predicted Kovats Retention Indices

Underivatized

MS/MS Spectra