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Record Information

Version

5.0

Status

Detected but not Quantified

Creation Date

2021-09-10 21:49:34 UTC

Update Date

2021-09-26 22:52:36 UTC

HMDB ID

HMDB0244682

Secondary Accession Numbers

None

Metabolite Identification

Common Name

5-Carboxytetramethylrhodamine succinimidyl ester

Description

5-Carboxytetramethylrhodamine succinimidyl ester, also known as tamra CPD, 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 5-Carboxytetramethylrhodamine succinimidyl ester. This compound has been identified in human blood as reported by (PMID: 31557052 ). 5-carboxytetramethylrhodamine succinimidyl ester is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically 5-Carboxytetramethylrhodamine 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          

 39 43  0  0  0  0            999 V2000
    5.7158    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0013    1.2375    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.0013    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868   -0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    1.2375    0.0000 N   0  3  0  0  0  0  0  0  0  0  0  0
   -0.7145    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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    1.4289    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434    1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -2.8875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -4.1250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -4.1250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -4.9500    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.0964   -5.4349    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8810   -5.1800    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.8414   -6.2195    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0164   -6.2195    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7615   -5.4349    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0231   -5.1800    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868   -1.6500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.0573   -0.5701    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  2  4  1  0  0  0  0
  4  5  2  0  0  0  0
  5  6  1  0  0  0  0
  6  7  2  0  0  0  0
  7  8  1  0  0  0  0
  8  9  2  0  0  0  0
  4  9  1  0  0  0  0
  7 10  1  0  0  0  0
 10 11  2  0  0  0  0
 11 12  1  0  0  0  0
 12 13  2  0  0  0  0
 13 14  1  0  0  0  0
 14 15  2  0  0  0  0
 15 16  1  0  0  0  0
 15 17  1  0  0  0  0
 14 18  1  0  0  0  0
 18 19  2  0  0  0  0
 11 19  1  0  0  0  0
 19 20  1  0  0  0  0
  6 20  1  0  0  0  0
 10 21  1  0  0  0  0
 21 22  2  0  0  0  0
 22 23  1  0  0  0  0
 23 24  2  0  0  0  0
 24 25  1  0  0  0  0
 25 26  2  0  0  0  0
 21 26  1  0  0  0  0
 24 27  1  0  0  0  0
 27 28  2  0  0  0  0
 27 29  1  0  0  0  0
 29 30  1  0  0  0  0
 30 31  1  0  0  0  0
 31 32  2  0  0  0  0
 31 33  1  0  0  0  0
 33 34  1  0  0  0  0
 34 35  1  0  0  0  0
 30 35  1  0  0  0  0
 35 36  2  0  0  0  0
 22 37  1  0  0  0  0
 37 38  2  0  0  0  0
 37 39  1  0  0  0  0
M  CHG  2  15   1  39  -1
M  END

HMDB0244682
     RDKit          3D
5-Carboxytetramethylrhodamine succinimidyl ester
 64 68  0  0  0  0  0  0  0  0999 V2000
   -5.6600    4.5092    0.2075 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2166    4.6221    0.2048 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5887    5.9204    0.2254 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4283    3.4444    0.1787 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0638    3.5488    0.1640 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3094    2.3751    0.1395 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8878    1.1283    0.1301 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1212   -0.0081    0.1056 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3269    0.0584    0.0945 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9598    0.0649    1.3323 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3331    0.1194    1.3968 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1052    0.1676    0.2643 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5470    0.2201    0.4056 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0910    0.2264    1.5409 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.4146    0.2656   -0.6784 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.7871    0.3152   -0.4807 N   0  0  0  0  0  0  0  0  0  0  0  0
    7.6082    1.3561   -0.0141 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.2205    2.5295    0.2196 O   0  0  0  0  0  0  0  0  0  0  0  0
    9.0037    0.8840    0.1680 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.8644   -0.6203    0.0889 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.6470   -0.7854   -0.7481 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.4598   -1.7373   -1.5282 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4859    0.1619   -0.9587 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1005    0.1073   -1.0437 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4313    0.1011   -2.3387 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8185    0.0541   -2.4187 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1435    0.1466   -3.5081 O   0  0  0  0  0  1  0  0  0  0  0  0
   -1.7169   -1.2287    0.0957 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9600   -2.3635    0.0716 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6112   -3.5766    0.0635 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9936   -3.6810    0.0792 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5331   -4.8511    0.0623 N   0  0  0  0  0  4  0  0  0  0  0  0
   -4.9676   -5.0165    0.0773 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6892   -6.0162    0.0268 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7868   -2.5282    0.1044 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1894   -1.2896    0.1130 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8692   -0.1711    0.1361 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2792    1.0066    0.1449 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0050    2.1812    0.1686 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.1391    5.5051    0.1315 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.0236    3.8634   -0.6264 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.9381    4.0572    1.2005 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7670    5.9365    0.9916 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3734    6.6662    0.5249 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2252    6.1496   -0.7949 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5624    4.5179    0.1711 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2367    2.4262    0.1278 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3632    0.0265    2.2528 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7785    0.1253    2.3915 H   0  0  0  0  0  0  0  0  0  0  0  0
    9.3907    1.1403    1.1632 H   0  0  0  0  0  0  0  0  0  0  0  0
    9.6819    1.2666   -0.6169 H   0  0  0  0  0  0  0  0  0  0  0  0
    9.7469   -1.1099   -0.3529 H   0  0  0  0  0  0  0  0  0  0  0  0
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    3.0573    0.2024   -1.8814 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1249   -2.2710    0.0608 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9792   -4.4782    0.0445 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4418   -4.4347    0.8866 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2630   -6.0732    0.2437 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3937   -4.7392   -0.9278 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0222   -6.0221    0.9132 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2555   -6.9562   -0.0129 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9952   -5.9959   -0.8638 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8639   -2.6063    0.1149 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1015    2.1500    0.1802 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  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  1  0
  9 10  2  0
 10 11  1  0
 11 12  2  0
 12 13  1  0
 13 14  2  0
 13 15  1  0
 15 16  1  0
 16 17  1  0
 17 18  2  0
 17 19  1  0
 19 20  1  0
 20 21  1  0
 21 22  2  0
 12 23  1  0
 23 24  2  0
 24 25  1  0
 25 26  2  0
 25 27  1  0
  8 28  2  0
 28 29  1  0
 29 30  2  0
 30 31  1  0
 31 32  2  3
 32 33  1  0
 32 34  1  0
 31 35  1  0
 35 36  2  0
 36 37  1  0
 37 38  1  0
 38 39  2  0
 39  4  1  0
 38  7  1  0
 24  9  1  0
 36 28  1  0
 21 16  1  0
  1 40  1  0
  1 41  1  0
  1 42  1  0
  3 43  1  0
  3 44  1  0
  3 45  1  0
  5 46  1  0
  6 47  1  0
 10 48  1  0
 11 49  1  0
 19 50  1  0
 19 51  1  0
 20 52  1  0
 20 53  1  0
 23 54  1  0
 29 55  1  0
 30 56  1  0
 33 57  1  0
 33 58  1  0
 33 59  1  0
 34 60  1  0
 34 61  1  0
 34 62  1  0
 35 63  1  0
 39 64  1  0
M  CHG  2  27  -1  32   1
M  END


  Mrv1652309102123492D          

 39 43  0  0  0  0            999 V2000
    5.7158    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0013    1.2375    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.0013    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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    3.5724   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868   -0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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    1.4289    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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  4  5  2  0  0  0  0
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 19 20  1  0  0  0  0
  6 20  1  0  0  0  0
 10 21  1  0  0  0  0
 21 22  2  0  0  0  0
 22 23  1  0  0  0  0
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 21 26  1  0  0  0  0
 24 27  1  0  0  0  0
 27 28  2  0  0  0  0
 27 29  1  0  0  0  0
 29 30  1  0  0  0  0
 30 31  1  0  0  0  0
 31 32  2  0  0  0  0
 31 33  1  0  0  0  0
 33 34  1  0  0  0  0
 34 35  1  0  0  0  0
 30 35  1  0  0  0  0
 35 36  2  0  0  0  0
 22 37  1  0  0  0  0
 37 38  2  0  0  0  0
 37 39  1  0  0  0  0
M  CHG  2  15   1  39  -1
M  END
> <DATABASE_ID>
HMDB0244682

> <DATABASE_NAME>
hmdb

> <SMILES>
CN(C)C1=CC2=C(C=C1)C(=C1C=CC(C=C1O2)=[N+](C)C)C1=C(C=C(C=C1)C(=O)ON1C(=O)CCC1=O)C([O-])=O

> <INCHI_IDENTIFIER>
InChI=1S/C29H25N3O7/c1-30(2)17-6-9-20-23(14-17)38-24-15-18(31(3)4)7-10-21(24)27(20)19-8-5-16(13-22(19)28(35)36)29(37)39-32-25(33)11-12-26(32)34/h5-10,13-15H,11-12H2,1-4H3

> <INCHI_KEY>
VWFRSNKRTNUMET-UHFFFAOYSA-N

> <FORMULA>
C29H25N3O7

> <MOLECULAR_WEIGHT>
527.533

> <EXACT_MASS>
527.169250157

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_ATOM_COUNT>
64

> <JCHEM_AVERAGE_POLARIZABILITY>
55.771476854850945

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2-[6-(dimethylamino)-3-(dimethyliminiumyl)-3H-xanthen-9-yl]-5-{[(2,5-dioxopyrrolidin-1-yl)oxy]carbonyl}benzoate

> <ALOGPS_LOGP>
0.18

> <JCHEM_LOGP>
-0.7618226580362168

> <ALOGPS_LOGS>
-5.83

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
17.69729760133662

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.6780311453991406

> <JCHEM_PKA_STRONGEST_BASIC>
3.074304525134718

> <JCHEM_POLAR_SURFACE_AREA>
119.28999999999999

> <JCHEM_REFRACTIVITY>
177.57280000000006

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
8.51e-04 g/l

> <JCHEM_TRADITIONAL_IUPAC>
2-[3-(dimethylamino)-6-(dimethyliminio)xanthen-9-yl]-5-{[(2,5-dioxopyrrolidin-1-yl)oxy]carbonyl}benzoate

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0244682
     RDKit          3D
5-Carboxytetramethylrhodamine succinimidyl ester
 64 68  0  0  0  0  0  0  0  0999 V2000
   -5.6600    4.5092    0.2075 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2166    4.6221    0.2048 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5887    5.9204    0.2254 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4283    3.4444    0.1787 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0638    3.5488    0.1640 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3094    2.3751    0.1395 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8878    1.1283    0.1301 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1212   -0.0081    0.1056 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3269    0.0584    0.0945 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9598    0.0649    1.3323 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3331    0.1194    1.3968 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1052    0.1676    0.2643 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5470    0.2201    0.4056 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0910    0.2264    1.5409 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.4146    0.2656   -0.6784 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.7871    0.3152   -0.4807 N   0  0  0  0  0  0  0  0  0  0  0  0
    7.6082    1.3561   -0.0141 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.2205    2.5295    0.2196 O   0  0  0  0  0  0  0  0  0  0  0  0
    9.0037    0.8840    0.1680 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.8644   -0.6203    0.0889 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.6470   -0.7854   -0.7481 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.4598   -1.7373   -1.5282 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4859    0.1619   -0.9587 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1005    0.1073   -1.0437 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4313    0.1011   -2.3387 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8185    0.0541   -2.4187 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1435    0.1466   -3.5081 O   0  0  0  0  0  1  0  0  0  0  0  0
   -1.7169   -1.2287    0.0957 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9600   -2.3635    0.0716 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6112   -3.5766    0.0635 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9936   -3.6810    0.0792 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5331   -4.8511    0.0623 N   0  0  0  0  0  4  0  0  0  0  0  0
   -4.9676   -5.0165    0.0773 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6892   -6.0162    0.0268 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7868   -2.5282    0.1044 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1894   -1.2896    0.1130 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8692   -0.1711    0.1361 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2792    1.0066    0.1449 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0050    2.1812    0.1686 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.1391    5.5051    0.1315 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.0236    3.8634   -0.6264 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.9381    4.0572    1.2005 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7670    5.9365    0.9916 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3734    6.6662    0.5249 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2252    6.1496   -0.7949 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5624    4.5179    0.1711 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2367    2.4262    0.1278 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3632    0.0265    2.2528 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7785    0.1253    2.3915 H   0  0  0  0  0  0  0  0  0  0  0  0
    9.3907    1.1403    1.1632 H   0  0  0  0  0  0  0  0  0  0  0  0
    9.6819    1.2666   -0.6169 H   0  0  0  0  0  0  0  0  0  0  0  0
    9.7469   -1.1099   -0.3529 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.6042   -0.9872    1.1036 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0573    0.2024   -1.8814 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1249   -2.2710    0.0608 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9792   -4.4782    0.0445 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4418   -4.4347    0.8866 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2630   -6.0732    0.2437 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3937   -4.7392   -0.9278 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0222   -6.0221    0.9132 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2555   -6.9562   -0.0129 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9952   -5.9959   -0.8638 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8639   -2.6063    0.1149 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1015    2.1500    0.1802 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  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  1  0
  9 10  2  0
 10 11  1  0
 11 12  2  0
 12 13  1  0
 13 14  2  0
 13 15  1  0
 15 16  1  0
 16 17  1  0
 17 18  2  0
 17 19  1  0
 19 20  1  0
 20 21  1  0
 21 22  2  0
 12 23  1  0
 23 24  2  0
 24 25  1  0
 25 26  2  0
 25 27  1  0
  8 28  2  0
 28 29  1  0
 29 30  2  0
 30 31  1  0
 31 32  2  3
 32 33  1  0
 32 34  1  0
 31 35  1  0
 35 36  2  0
 36 37  1  0
 37 38  1  0
 38 39  2  0
 39  4  1  0
 38  7  1  0
 24  9  1  0
 36 28  1  0
 21 16  1  0
  1 40  1  0
  1 41  1  0
  1 42  1  0
  3 43  1  0
  3 44  1  0
  3 45  1  0
  5 46  1  0
  6 47  1  0
 10 48  1  0
 11 49  1  0
 19 50  1  0
 19 51  1  0
 20 52  1  0
 20 53  1  0
 23 54  1  0
 29 55  1  0
 30 56  1  0
 33 57  1  0
 33 58  1  0
 33 59  1  0
 34 60  1  0
 34 61  1  0
 34 62  1  0
 35 63  1  0
 39 64  1  0
M  CHG  2  27  -1  32   1
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      10.669   1.540   0.000  0.00  0.00           C+0
HETATM    2  N   UNK     0       9.336   2.310   0.000  0.00  0.00           N+0
HETATM    3  C   UNK     0       9.336   3.850   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       8.002   1.540   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       6.668   2.310   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       5.335   1.540   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       5.335   0.000   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       6.668  -0.770   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       8.002  -0.000   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       4.001  -0.770   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       2.667  -0.000   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       1.334  -0.770   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   1.540   0.000  0.00  0.00           C+0
HETATM   15  N   UNK     0      -1.334   2.310   0.000  0.00  0.00           N+1
HETATM   16  C   UNK     0      -1.334   3.850   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      -2.667   1.540   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
HETATM   20  O   UNK     0       4.001   2.310   0.000  0.00  0.00           O+0
HETATM   21  C   UNK     0       4.001  -2.310   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       5.335  -3.080   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       5.335  -4.620   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       4.001  -5.390   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       2.667  -4.620   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       2.667  -3.080   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0       4.001  -6.930   0.000  0.00  0.00           C+0
HETATM   28  O   UNK     0       5.335  -7.700   0.000  0.00  0.00           O+0
HETATM   29  O   UNK     0       2.667  -7.700   0.000  0.00  0.00           O+0
HETATM   30  N   UNK     0       2.667  -9.240   0.000  0.00  0.00           N+0
HETATM   31  C   UNK     0       3.913 -10.145   0.000  0.00  0.00           C+0
HETATM   32  O   UNK     0       5.378  -9.669   0.000  0.00  0.00           O+0
HETATM   33  C   UNK     0       3.437 -11.610   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0       1.897 -11.610   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0       1.421 -10.145   0.000  0.00  0.00           C+0
HETATM   36  O   UNK     0      -0.043  -9.669   0.000  0.00  0.00           O+0
HETATM   37  C   UNK     0       6.668  -2.310   0.000  0.00  0.00           C+0
HETATM   38  O   UNK     0       8.002  -3.080   0.000  0.00  0.00           O+0
HETATM   39  O   UNK     0       7.574  -1.064   0.000  0.00  0.00           O-1
CONECT    1    2                                                            
CONECT    2    1    3    4                                                  
CONECT    3    2                                                            
CONECT    4    2    5    9                                                  
CONECT    5    4    6                                                       
CONECT    6    5    7   20                                                  
CONECT    7    6    8   10                                                  
CONECT    8    7    9                                                       
CONECT    9    8    4                                                       
CONECT   10    7   11   21                                                  
CONECT   11   10   12   19                                                  
CONECT   12   11   13                                                       
CONECT   13   12   14                                                       
CONECT   14   13   15   18                                                  
CONECT   15   14   16   17                                                  
CONECT   16   15                                                            
CONECT   17   15                                                            
CONECT   18   14   19                                                       
CONECT   19   18   11   20                                                  
CONECT   20   19    6                                                       
CONECT   21   10   22   26                                                  
CONECT   22   21   23   37                                                  
CONECT   23   22   24                                                       
CONECT   24   23   25   27                                                  
CONECT   25   24   26                                                       
CONECT   26   25   21                                                       
CONECT   27   24   28   29                                                  
CONECT   28   27                                                            
CONECT   29   27   30                                                       
CONECT   30   29   31   35                                                  
CONECT   31   30   32   33                                                  
CONECT   32   31                                                            
CONECT   33   31   34                                                       
CONECT   34   33   35                                                       
CONECT   35   34   30   36                                                  
CONECT   36   35                                                            
CONECT   37   22   38   39                                                  
CONECT   38   37                                                            
CONECT   39   37                                                            
MASTER        0    0    0    0    0    0    0    0   39    0   86    0
END

COMPND    HMDB0244682
HETATM    1  C1  UNL     1      -5.660   4.509   0.207  1.00  0.00           C  
HETATM    2  N1  UNL     1      -4.217   4.622   0.205  1.00  0.00           N  
HETATM    3  C2  UNL     1      -3.589   5.920   0.225  1.00  0.00           C  
HETATM    4  C3  UNL     1      -3.428   3.444   0.179  1.00  0.00           C  
HETATM    5  C4  UNL     1      -2.064   3.549   0.164  1.00  0.00           C  
HETATM    6  C5  UNL     1      -1.309   2.375   0.139  1.00  0.00           C  
HETATM    7  C6  UNL     1      -1.888   1.128   0.130  1.00  0.00           C  
HETATM    8  C7  UNL     1      -1.121  -0.008   0.106  1.00  0.00           C  
HETATM    9  C8  UNL     1       0.327   0.058   0.095  1.00  0.00           C  
HETATM   10  C9  UNL     1       0.960   0.065   1.332  1.00  0.00           C  
HETATM   11  C10 UNL     1       2.333   0.119   1.397  1.00  0.00           C  
HETATM   12  C11 UNL     1       3.105   0.168   0.264  1.00  0.00           C  
HETATM   13  C12 UNL     1       4.547   0.220   0.406  1.00  0.00           C  
HETATM   14  O1  UNL     1       5.091   0.226   1.541  1.00  0.00           O  
HETATM   15  O2  UNL     1       5.415   0.266  -0.678  1.00  0.00           O  
HETATM   16  N2  UNL     1       6.787   0.315  -0.481  1.00  0.00           N  
HETATM   17  C13 UNL     1       7.608   1.356  -0.014  1.00  0.00           C  
HETATM   18  O3  UNL     1       7.221   2.529   0.220  1.00  0.00           O  
HETATM   19  C14 UNL     1       9.004   0.884   0.168  1.00  0.00           C  
HETATM   20  C15 UNL     1       8.864  -0.620   0.089  1.00  0.00           C  
HETATM   21  C16 UNL     1       7.647  -0.785  -0.748  1.00  0.00           C  
HETATM   22  O4  UNL     1       7.460  -1.737  -1.528  1.00  0.00           O  
HETATM   23  C17 UNL     1       2.486   0.162  -0.959  1.00  0.00           C  
HETATM   24  C18 UNL     1       1.100   0.107  -1.044  1.00  0.00           C  
HETATM   25  C19 UNL     1       0.431   0.101  -2.339  1.00  0.00           C  
HETATM   26  O5  UNL     1      -0.819   0.054  -2.419  1.00  0.00           O  
HETATM   27  O6  UNL     1       1.143   0.147  -3.508  1.00  0.00           O1-
HETATM   28  C20 UNL     1      -1.717  -1.229   0.096  1.00  0.00           C  
HETATM   29  C21 UNL     1      -0.960  -2.364   0.072  1.00  0.00           C  
HETATM   30  C22 UNL     1      -1.611  -3.577   0.064  1.00  0.00           C  
HETATM   31  C23 UNL     1      -2.994  -3.681   0.079  1.00  0.00           C  
HETATM   32  N3  UNL     1      -3.533  -4.851   0.062  1.00  0.00           N1+
HETATM   33  C24 UNL     1      -4.968  -5.017   0.077  1.00  0.00           C  
HETATM   34  C25 UNL     1      -2.689  -6.016   0.027  1.00  0.00           C  
HETATM   35  C26 UNL     1      -3.787  -2.528   0.104  1.00  0.00           C  
HETATM   36  C27 UNL     1      -3.189  -1.290   0.113  1.00  0.00           C  
HETATM   37  O7  UNL     1      -3.869  -0.171   0.136  1.00  0.00           O  
HETATM   38  C28 UNL     1      -3.279   1.007   0.145  1.00  0.00           C  
HETATM   39  C29 UNL     1      -4.005   2.181   0.169  1.00  0.00           C  
HETATM   40  H1  UNL     1      -6.139   5.505   0.131  1.00  0.00           H  
HETATM   41  H2  UNL     1      -6.024   3.863  -0.626  1.00  0.00           H  
HETATM   42  H3  UNL     1      -5.938   4.057   1.200  1.00  0.00           H  
HETATM   43  H4  UNL     1      -2.767   5.937   0.992  1.00  0.00           H  
HETATM   44  H5  UNL     1      -4.373   6.666   0.525  1.00  0.00           H  
HETATM   45  H6  UNL     1      -3.225   6.150  -0.795  1.00  0.00           H  
HETATM   46  H7  UNL     1      -1.562   4.518   0.171  1.00  0.00           H  
HETATM   47  H8  UNL     1      -0.237   2.426   0.128  1.00  0.00           H  
HETATM   48  H9  UNL     1       0.363   0.026   2.253  1.00  0.00           H  
HETATM   49  H10 UNL     1       2.779   0.125   2.391  1.00  0.00           H  
HETATM   50  H11 UNL     1       9.391   1.140   1.163  1.00  0.00           H  
HETATM   51  H12 UNL     1       9.682   1.267  -0.617  1.00  0.00           H  
HETATM   52  H13 UNL     1       9.747  -1.110  -0.353  1.00  0.00           H  
HETATM   53  H14 UNL     1       8.604  -0.987   1.104  1.00  0.00           H  
HETATM   54  H15 UNL     1       3.057   0.202  -1.881  1.00  0.00           H  
HETATM   55  H16 UNL     1       0.125  -2.271   0.061  1.00  0.00           H  
HETATM   56  H17 UNL     1      -0.979  -4.478   0.044  1.00  0.00           H  
HETATM   57  H18 UNL     1      -5.442  -4.435   0.887  1.00  0.00           H  
HETATM   58  H19 UNL     1      -5.263  -6.073   0.244  1.00  0.00           H  
HETATM   59  H20 UNL     1      -5.394  -4.739  -0.928  1.00  0.00           H  
HETATM   60  H21 UNL     1      -2.022  -6.022   0.913  1.00  0.00           H  
HETATM   61  H22 UNL     1      -3.255  -6.956  -0.013  1.00  0.00           H  
HETATM   62  H23 UNL     1      -1.995  -5.996  -0.864  1.00  0.00           H  
HETATM   63  H24 UNL     1      -4.864  -2.606   0.115  1.00  0.00           H  
HETATM   64  H25 UNL     1      -5.102   2.150   0.180  1.00  0.00           H  
CONECT    1    2   40   41   42
CONECT    2    3    4
CONECT    3   43   44   45
CONECT    4    5    5   39
CONECT    5    6   46
CONECT    6    7    7   47
CONECT    7    8   38
CONECT    8    9   28   28
CONECT    9   10   10   24
CONECT   10   11   48
CONECT   11   12   12   49
CONECT   12   13   23
CONECT   13   14   14   15
CONECT   15   16
CONECT   16   17   21
CONECT   17   18   18   19
CONECT   19   20   50   51
CONECT   20   21   52   53
CONECT   21   22   22
CONECT   23   24   24   54
CONECT   24   25
CONECT   25   26   26   27
CONECT   28   29   36
CONECT   29   30   30   55
CONECT   30   31   56
CONECT   31   32   32   35
CONECT   32   33   34
CONECT   33   57   58   59
CONECT   34   60   61   62
CONECT   35   36   36   63
CONECT   36   37
CONECT   37   38
CONECT   38   39   39
CONECT   39   64
END

HMDB0244682
     RDKit          3D
5-Carboxytetramethylrhodamine succinimidyl ester
 64 68  0  0  0  0  0  0  0  0999 V2000
   -5.6600    4.5092    0.2075 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2166    4.6221    0.2048 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5887    5.9204    0.2254 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4283    3.4444    0.1787 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0638    3.5488    0.1640 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3094    2.3751    0.1395 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8878    1.1283    0.1301 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1212   -0.0081    0.1056 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3269    0.0584    0.0945 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9598    0.0649    1.3323 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3331    0.1194    1.3968 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1052    0.1676    0.2643 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5470    0.2201    0.4056 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0910    0.2264    1.5409 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.4146    0.2656   -0.6784 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.7871    0.3152   -0.4807 N   0  0  0  0  0  0  0  0  0  0  0  0
    7.6082    1.3561   -0.0141 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.2205    2.5295    0.2196 O   0  0  0  0  0  0  0  0  0  0  0  0
    9.0037    0.8840    0.1680 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.8644   -0.6203    0.0889 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.6470   -0.7854   -0.7481 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.4598   -1.7373   -1.5282 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4859    0.1619   -0.9587 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1005    0.1073   -1.0437 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4313    0.1011   -2.3387 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8185    0.0541   -2.4187 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1435    0.1466   -3.5081 O   0  0  0  0  0  1  0  0  0  0  0  0
   -1.7169   -1.2287    0.0957 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9600   -2.3635    0.0716 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6112   -3.5766    0.0635 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9936   -3.6810    0.0792 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5331   -4.8511    0.0623 N   0  0  0  0  0  4  0  0  0  0  0  0
   -4.9676   -5.0165    0.0773 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6892   -6.0162    0.0268 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7868   -2.5282    0.1044 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1894   -1.2896    0.1130 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8692   -0.1711    0.1361 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2792    1.0066    0.1449 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0050    2.1812    0.1686 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.1391    5.5051    0.1315 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.0236    3.8634   -0.6264 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.9381    4.0572    1.2005 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7670    5.9365    0.9916 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3734    6.6662    0.5249 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2252    6.1496   -0.7949 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5624    4.5179    0.1711 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2367    2.4262    0.1278 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3632    0.0265    2.2528 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7785    0.1253    2.3915 H   0  0  0  0  0  0  0  0  0  0  0  0
    9.3907    1.1403    1.1632 H   0  0  0  0  0  0  0  0  0  0  0  0
    9.6819    1.2666   -0.6169 H   0  0  0  0  0  0  0  0  0  0  0  0
    9.7469   -1.1099   -0.3529 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.6042   -0.9872    1.1036 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0573    0.2024   -1.8814 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1249   -2.2710    0.0608 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9792   -4.4782    0.0445 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4418   -4.4347    0.8866 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2630   -6.0732    0.2437 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3937   -4.7392   -0.9278 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0222   -6.0221    0.9132 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2555   -6.9562   -0.0129 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9952   -5.9959   -0.8638 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8639   -2.6063    0.1149 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1015    2.1500    0.1802 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  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  1  0
  9 10  2  0
 10 11  1  0
 11 12  2  0
 12 13  1  0
 13 14  2  0
 13 15  1  0
 15 16  1  0
 16 17  1  0
 17 18  2  0
 17 19  1  0
 19 20  1  0
 20 21  1  0
 21 22  2  0
 12 23  1  0
 23 24  2  0
 24 25  1  0
 25 26  2  0
 25 27  1  0
  8 28  2  0
 28 29  1  0
 29 30  2  0
 30 31  1  0
 31 32  2  3
 32 33  1  0
 32 34  1  0
 31 35  1  0
 35 36  2  0
 36 37  1  0
 37 38  1  0
 38 39  2  0
 39  4  1  0
 38  7  1  0
 24  9  1  0
 36 28  1  0
 21 16  1  0
  1 40  1  0
  1 41  1  0
  1 42  1  0
  3 43  1  0
  3 44  1  0
  3 45  1  0
  5 46  1  0
  6 47  1  0
 10 48  1  0
 11 49  1  0
 19 50  1  0
 19 51  1  0
 20 52  1  0
 20 53  1  0
 23 54  1  0
 29 55  1  0
 30 56  1  0
 33 57  1  0
 33 58  1  0
 33 59  1  0
 34 60  1  0
 34 61  1  0
 34 62  1  0
 35 63  1  0
 39 64  1  0
M  CHG  2  27  -1  32   1
M  END

View in JSmol View NMR Assignments View Stereo Labels

Synonyms

Value	Source
TAMRA CPD	HMDB

Chemical Formula

C₂₉H₂₅N₃O₇

Average Molecular Weight

527.533

Monoisotopic Molecular Weight

527.169250157

IUPAC Name

2-[6-(dimethylamino)-3-(dimethyliminiumyl)-3H-xanthen-9-yl]-5-{[(2,5-dioxopyrrolidin-1-yl)oxy]carbonyl}benzoate

Traditional Name

2-[3-(dimethylamino)-6-(dimethyliminio)xanthen-9-yl]-5-{[(2,5-dioxopyrrolidin-1-yl)oxy]carbonyl}benzoate

CAS Registry Number

Not Available

SMILES

CN(C)C1=CC2=C(C=C1)C(=C1C=CC(C=C1O2)=[N+](C)C)C1=C(C=C(C=C1)C(=O)ON1C(=O)CCC1=O)C([O-])=O

InChI Identifier

InChI=1S/C29H25N3O7/c1-30(2)17-6-9-20-23(14-17)38-24-15-18(31(3)4)7-10-21(24)27(20)19-8-5-16(13-22(19)28(35)36)29(37)39-32-25(33)11-12-26(32)34/h5-10,13-15H,11-12H2,1-4H3

InChI Key

VWFRSNKRTNUMET-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
Benzoic acid or derivatives
Benzoic acid
Benzoyl
Tertiary aliphatic/aromatic amine
Dialkylarylamine
Monocyclic benzene moiety
Dicarboxylic acid or derivatives
Pyrrolidone
2-pyrrolidone
Benzenoid
Secondary ketimine
Heteroaromatic compound
Pyrrolidine
Dicarboximide
Tertiary amine
Amino acid
Carboxylic acid salt
Lactam
Amino acid or derivatives
Oxacycle
Azacycle
Carboxylic acid derivative
Carboxylic acid
Organic zwitterion
Organic oxide
Organonitrogen compound
Organooxygen compound
Carbonyl group
Organopnictogen compound
Organic oxygen compound
Organic nitrogen compound
Organic salt
Amine
Hydrocarbon derivative
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

Not Available

Ontology

Physiological effect

Not Available

Disposition

Biological location

Non-excretory biofluid

Biofluid or Excreta

Blood (PMID: 31557052)

Process

Not Available

Role

Not Available

Physical Properties

State

Not Available

Experimental Molecular Properties

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

Experimental Chromatographic Properties

Not Available

Predicted Molecular Properties

Property	Value	Source
logP	0.18	ALOGPS
logP	-0.76	ChemAxon
logS	-5.8	ALOGPS
pKa (Strongest Acidic)	3.68	ChemAxon
pKa (Strongest Basic)	3.07	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	7	ChemAxon
Hydrogen Donor Count	0	ChemAxon
Polar Surface Area	119.29 Å²	ChemAxon
Rotatable Bond Count	5	ChemAxon
Refractivity	177.57 m³·mol⁻¹	ChemAxon
Polarizability	55.77 Å³	ChemAxon
Number of Rings	5	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	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]+	211.158	30932474
DeepCCS	[M-H]-	208.762	30932474
DeepCCS	[M-2H]-	241.685	30932474
DeepCCS	[M+Na]+	217.05	30932474
AllCCS	[M+H]+	222.0	32859911
AllCCS	[M+H-H2O]+	220.2	32859911
AllCCS	[M+NH4]+	223.6	32859911
AllCCS	[M+Na]+	224.1	32859911
AllCCS	[M-H]-	218.3	32859911
AllCCS	[M+Na-2H]-	219.6	32859911
AllCCS	[M+HCOO]-	221.1	32859911

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
5-Carboxytetramethylrhodamine succinimidyl ester	CN(C)C1=CC2=C(C=C1)C(=C1C=CC(C=C1O2)=[N+](C)C)C1=C(C=C(C=C1)C(=O)ON1C(=O)CCC1=O)C([O-])=O	5788.7	Standard polar	33892256
5-Carboxytetramethylrhodamine succinimidyl ester	CN(C)C1=CC2=C(C=C1)C(=C1C=CC(C=C1O2)=[N+](C)C)C1=C(C=C(C=C1)C(=O)ON1C(=O)CCC1=O)C([O-])=O	4628.3	Standard non polar	33892256
5-Carboxytetramethylrhodamine succinimidyl ester	CN(C)C1=CC2=C(C=C1)C(=C1C=CC(C=C1O2)=[N+](C)C)C1=C(C=C(C=C1)C(=O)ON1C(=O)CCC1=O)C([O-])=O	4802.2	Semi standard non polar	33892256

Spectra

NMR Spectra

Spectrum Type	Description	Deposition Date	Source	View
Predicted 1D NMR	¹³C NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	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

2043316

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

2762600

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 5-Carboxytetramethylrhodamine succinimidyl ester (HMDB0244682)

MOL for HMDB0244682 (5-Carboxytetramethylrhodamine succinimidyl ester)

3D MOL for HMDB0244682 (5-Carboxytetramethylrhodamine succinimidyl ester)

3D SDF for HMDB0244682 (5-Carboxytetramethylrhodamine succinimidyl ester)

3D-SDF for HMDB0244682 (5-Carboxytetramethylrhodamine succinimidyl ester)

PDB for HMDB0244682 (5-Carboxytetramethylrhodamine succinimidyl ester)

3D PDB for HMDB0244682 (5-Carboxytetramethylrhodamine succinimidyl ester)

SMILES for HMDB0244682 (5-Carboxytetramethylrhodamine succinimidyl ester)

INCHI for HMDB0244682 (5-Carboxytetramethylrhodamine succinimidyl ester)

Structure for HMDB0244682 (5-Carboxytetramethylrhodamine succinimidyl ester)

3D Structure for HMDB0244682 (5-Carboxytetramethylrhodamine succinimidyl ester)

Predicted Collision Cross Sections

Predicted Kovats Retention Indices

Underivatized

NMR Spectra