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Record Information

Version

5.0

Status

Detected but not Quantified

Creation Date

2021-09-11 04:03:02 UTC

Update Date

2021-09-26 23:00:29 UTC

HMDB ID

HMDB0249540

Secondary Accession Numbers

None

Metabolite Identification

Common Name

Calcein-AM

Description

Calcein-AM 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 Calcein-AM. This compound has been identified in human blood as reported by (PMID: 31557052 ). Calcein-am is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically Calcein-AM 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


  Mrv1652309112106032D          

 71 75  0  0  0  0            999 V2000
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M  END

HMDB0249540
     RDKit          3D
Calcein-AM
117121  0  0  0  0  0  0  0  0999 V2000
    4.9580    6.4982   -4.1106 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7921    6.0462   -2.6842 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3480    6.7032   -1.7745 O   0  0  0  0  0  0  0  0  0  0  0  0
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    3.9405    4.5823   -0.9508 C   0  0  0  0  0  0  0  0  0  0  0  0
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    1.8558    3.2797   -1.2297 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3635    4.3327   -1.7911 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9873    2.0907   -1.1097 C   0  0  0  0  0  0  0  0  0  0  0  0
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 70117  1  0
M  END


  Mrv1652309112106032D          

 71 75  0  0  0  0            999 V2000
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 69 71  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0249540

> <DATABASE_NAME>
hmdb

> <SMILES>
CC(=O)OCOC(=O)CN(CC(=O)OCOC(C)=O)CC1=C(OC(C)=O)C=CC2=C1OC1=C(C=CC(OC(C)=O)=C1CN(CC(=O)OCOC(C)=O)CC(=O)OCOC(C)=O)C21OC(=O)C2=CC=CC=C12

> <INCHI_IDENTIFIER>
InChI=1S/C46H46N2O23/c1-25(49)60-21-64-39(55)17-47(18-40(56)65-22-61-26(2)50)15-32-37(68-29(5)53)13-11-35-43(32)70-44-33(16-48(19-41(57)66-23-62-27(3)51)20-42(58)67-24-63-28(4)52)38(69-30(6)54)14-12-36(44)46(35)34-10-8-7-9-31(34)45(59)71-46/h7-14H,15-24H2,1-6H3

> <INCHI_KEY>
XKFSBWQWNMZWFA-UHFFFAOYSA-N

> <FORMULA>
C46H46N2O23

> <MOLECULAR_WEIGHT>
994.865

> <EXACT_MASS>
994.249135749

> <JCHEM_ACCEPTOR_COUNT>
13

> <JCHEM_ATOM_COUNT>
117

> <JCHEM_AVERAGE_POLARIZABILITY>
95.55416592646152

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(acetyloxy)methyl 2-({2-[(acetyloxy)methoxy]-2-oxoethyl}({[3',6'-bis(acetyloxy)-5'-{[bis({2-[(acetyloxy)methoxy]-2-oxoethyl})amino]methyl}-3-oxo-3H-spiro[2-benzofuran-1,9'-xanthene]-4'-yl]methyl})amino)acetate

> <ALOGPS_LOGP>
2.69

> <JCHEM_LOGP>
1.5247957693333338

> <ALOGPS_LOGS>
-5.02

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_BASIC>
3.039186827376699

> <JCHEM_POLAR_SURFACE_AREA>
305.01

> <JCHEM_REFRACTIVITY>
231.03650000000016

> <JCHEM_ROTATABLE_BOND_COUNT>
32

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
9.49e-03 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(acetyloxy)methyl ({2-[(acetyloxy)methoxy]-2-oxoethyl}[3',6'-bis(acetyloxy)-5'-{[bis({2-[(acetyloxy)methoxy]-2-oxoethyl})amino]methyl}-3-oxospiro[2-benzofuran-1,9'-xanthene]-4'-ylmethyl]amino)acetate

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0249540
     RDKit          3D
Calcein-AM
117121  0  0  0  0  0  0  0  0999 V2000
    4.9580    6.4982   -4.1106 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7921    6.0462   -2.6842 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3480    6.7032   -1.7745 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.0502    4.9333   -2.3268 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.9405    4.5823   -0.9508 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1514    3.4182   -0.8130 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.8558    3.2797   -1.2297 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3635    4.3327   -1.7911 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9873    2.0907   -1.1097 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5585    1.0233   -0.3296 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.6109    1.5618    1.0351 C   0  0  0  0  0  0  0  0  0  0  0  0
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M  END

HEADER    PROTEIN                                 11-SEP-21   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   11-SEP-21         0                                  
HETATM    1  C   UNK     0      -2.183 -16.786   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -0.643 -16.786   0.000  0.00  0.00           C+0
HETATM    3  O   UNK     0       0.127 -18.120   0.000  0.00  0.00           O+0
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HETATM    5  C   UNK     0       1.667 -15.453   0.000  0.00  0.00           C+0
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HETATM   61  O   UNK     0      11.955 -14.067   0.000  0.00  0.00           O+0
HETATM   62  C   UNK     0      11.521 -15.687   0.000  0.00  0.00           C+0
HETATM   63  C   UNK     0       7.057 -14.119   0.000  0.00  0.00           C+0
HETATM   64  C   UNK     0       8.597 -14.119   0.000  0.00  0.00           C+0
HETATM   65  O   UNK     0       9.367 -12.785   0.000  0.00  0.00           O+0
HETATM   66  O   UNK     0       9.367 -15.453   0.000  0.00  0.00           O+0
HETATM   67  C   UNK     0      10.907 -15.453   0.000  0.00  0.00           C+0
HETATM   68  O   UNK     0      11.677 -16.786   0.000  0.00  0.00           O+0
HETATM   69  C   UNK     0      13.217 -16.786   0.000  0.00  0.00           C+0
HETATM   70  O   UNK     0      13.987 -15.453   0.000  0.00  0.00           O+0
HETATM   71  C   UNK     0      13.987 -18.120   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3    4                                                  
CONECT    3    2                                                            
CONECT    4    2    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6    8    9                                                  
CONECT    8    7                                                            
CONECT    9    7   10                                                       
CONECT   10    9   11   63                                                  
CONECT   11   10   12                                                       
CONECT   12   11   13   17                                                  
CONECT   13   12   14   59                                                  
CONECT   14   13   15                                                       
CONECT   15   14   16                                                       
CONECT   16   15   17   21                                                  
CONECT   17   16   12   18                                                  
CONECT   18   17   19                                                       
CONECT   19   18   20   34                                                  
CONECT   20   19   21   31                                                  
CONECT   21   20   16   22   30                                             
CONECT   22   21   23   27                                                  
CONECT   23   22   24                                                       
CONECT   24   23   25                                                       
CONECT   25   24   26                                                       
CONECT   26   25   27                                                       
CONECT   27   26   22   28                                                  
CONECT   28   27   29   30                                                  
CONECT   29   28                                                            
CONECT   30   28   21                                                       
CONECT   31   20   32                                                       
CONECT   32   31   33                                                       
CONECT   33   32   34   55                                                  
CONECT   34   33   19   35                                                  
CONECT   35   34   36                                                       
CONECT   36   35   37   46                                                  
CONECT   37   36   38                                                       
CONECT   38   37   39   40                                                  
CONECT   39   38                                                            
CONECT   40   38   41                                                       
CONECT   41   40   42                                                       
CONECT   42   41   43                                                       
CONECT   43   42   44   45                                                  
CONECT   44   43                                                            
CONECT   45   43                                                            
CONECT   46   36   47                                                       
CONECT   47   46   48   49                                                  
CONECT   48   47                                                            
CONECT   49   47   50                                                       
CONECT   50   49   51                                                       
CONECT   51   50   52                                                       
CONECT   52   51   53   54                                                  
CONECT   53   52                                                            
CONECT   54   52                                                            
CONECT   55   33   56                                                       
CONECT   56   55   57   58                                                  
CONECT   57   56                                                            
CONECT   58   56                                                            
CONECT   59   13   60                                                       
CONECT   60   59   61   62                                                  
CONECT   61   60                                                            
CONECT   62   60                                                            
CONECT   63   10   64                                                       
CONECT   64   63   65   66                                                  
CONECT   65   64                                                            
CONECT   66   64   67                                                       
CONECT   67   66   68                                                       
CONECT   68   67   69                                                       
CONECT   69   68   70   71                                                  
CONECT   70   69                                                            
CONECT   71   69                                                            
MASTER        0    0    0    0    0    0    0    0   71    0  150    0
END

COMPND    HMDB0249540
HETATM    1  C1  UNL     1       4.958   6.498  -4.111  1.00  0.00           C  
HETATM    2  C2  UNL     1       4.792   6.046  -2.684  1.00  0.00           C  
HETATM    3  O1  UNL     1       5.348   6.703  -1.775  1.00  0.00           O  
HETATM    4  O2  UNL     1       4.050   4.933  -2.327  1.00  0.00           O  
HETATM    5  C3  UNL     1       3.941   4.582  -0.951  1.00  0.00           C  
HETATM    6  O3  UNL     1       3.151   3.418  -0.813  1.00  0.00           O  
HETATM    7  C4  UNL     1       1.856   3.280  -1.230  1.00  0.00           C  
HETATM    8  O4  UNL     1       1.363   4.333  -1.791  1.00  0.00           O  
HETATM    9  C5  UNL     1       0.987   2.091  -1.110  1.00  0.00           C  
HETATM   10  N1  UNL     1       1.558   1.023  -0.330  1.00  0.00           N  
HETATM   11  C6  UNL     1       1.611   1.562   1.035  1.00  0.00           C  
HETATM   12  C7  UNL     1       2.176   0.598   2.018  1.00  0.00           C  
HETATM   13  O5  UNL     1       2.695   1.166   3.034  1.00  0.00           O  
HETATM   14  O6  UNL     1       2.191  -0.718   1.944  1.00  0.00           O  
HETATM   15  C8  UNL     1       2.661  -1.720   2.741  1.00  0.00           C  
HETATM   16  O7  UNL     1       2.232  -1.925   4.019  1.00  0.00           O  
HETATM   17  C9  UNL     1       2.224  -1.395   5.206  1.00  0.00           C  
HETATM   18  C10 UNL     1       1.570  -2.011   6.430  1.00  0.00           C  
HETATM   19  O8  UNL     1       2.779  -0.298   5.425  1.00  0.00           O  
HETATM   20  C11 UNL     1       2.868   0.712  -0.800  1.00  0.00           C  
HETATM   21  C12 UNL     1       3.126  -0.646  -1.263  1.00  0.00           C  
HETATM   22  C13 UNL     1       4.421  -0.941  -1.631  1.00  0.00           C  
HETATM   23  O9  UNL     1       5.445  -0.002  -1.515  1.00  0.00           O  
HETATM   24  C14 UNL     1       5.675   0.857  -2.583  1.00  0.00           C  
HETATM   25  C15 UNL     1       6.763   1.893  -2.527  1.00  0.00           C  
HETATM   26  O10 UNL     1       4.933   0.734  -3.602  1.00  0.00           O  
HETATM   27  C16 UNL     1       4.740  -2.182  -2.127  1.00  0.00           C  
HETATM   28  C17 UNL     1       3.752  -3.137  -2.256  1.00  0.00           C  
HETATM   29  C18 UNL     1       2.454  -2.867  -1.898  1.00  0.00           C  
HETATM   30  C19 UNL     1       2.161  -1.617  -1.405  1.00  0.00           C  
HETATM   31  O11 UNL     1       0.826  -1.366  -1.059  1.00  0.00           O  
HETATM   32  C20 UNL     1      -0.191  -2.319  -1.201  1.00  0.00           C  
HETATM   33  C21 UNL     1       0.107  -3.549  -1.691  1.00  0.00           C  
HETATM   34  C22 UNL     1      -0.918  -4.477  -1.832  1.00  0.00           C  
HETATM   35  C23 UNL     1      -2.196  -4.174  -1.490  1.00  0.00           C  
HETATM   36  C24 UNL     1      -2.485  -2.901  -0.983  1.00  0.00           C  
HETATM   37  O12 UNL     1      -3.846  -2.696  -0.652  1.00  0.00           O  
HETATM   38  C25 UNL     1      -4.480  -3.436   0.342  1.00  0.00           C  
HETATM   39  C26 UNL     1      -5.925  -3.138   0.612  1.00  0.00           C  
HETATM   40  O13 UNL     1      -3.838  -4.310   0.967  1.00  0.00           O  
HETATM   41  C27 UNL     1      -1.507  -1.981  -0.838  1.00  0.00           C  
HETATM   42  C28 UNL     1      -1.700  -0.634  -0.275  1.00  0.00           C  
HETATM   43  N2  UNL     1      -2.983  -0.160   0.007  1.00  0.00           N  
HETATM   44  C29 UNL     1      -3.790   0.215  -1.053  1.00  0.00           C  
HETATM   45  C30 UNL     1      -5.097   0.834  -0.834  1.00  0.00           C  
HETATM   46  O14 UNL     1      -5.464   1.448   0.209  1.00  0.00           O  
HETATM   47  O15 UNL     1      -6.109   0.791  -1.828  1.00  0.00           O  
HETATM   48  C31 UNL     1      -7.366   1.400  -1.596  1.00  0.00           C  
HETATM   49  O16 UNL     1      -7.205   2.806  -1.368  1.00  0.00           O  
HETATM   50  C32 UNL     1      -8.324   3.579  -1.122  1.00  0.00           C  
HETATM   51  C33 UNL     1      -8.216   5.029  -0.892  1.00  0.00           C  
HETATM   52  O17 UNL     1      -9.442   3.024  -1.099  1.00  0.00           O  
HETATM   53  C34 UNL     1      -3.506  -0.223   1.288  1.00  0.00           C  
HETATM   54  C35 UNL     1      -2.950   0.723   2.307  1.00  0.00           C  
HETATM   55  O18 UNL     1      -3.460   0.551   3.477  1.00  0.00           O  
HETATM   56  O19 UNL     1      -2.026   1.680   2.142  1.00  0.00           O  
HETATM   57  C36 UNL     1      -1.540   2.550   3.153  1.00  0.00           C  
HETATM   58  O20 UNL     1      -2.663   3.276   3.651  1.00  0.00           O  
HETATM   59  C37 UNL     1      -2.395   4.207   4.682  1.00  0.00           C  
HETATM   60  C38 UNL     1      -3.559   4.964   5.195  1.00  0.00           C  
HETATM   61  O21 UNL     1      -1.248   4.380   5.132  1.00  0.00           O  
HETATM   62  C39 UNL     1       1.461  -3.966  -2.085  1.00  0.00           C  
HETATM   63  O22 UNL     1       1.536  -4.477  -3.397  1.00  0.00           O  
HETATM   64  C40 UNL     1       2.155  -5.714  -3.423  1.00  0.00           C  
HETATM   65  O23 UNL     1       2.455  -6.401  -4.445  1.00  0.00           O  
HETATM   66  C41 UNL     1       2.405  -6.088  -2.031  1.00  0.00           C  
HETATM   67  C42 UNL     1       2.943  -7.223  -1.444  1.00  0.00           C  
HETATM   68  C43 UNL     1       3.001  -7.325  -0.072  1.00  0.00           C  
HETATM   69  C44 UNL     1       2.534  -6.320   0.737  1.00  0.00           C  
HETATM   70  C45 UNL     1       2.002  -5.196   0.125  1.00  0.00           C  
HETATM   71  C46 UNL     1       1.941  -5.082  -1.235  1.00  0.00           C  
HETATM   72  H1  UNL     1       4.069   6.264  -4.718  1.00  0.00           H  
HETATM   73  H2  UNL     1       5.036   7.613  -4.076  1.00  0.00           H  
HETATM   74  H3  UNL     1       5.844   6.035  -4.576  1.00  0.00           H  
HETATM   75  H4  UNL     1       3.600   5.408  -0.321  1.00  0.00           H  
HETATM   76  H5  UNL     1       4.975   4.282  -0.617  1.00  0.00           H  
HETATM   77  H6  UNL     1       0.708   1.719  -2.137  1.00  0.00           H  
HETATM   78  H7  UNL     1       0.009   2.415  -0.679  1.00  0.00           H  
HETATM   79  H8  UNL     1       0.577   1.745   1.343  1.00  0.00           H  
HETATM   80  H9  UNL     1       2.243   2.444   1.015  1.00  0.00           H  
HETATM   81  H10 UNL     1       2.524  -2.719   2.191  1.00  0.00           H  
HETATM   82  H11 UNL     1       3.816  -1.701   2.785  1.00  0.00           H  
HETATM   83  H12 UNL     1       0.621  -1.507   6.643  1.00  0.00           H  
HETATM   84  H13 UNL     1       1.364  -3.072   6.146  1.00  0.00           H  
HETATM   85  H14 UNL     1       2.295  -1.999   7.270  1.00  0.00           H  
HETATM   86  H15 UNL     1       3.611   1.070  -0.036  1.00  0.00           H  
HETATM   87  H16 UNL     1       3.090   1.420  -1.686  1.00  0.00           H  
HETATM   88  H17 UNL     1       7.626   1.573  -1.920  1.00  0.00           H  
HETATM   89  H18 UNL     1       7.068   2.079  -3.594  1.00  0.00           H  
HETATM   90  H19 UNL     1       6.347   2.850  -2.106  1.00  0.00           H  
HETATM   91  H20 UNL     1       5.768  -2.422  -2.424  1.00  0.00           H  
HETATM   92  H21 UNL     1       4.015  -4.105  -2.647  1.00  0.00           H  
HETATM   93  H22 UNL     1      -0.727  -5.476  -2.222  1.00  0.00           H  
HETATM   94  H23 UNL     1      -3.016  -4.871  -1.584  1.00  0.00           H  
HETATM   95  H24 UNL     1      -6.478  -4.074   0.851  1.00  0.00           H  
HETATM   96  H25 UNL     1      -6.383  -2.700  -0.312  1.00  0.00           H  
HETATM   97  H26 UNL     1      -6.030  -2.353   1.391  1.00  0.00           H  
HETATM   98  H27 UNL     1      -1.011  -0.579   0.619  1.00  0.00           H  
HETATM   99  H28 UNL     1      -1.208   0.122  -0.979  1.00  0.00           H  
HETATM  100  H29 UNL     1      -3.883  -0.516  -1.886  1.00  0.00           H  
HETATM  101  H30 UNL     1      -3.183   1.059  -1.623  1.00  0.00           H  
HETATM  102  H31 UNL     1      -7.916   0.944  -0.766  1.00  0.00           H  
HETATM  103  H32 UNL     1      -7.969   1.258  -2.523  1.00  0.00           H  
HETATM  104  H33 UNL     1      -8.842   5.596  -1.630  1.00  0.00           H  
HETATM  105  H34 UNL     1      -7.153   5.342  -1.116  1.00  0.00           H  
HETATM  106  H35 UNL     1      -8.480   5.361   0.110  1.00  0.00           H  
HETATM  107  H36 UNL     1      -3.351  -1.290   1.748  1.00  0.00           H  
HETATM  108  H37 UNL     1      -4.601  -0.140   1.325  1.00  0.00           H  
HETATM  109  H38 UNL     1      -1.002   2.030   3.967  1.00  0.00           H  
HETATM  110  H39 UNL     1      -0.812   3.239   2.675  1.00  0.00           H  
HETATM  111  H40 UNL     1      -3.907   5.704   4.467  1.00  0.00           H  
HETATM  112  H41 UNL     1      -3.240   5.495   6.115  1.00  0.00           H  
HETATM  113  H42 UNL     1      -4.391   4.254   5.394  1.00  0.00           H  
HETATM  114  H43 UNL     1       3.317  -8.026  -2.093  1.00  0.00           H  
HETATM  115  H44 UNL     1       3.431  -8.224   0.399  1.00  0.00           H  
HETATM  116  H45 UNL     1       2.572  -6.390   1.818  1.00  0.00           H  
HETATM  117  H46 UNL     1       1.639  -4.425   0.796  1.00  0.00           H  
CONECT    1    2   72   73   74
CONECT    2    3    3    4
CONECT    4    5
CONECT    5    6   75   76
CONECT    6    7
CONECT    7    8    8    9
CONECT    9   10   77   78
CONECT   10   11   20
CONECT   11   12   79   80
CONECT   12   13   13   14
CONECT   14   15
CONECT   15   16   81   82
CONECT   16   17
CONECT   17   18   19   19
CONECT   18   83   84   85
CONECT   20   21   86   87
CONECT   21   22   22   30
CONECT   22   23   27
CONECT   23   24
CONECT   24   25   26   26
CONECT   25   88   89   90
CONECT   27   28   28   91
CONECT   28   29   92
CONECT   29   30   30   62
CONECT   30   31
CONECT   31   32
CONECT   32   33   33   41
CONECT   33   34   62
CONECT   34   35   35   93
CONECT   35   36   94
CONECT   36   37   41   41
CONECT   37   38
CONECT   38   39   40   40
CONECT   39   95   96   97
CONECT   41   42
CONECT   42   43   98   99
CONECT   43   44   53
CONECT   44   45  100  101
CONECT   45   46   46   47
CONECT   47   48
CONECT   48   49  102  103
CONECT   49   50
CONECT   50   51   52   52
CONECT   51  104  105  106
CONECT   53   54  107  108
CONECT   54   55   55   56
CONECT   56   57
CONECT   57   58  109  110
CONECT   58   59
CONECT   59   60   61   61
CONECT   60  111  112  113
CONECT   62   63   71
CONECT   63   64
CONECT   64   65   65   66
CONECT   66   67   67   71
CONECT   67   68  114
CONECT   68   69   69  115
CONECT   69   70  116
CONECT   70   71   71  117
END

HMDB0249540
     RDKit          3D
Calcein-AM
117121  0  0  0  0  0  0  0  0999 V2000
    4.9580    6.4982   -4.1106 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7921    6.0462   -2.6842 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3480    6.7032   -1.7745 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.0502    4.9333   -2.3268 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.9405    4.5823   -0.9508 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1514    3.4182   -0.8130 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.8558    3.2797   -1.2297 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3635    4.3327   -1.7911 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9873    2.0907   -1.1097 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5585    1.0233   -0.3296 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.6109    1.5618    1.0351 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1763    0.5980    2.0178 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6950    1.1657    3.0345 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1910   -0.7175    1.9435 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6611   -1.7201    2.7413 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2321   -1.9252    4.0188 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.2235   -1.3955    5.2059 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5700   -2.0112    6.4298 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7788   -0.2977    5.4248 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8682    0.7124   -0.7996 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1260   -0.6457   -1.2635 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4212   -0.9408   -1.6309 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.4448   -0.0022   -1.5152 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.6746    0.8574   -2.5834 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.7629    1.8927   -2.5272 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9331    0.7337   -3.6024 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.7399   -2.1820   -2.1267 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7515   -3.1374   -2.2559 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4537   -2.8673   -1.8983 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1606   -1.6165   -1.4052 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8264   -1.3663   -1.0590 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1911   -2.3192   -1.2007 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1066   -3.5491   -1.6909 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9179   -4.4772   -1.8323 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1959   -4.1744   -1.4897 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4848   -2.9013   -0.9829 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8456   -2.6955   -0.6518 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4803   -3.4359    0.3423 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.9248   -3.1385    0.6121 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8378   -4.3097    0.9668 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5072   -1.9809   -0.8377 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6996   -0.6342   -0.2754 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9834   -0.1602    0.0067 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7901    0.2149   -1.0528 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0970    0.8342   -0.8341 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4642    1.4477    0.2086 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.1092    0.7909   -1.8277 O   0  0  0  0  0  0  0  0  0  0  0  0
   -7.3659    1.4000   -1.5958 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.2047    2.8063   -1.3678 O   0  0  0  0  0  0  0  0  0  0  0  0
   -8.3236    3.5793   -1.1224 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.2158    5.0289   -0.8922 C   0  0  0  0  0  0  0  0  0  0  0  0
   -9.4419    3.0244   -1.0988 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5060   -0.2234    1.2880 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9503    0.7226    2.3067 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4597    0.5513    3.4770 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0262    1.6801    2.1415 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5396    2.5495    3.1528 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6631    3.2760    3.6508 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3954    4.2068    4.6816 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5593    4.9639    5.1946 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2482    4.3802    5.1319 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4614   -3.9664   -2.0848 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5364   -4.4775   -3.3975 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1550   -5.7138   -3.4234 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4548   -6.4015   -4.4446 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4050   -6.0884   -2.0314 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9432   -7.2234   -1.4441 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0007   -7.3255   -0.0719 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5342   -6.3199    0.7371 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0024   -5.1956    0.1247 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9407   -5.0823   -1.2346 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0691    6.2643   -4.7184 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.0358    7.6133   -4.0756 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.8442    6.0355   -4.5765 H   0  0  0  0  0  0  0  0  0  0  0  0
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    3.0895    1.4202   -1.6859 H   0  0  0  0  0  0  0  0  0  0  0  0
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    7.0681    2.0790   -3.5936 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.3474    2.8495   -2.1056 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.7675   -2.4225   -2.4242 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.0152   -4.1054   -2.6467 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7271   -5.4762   -2.2218 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0157   -4.8710   -1.5841 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.4784   -4.0741    0.8506 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.3831   -2.7003   -0.3122 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.0301   -2.3535    1.3911 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0105   -0.5786    0.6188 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2077    0.1222   -0.9789 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8832   -0.5155   -1.8860 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1827    1.0589   -1.6232 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.9160    0.9439   -0.7664 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.9694    1.2580   -2.5231 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.8417    5.5959   -1.6295 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.1534    5.3424   -1.1156 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.4797    5.3609    0.1103 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3513   -1.2896    1.7477 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6011   -0.1400    1.3246 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0025    2.0301    3.9668 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8125    3.2393    2.6748 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9072    5.7041    4.4669 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2403    5.4946    6.1151 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3909    4.2538    5.3935 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3170   -8.0261   -2.0926 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4311   -8.2241    0.3991 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5719   -6.3904    1.8177 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6387   -4.4254    0.7963 H   0  0  0  0  0  0  0  0  0  0  0  0
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M  END

View in JSmol View Stereo Labels

Synonyms

Not Available

Chemical Formula

C₄₆H₄₆N₂O₂₃

Average Molecular Weight

994.865

Monoisotopic Molecular Weight

994.249135749

IUPAC Name

(acetyloxy)methyl 2-({2-[(acetyloxy)methoxy]-2-oxoethyl}({[3',6'-bis(acetyloxy)-5'-{[bis({2-[(acetyloxy)methoxy]-2-oxoethyl})amino]methyl}-3-oxo-3H-spiro[2-benzofuran-1,9'-xanthene]-4'-yl]methyl})amino)acetate

Traditional Name

(acetyloxy)methyl ({2-[(acetyloxy)methoxy]-2-oxoethyl}[3',6'-bis(acetyloxy)-5'-{[bis({2-[(acetyloxy)methoxy]-2-oxoethyl})amino]methyl}-3-oxospiro[2-benzofuran-1,9'-xanthene]-4'-ylmethyl]amino)acetate

CAS Registry Number

Not Available

SMILES

CC(=O)OCOC(=O)CN(CC(=O)OCOC(C)=O)CC1=C(OC(C)=O)C=CC2=C1OC1=C(C=CC(OC(C)=O)=C1CN(CC(=O)OCOC(C)=O)CC(=O)OCOC(C)=O)C21OC(=O)C2=CC=CC=C12

InChI Identifier

InChI=1S/C46H46N2O23/c1-25(49)60-21-64-39(55)17-47(18-40(56)65-22-61-26(2)50)15-32-37(68-29(5)53)13-11-35-43(32)70-44-33(16-48(19-41(57)66-23-62-27(3)51)20-42(58)67-24-63-28(4)52)38(69-30(6)54)14-12-36(44)46(35)34-10-8-7-9-31(34)45(59)71-46/h7-14H,15-24H2,1-6H3

InChI Key

XKFSBWQWNMZWFA-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
Alpha-amino acid ester
Diaryl ether
Benzofuranone
Isobenzofuranone
Alpha-amino acid or derivatives
Phthalide
Isocoumaran
Isobenzofuran
Acylal
Aralkylamine
Benzenoid
Carboxylic acid ester
Lactone
Tertiary aliphatic amine
Tertiary amine
Amino acid or derivatives
Acetal
Carboxylic acid derivative
Oxacycle
Ether
Hydrocarbon derivative
Organic nitrogen compound
Carbonyl group
Organic oxide
Organopnictogen compound
Organic oxygen compound
Amine
Organooxygen compound
Organonitrogen compound
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	2.69	ALOGPS
logP	1.52	ChemAxon
logS	-5	ALOGPS
pKa (Strongest Basic)	3.04	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	13	ChemAxon
Hydrogen Donor Count	0	ChemAxon
Polar Surface Area	305.01 Å²	ChemAxon
Rotatable Bond Count	32	ChemAxon
Refractivity	231.04 m³·mol⁻¹	ChemAxon
Polarizability	95.55 Å³	ChemAxon
Number of Rings	5	ChemAxon
Bioavailability	No	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-2H]-	310.442	30932474
DeepCCS	[M+Na]+	284.533	30932474

Predicted Retention Times

Underivatized

Chromatographic Method	Retention Time	Reference
Predicted by Siyang on May 30, 2022	20.8649 minutes	33406817
Predicted by Siyang using ReTip algorithm on June 8, 2022	3.05 minutes	32390414
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid	4211.3 seconds	40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid	161.7 seconds	40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid	159.3 seconds	40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid	117.8 seconds	40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	134.0 seconds	40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid	942.2 seconds	40023050
BfG_NTS_RP1 =Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) with Water:ACN and 0.1% Formic Acid	1167.1 seconds	40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)	114.7 seconds	40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid	1820.8 seconds	40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid	847.3 seconds	40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid	3208.3 seconds	40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	603.4 seconds	40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	606.9 seconds	40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate	541.6 seconds	40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA	39.7 seconds	40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water	224.4 seconds	40023050

Predicted Kovats Retention Indices

Not Available

Spectra

MS/MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Calcein-AM 10V, Positive-QTOF	splash10-0cg0-0000000195-091e4f6e09cad588c86c	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Calcein-AM 20V, Positive-QTOF	splash10-02w9-0000004292-1d0d07f3b9675844fbde	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Calcein-AM 40V, Positive-QTOF	splash10-00bc-1000209044-07cbfa4d8ab5c38275d2	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Calcein-AM 10V, Negative-QTOF	splash10-004i-1000000090-8609870b59428adcd6b6	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Calcein-AM 20V, Negative-QTOF	splash10-001i-1000000090-badb35bda077e68dd1ea	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Calcein-AM 40V, Negative-QTOF	splash10-0a4l-9000000220-9f98b19ab9ab953b8460	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

3339537

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

4126474

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 Calcein-AM (HMDB0249540)

MOL for HMDB0249540 (Calcein-AM)

3D MOL for HMDB0249540 (Calcein-AM)

3D SDF for HMDB0249540 (Calcein-AM)

3D-SDF for HMDB0249540 (Calcein-AM)

PDB for HMDB0249540 (Calcein-AM)

3D PDB for HMDB0249540 (Calcein-AM)

SMILES for HMDB0249540 (Calcein-AM)

INCHI for HMDB0249540 (Calcein-AM)

Structure for HMDB0249540 (Calcein-AM)

3D Structure for HMDB0249540 (Calcein-AM)

Predicted Collision Cross Sections

Predicted Retention Times

Underivatized

Predicted Kovats Retention Indices

MS/MS Spectra