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Record Information

Version

5.0

Status

Detected but not Quantified

Creation Date

2021-09-11 15:08:52 UTC

Update Date

2021-09-26 23:10:20 UTC

HMDB ID

HMDB0255500

Secondary Accession Numbers

None

Metabolite Identification

Common Name

5-(1H-Indol-3-ylmethyl)-3-methyl-2-thioxo-4-Imidazolidinone

Description

4-[(1H-indol-3-yl)methyl]-1-methyl-2-sulfanyl-4,5-dihydro-1H-imidazol-5-one belongs to the class of organic compounds known as alpha amino acids and derivatives. These are amino acids in which the amino group is attached to the carbon atom immediately adjacent to the carboxylate group (alpha carbon), or a derivative thereof. Based on a literature review very few articles have been published on 4-[(1H-indol-3-yl)methyl]-1-methyl-2-sulfanyl-4,5-dihydro-1H-imidazol-5-one. This compound has been identified in human blood as reported by (PMID: 31557052 ). 5-(1h-indol-3-ylmethyl)-3-methyl-2-thioxo-4-imidazolidinone is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically 5-(1H-Indol-3-ylmethyl)-3-methyl-2-thioxo-4-Imidazolidinone 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

HMDB0255500
     RDKit          3D
5-(1H-Indol-3-ylmethyl)-3-methyl-2-thioxo-4-Imidazolidinone
 31 33  0  0  0  0  0  0  0  0999 V2000
   -5.0000    0.2395   -0.4694 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5892    0.2634   -0.1588 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5940   -0.4406   -0.8678 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8184   -1.3696   -1.7134 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2223    0.0762   -0.4707 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3768   -1.0995   -0.4678 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0206   -1.0707   -0.1453 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7447   -2.2585    0.0240 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9925   -1.9434    0.3203 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.1825   -0.6218    0.3682 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2831    0.1975    0.6311 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1583    1.5709    0.6041 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9061    2.0825    0.3076 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8093    1.2877    0.0459 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9421   -0.0726    0.0752 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5109    0.6718    0.7840 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8961    0.9485    0.8632 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6801    1.9108    1.9489 S   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2407    0.7861   -1.4139 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3378   -0.8205   -0.6743 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6209    0.6001    0.3651 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0227    0.8138   -1.3046 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4768   -1.6082   -1.4764 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8759   -1.8552    0.2177 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3846   -3.2856   -0.0623 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7611   -2.6331    0.5016 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.2090   -0.3074    0.8503 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.0218    2.1792    0.8102 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8265    3.1605    0.2890 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8686    1.7039   -0.1785 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8483    0.8942    1.5619 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  0
  3  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  2  0
  8  9  1  0
  9 10  1  0
 10 11  2  0
 11 12  1  0
 12 13  2  0
 13 14  1  0
 14 15  2  0
  5 16  1  0
 16 17  1  0
 17 18  2  0
 17  2  1  0
 15  7  1  0
 15 10  1  0
  1 19  1  0
  1 20  1  0
  1 21  1  0
  5 22  1  0
  6 23  1  0
  6 24  1  0
  8 25  1  0
  9 26  1  0
 11 27  1  0
 12 28  1  0
 13 29  1  0
 14 30  1  0
 16 31  1  0
M  END


  Mrv1652309112117092D          

 18 20  0  0  0  0            999 V2000
   -2.0044   -1.8464    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2508   -2.1820    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5363   -1.7695    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4500   -0.9490    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0768   -2.3215    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2587   -3.0752    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0792   -2.9890    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6313   -3.6021    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
    0.8838   -2.1500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1387   -1.3654    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6538   -0.6979    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1387   -0.0305    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.9233   -0.2854    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6378    0.1271    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3523   -0.2854    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3523   -1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6378   -1.5229    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9233   -1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  2  0  0  0  0
  3  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  2  7  1  0  0  0  0
  7  8  2  0  0  0  0
  5  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  2  0  0  0  0
 11 12  1  0  0  0  0
 12 13  1  0  0  0  0
 13 14  2  0  0  0  0
 14 15  1  0  0  0  0
 15 16  2  0  0  0  0
 16 17  1  0  0  0  0
 17 18  2  0  0  0  0
 13 18  1  0  0  0  0
 10 18  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0255500

> <DATABASE_NAME>
hmdb

> <SMILES>
CN1C(=S)NC(CC2=CNC3=CC=CC=C23)C1=O

> <INCHI_IDENTIFIER>
InChI=1S/C13H13N3OS/c1-16-12(17)11(15-13(16)18)6-8-7-14-10-5-3-2-4-9(8)10/h2-5,7,11,14H,6H2,1H3,(H,15,18)

> <INCHI_KEY>
TXUWMXQFNYDOEZ-UHFFFAOYSA-N

> <FORMULA>
C13H13N3OS

> <MOLECULAR_WEIGHT>
259.33

> <EXACT_MASS>
259.077933225

> <JCHEM_ACCEPTOR_COUNT>
1

> <JCHEM_ATOM_COUNT>
31

> <JCHEM_AVERAGE_POLARIZABILITY>
27.367701886165683

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
5-[(1H-indol-3-yl)methyl]-3-methyl-2-sulfanylideneimidazolidin-4-one

> <ALOGPS_LOGP>
2.08

> <JCHEM_LOGP>
1.987177785333334

> <ALOGPS_LOGS>
-3.75

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
15.455551288378512

> <JCHEM_PKA_STRONGEST_ACIDIC>
11.063026584694121

> <JCHEM_PKA_STRONGEST_BASIC>
-8.341598681782296

> <JCHEM_POLAR_SURFACE_AREA>
48.13

> <JCHEM_REFRACTIVITY>
74.1331

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
4.65e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
5-(1H-indol-3-ylmethyl)-3-methyl-2-sulfanylideneimidazolidin-4-one

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0255500
     RDKit          3D
5-(1H-Indol-3-ylmethyl)-3-methyl-2-thioxo-4-Imidazolidinone
 31 33  0  0  0  0  0  0  0  0999 V2000
   -5.0000    0.2395   -0.4694 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5892    0.2634   -0.1588 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5940   -0.4406   -0.8678 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8184   -1.3696   -1.7134 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2223    0.0762   -0.4707 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3768   -1.0995   -0.4678 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0206   -1.0707   -0.1453 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7447   -2.2585    0.0240 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9925   -1.9434    0.3203 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.1825   -0.6218    0.3682 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2831    0.1975    0.6311 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1583    1.5709    0.6041 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9061    2.0825    0.3076 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8093    1.2877    0.0459 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9421   -0.0726    0.0752 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5109    0.6718    0.7840 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8961    0.9485    0.8632 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6801    1.9108    1.9489 S   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2407    0.7861   -1.4139 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3378   -0.8205   -0.6743 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6209    0.6001    0.3651 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0227    0.8138   -1.3046 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4768   -1.6082   -1.4764 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8759   -1.8552    0.2177 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3846   -3.2856   -0.0623 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7611   -2.6331    0.5016 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.2090   -0.3074    0.8503 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.0218    2.1792    0.8102 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8265    3.1605    0.2890 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8686    1.7039   -0.1785 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8483    0.8942    1.5619 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  0
  3  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  2  0
  8  9  1  0
  9 10  1  0
 10 11  2  0
 11 12  1  0
 12 13  2  0
 13 14  1  0
 14 15  2  0
  5 16  1  0
 16 17  1  0
 17 18  2  0
 17  2  1  0
 15  7  1  0
 15 10  1  0
  1 19  1  0
  1 20  1  0
  1 21  1  0
  5 22  1  0
  6 23  1  0
  6 24  1  0
  8 25  1  0
  9 26  1  0
 11 27  1  0
 12 28  1  0
 13 29  1  0
 14 30  1  0
 16 31  1  0
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      -3.742  -3.447   0.000  0.00  0.00           C+0
HETATM    2  N   UNK     0      -2.335  -4.073   0.000  0.00  0.00           N+0
HETATM    3  C   UNK     0      -1.001  -3.303   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0      -0.840  -1.771   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0       0.143  -4.334   0.000  0.00  0.00           C+0
HETATM    6  N   UNK     0      -0.483  -5.740   0.000  0.00  0.00           N+0
HETATM    7  C   UNK     0      -2.015  -5.579   0.000  0.00  0.00           C+0
HETATM    8  S   UNK     0      -3.045  -6.724   0.000  0.00  0.00           S+0
HETATM    9  C   UNK     0       1.650  -4.013   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       2.126  -2.549   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       1.220  -1.303   0.000  0.00  0.00           C+0
HETATM   12  N   UNK     0       2.126  -0.057   0.000  0.00  0.00           N+0
HETATM   13  C   UNK     0       3.590  -0.533   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       4.924   0.237   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       6.258  -0.533   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       6.258  -2.073   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       4.924  -2.843   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       3.590  -2.073   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3    7                                                  
CONECT    3    2    4    5                                                  
CONECT    4    3                                                            
CONECT    5    3    6    9                                                  
CONECT    6    5    7                                                       
CONECT    7    6    2    8                                                  
CONECT    8    7                                                            
CONECT    9    5   10                                                       
CONECT   10    9   11   18                                                  
CONECT   11   10   12                                                       
CONECT   12   11   13                                                       
CONECT   13   12   14   18                                                  
CONECT   14   13   15                                                       
CONECT   15   14   16                                                       
CONECT   16   15   17                                                       
CONECT   17   16   18                                                       
CONECT   18   17   13   10                                                  
MASTER        0    0    0    0    0    0    0    0   18    0   40    0
END

COMPND    HMDB0255500
HETATM    1  C1  UNL     1      -5.000   0.239  -0.469  1.00  0.00           C  
HETATM    2  N1  UNL     1      -3.589   0.263  -0.159  1.00  0.00           N  
HETATM    3  C2  UNL     1      -2.594  -0.441  -0.868  1.00  0.00           C  
HETATM    4  O1  UNL     1      -2.818  -1.370  -1.713  1.00  0.00           O  
HETATM    5  C3  UNL     1      -1.222   0.076  -0.471  1.00  0.00           C  
HETATM    6  C4  UNL     1      -0.377  -1.099  -0.468  1.00  0.00           C  
HETATM    7  C5  UNL     1       1.021  -1.071  -0.145  1.00  0.00           C  
HETATM    8  C6  UNL     1       1.745  -2.259   0.024  1.00  0.00           C  
HETATM    9  N2  UNL     1       2.993  -1.943   0.320  1.00  0.00           N  
HETATM   10  C7  UNL     1       3.182  -0.622   0.368  1.00  0.00           C  
HETATM   11  C8  UNL     1       4.283   0.197   0.631  1.00  0.00           C  
HETATM   12  C9  UNL     1       4.158   1.571   0.604  1.00  0.00           C  
HETATM   13  C10 UNL     1       2.906   2.082   0.308  1.00  0.00           C  
HETATM   14  C11 UNL     1       1.809   1.288   0.046  1.00  0.00           C  
HETATM   15  C12 UNL     1       1.942  -0.073   0.075  1.00  0.00           C  
HETATM   16  N3  UNL     1      -1.511   0.672   0.784  1.00  0.00           N  
HETATM   17  C13 UNL     1      -2.896   0.948   0.863  1.00  0.00           C  
HETATM   18  S1  UNL     1      -3.680   1.911   1.949  1.00  0.00           S  
HETATM   19  H1  UNL     1      -5.241   0.786  -1.414  1.00  0.00           H  
HETATM   20  H2  UNL     1      -5.338  -0.820  -0.674  1.00  0.00           H  
HETATM   21  H3  UNL     1      -5.621   0.600   0.365  1.00  0.00           H  
HETATM   22  H4  UNL     1      -1.023   0.814  -1.305  1.00  0.00           H  
HETATM   23  H5  UNL     1      -0.477  -1.608  -1.476  1.00  0.00           H  
HETATM   24  H6  UNL     1      -0.876  -1.855   0.218  1.00  0.00           H  
HETATM   25  H7  UNL     1       1.385  -3.286  -0.062  1.00  0.00           H  
HETATM   26  H8  UNL     1       3.761  -2.633   0.502  1.00  0.00           H  
HETATM   27  H9  UNL     1       5.209  -0.307   0.850  1.00  0.00           H  
HETATM   28  H10 UNL     1       5.022   2.179   0.810  1.00  0.00           H  
HETATM   29  H11 UNL     1       2.827   3.161   0.289  1.00  0.00           H  
HETATM   30  H12 UNL     1       0.869   1.704  -0.179  1.00  0.00           H  
HETATM   31  H13 UNL     1      -0.848   0.894   1.562  1.00  0.00           H  
CONECT    1    2   19   20   21
CONECT    2    3   17
CONECT    3    4    4    5
CONECT    5    6   16   22
CONECT    6    7   23   24
CONECT    7    8    8   15
CONECT    8    9   25
CONECT    9   10   26
CONECT   10   11   11   15
CONECT   11   12   27
CONECT   12   13   13   28
CONECT   13   14   29
CONECT   14   15   15   30
CONECT   16   17   31
CONECT   17   18   18
END

HMDB0255500
     RDKit          3D
5-(1H-Indol-3-ylmethyl)-3-methyl-2-thioxo-4-Imidazolidinone
 31 33  0  0  0  0  0  0  0  0999 V2000
   -5.0000    0.2395   -0.4694 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5892    0.2634   -0.1588 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5940   -0.4406   -0.8678 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8184   -1.3696   -1.7134 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2223    0.0762   -0.4707 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3768   -1.0995   -0.4678 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0206   -1.0707   -0.1453 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7447   -2.2585    0.0240 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9925   -1.9434    0.3203 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.1825   -0.6218    0.3682 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2831    0.1975    0.6311 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1583    1.5709    0.6041 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9061    2.0825    0.3076 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8093    1.2877    0.0459 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9421   -0.0726    0.0752 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5109    0.6718    0.7840 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8961    0.9485    0.8632 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6801    1.9108    1.9489 S   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2407    0.7861   -1.4139 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3378   -0.8205   -0.6743 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6209    0.6001    0.3651 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0227    0.8138   -1.3046 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4768   -1.6082   -1.4764 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8759   -1.8552    0.2177 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3846   -3.2856   -0.0623 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7611   -2.6331    0.5016 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.2090   -0.3074    0.8503 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.0218    2.1792    0.8102 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8265    3.1605    0.2890 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8686    1.7039   -0.1785 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8483    0.8942    1.5619 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  0
  3  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  2  0
  8  9  1  0
  9 10  1  0
 10 11  2  0
 11 12  1  0
 12 13  2  0
 13 14  1  0
 14 15  2  0
  5 16  1  0
 16 17  1  0
 17 18  2  0
 17  2  1  0
 15  7  1  0
 15 10  1  0
  1 19  1  0
  1 20  1  0
  1 21  1  0
  5 22  1  0
  6 23  1  0
  6 24  1  0
  8 25  1  0
  9 26  1  0
 11 27  1  0
 12 28  1  0
 13 29  1  0
 14 30  1  0
 16 31  1  0
M  END

View in JSmol View Stereo Labels

Synonyms

Value	Source
4-[(1H-indol-3-yl)Methyl]-1-methyl-2-sulphanyl-4,5-dihydro-1H-imidazol-5-one	Generator

Chemical Formula

C₁₃H₁₃N₃OS

Average Molecular Weight

259.33

Monoisotopic Molecular Weight

259.077933225

IUPAC Name

5-[(1H-indol-3-yl)methyl]-3-methyl-2-sulfanylideneimidazolidin-4-one

Traditional Name

5-(1H-indol-3-ylmethyl)-3-methyl-2-sulfanylideneimidazolidin-4-one

CAS Registry Number

Not Available

SMILES

CN1C(=S)NC(CC2=CNC3=CC=CC=C23)C1=O

InChI Identifier

InChI=1S/C13H13N3OS/c1-16-12(17)11(15-13(16)18)6-8-7-14-10-5-3-2-4-9(8)10/h2-5,7,11,14H,6H2,1H3,(H,15,18)

InChI Key

TXUWMXQFNYDOEZ-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as alpha amino acids and derivatives. These are amino acids in which the amino group is attached to the carbon atom immediately adjacent to the carboxylate group (alpha carbon), or a derivative thereof.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Carboxylic acids and derivatives

Sub Class

Amino acids, peptides, and analogues

Direct Parent

Alpha amino acids and derivatives

Alternative Parents

Substituents

Alpha-amino acid or derivatives
3-alkylindole
Indole
Indole or derivatives
Imidazolidinone
Substituted pyrrole
Benzenoid
Pyrrole
Imidazolidine
Heteroaromatic compound
Thiourea
Organoheterocyclic compound
Azacycle
Carbonyl group
Organic oxide
Organosulfur compound
Organooxygen compound
Organonitrogen compound
Organopnictogen compound
Organic oxygen compound
Organic nitrogen compound
Hydrocarbon derivative
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

Not Available

Ontology

Physiological effect

Not Available

Disposition

Biological location

Non-excretory biofluid

Biofluid or Excreta

Blood (PMID: 31557052)

Process

Not Available

Role

Not Available

Physical Properties

State

Not Available

Experimental Molecular Properties

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

Experimental Chromatographic Properties

Not Available

Predicted Molecular Properties

Property	Value	Source
logP	2.08	ALOGPS
logP	1.99	ChemAxon
logS	-3.8	ALOGPS
pKa (Strongest Acidic)	11.06	ChemAxon
pKa (Strongest Basic)	-8.3	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	1	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	48.13 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	74.13 m³·mol⁻¹	ChemAxon
Polarizability	27.37 Å³	ChemAxon
Number of Rings	3	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Predicted Chromatographic Properties

Predicted Collision Cross Sections

Predictor	Adduct Type	CCS Value (Å²)	Reference
DeepCCS	[M-2H]-	188.039	30932474
DeepCCS	[M+Na]+	163.466	30932474
AllCCS	[M+H]+	158.9	32859911
AllCCS	[M+H-H2O]+	155.1	32859911
AllCCS	[M+NH4]+	162.5	32859911
AllCCS	[M+Na]+	163.5	32859911
AllCCS	[M-H]-	161.4	32859911
AllCCS	[M+Na-2H]-	161.1	32859911
AllCCS	[M+HCOO]-	160.9	32859911

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
5-(1H-Indol-3-ylmethyl)-3-methyl-2-thioxo-4-Imidazolidinone	CN1C(=S)NC(CC2=CNC3=CC=CC=C23)C1=O	4059.4	Standard polar	33892256
5-(1H-Indol-3-ylmethyl)-3-methyl-2-thioxo-4-Imidazolidinone	CN1C(=S)NC(CC2=CNC3=CC=CC=C23)C1=O	2542.5	Standard non polar	33892256
5-(1H-Indol-3-ylmethyl)-3-methyl-2-thioxo-4-Imidazolidinone	CN1C(=S)NC(CC2=CNC3=CC=CC=C23)C1=O	2821.1	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
5-(1H-Indol-3-ylmethyl)-3-methyl-2-thioxo-4-Imidazolidinone,1TMS,isomer #1	CN1C(=O)C(CC2=C[NH]C3=CC=CC=C23)N([Si](C)(C)C)C1=S	2640.5	Semi standard non polar	33892256
5-(1H-Indol-3-ylmethyl)-3-methyl-2-thioxo-4-Imidazolidinone,1TMS,isomer #1	CN1C(=O)C(CC2=C[NH]C3=CC=CC=C23)N([Si](C)(C)C)C1=S	2535.9	Standard non polar	33892256
5-(1H-Indol-3-ylmethyl)-3-methyl-2-thioxo-4-Imidazolidinone,1TMS,isomer #1	CN1C(=O)C(CC2=C[NH]C3=CC=CC=C23)N([Si](C)(C)C)C1=S	3484.6	Standard polar	33892256
5-(1H-Indol-3-ylmethyl)-3-methyl-2-thioxo-4-Imidazolidinone,1TMS,isomer #2	CN1C(=O)C(CC2=CN([Si](C)(C)C)C3=CC=CC=C23)NC1=S	2760.2	Semi standard non polar	33892256
5-(1H-Indol-3-ylmethyl)-3-methyl-2-thioxo-4-Imidazolidinone,1TMS,isomer #2	CN1C(=O)C(CC2=CN([Si](C)(C)C)C3=CC=CC=C23)NC1=S	2649.2	Standard non polar	33892256
5-(1H-Indol-3-ylmethyl)-3-methyl-2-thioxo-4-Imidazolidinone,1TMS,isomer #2	CN1C(=O)C(CC2=CN([Si](C)(C)C)C3=CC=CC=C23)NC1=S	3981.7	Standard polar	33892256
5-(1H-Indol-3-ylmethyl)-3-methyl-2-thioxo-4-Imidazolidinone,2TMS,isomer #1	CN1C(=O)C(CC2=CN([Si](C)(C)C)C3=CC=CC=C23)N([Si](C)(C)C)C1=S	2639.6	Semi standard non polar	33892256
5-(1H-Indol-3-ylmethyl)-3-methyl-2-thioxo-4-Imidazolidinone,2TMS,isomer #1	CN1C(=O)C(CC2=CN([Si](C)(C)C)C3=CC=CC=C23)N([Si](C)(C)C)C1=S	2628.1	Standard non polar	33892256
5-(1H-Indol-3-ylmethyl)-3-methyl-2-thioxo-4-Imidazolidinone,2TMS,isomer #1	CN1C(=O)C(CC2=CN([Si](C)(C)C)C3=CC=CC=C23)N([Si](C)(C)C)C1=S	3261.0	Standard polar	33892256
5-(1H-Indol-3-ylmethyl)-3-methyl-2-thioxo-4-Imidazolidinone,1TBDMS,isomer #1	CN1C(=O)C(CC2=C[NH]C3=CC=CC=C23)N([Si](C)(C)C(C)(C)C)C1=S	2924.5	Semi standard non polar	33892256
5-(1H-Indol-3-ylmethyl)-3-methyl-2-thioxo-4-Imidazolidinone,1TBDMS,isomer #1	CN1C(=O)C(CC2=C[NH]C3=CC=CC=C23)N([Si](C)(C)C(C)(C)C)C1=S	2757.6	Standard non polar	33892256
5-(1H-Indol-3-ylmethyl)-3-methyl-2-thioxo-4-Imidazolidinone,1TBDMS,isomer #1	CN1C(=O)C(CC2=C[NH]C3=CC=CC=C23)N([Si](C)(C)C(C)(C)C)C1=S	3548.9	Standard polar	33892256
5-(1H-Indol-3-ylmethyl)-3-methyl-2-thioxo-4-Imidazolidinone,1TBDMS,isomer #2	CN1C(=O)C(CC2=CN([Si](C)(C)C(C)(C)C)C3=CC=CC=C23)NC1=S	2981.0	Semi standard non polar	33892256
5-(1H-Indol-3-ylmethyl)-3-methyl-2-thioxo-4-Imidazolidinone,1TBDMS,isomer #2	CN1C(=O)C(CC2=CN([Si](C)(C)C(C)(C)C)C3=CC=CC=C23)NC1=S	2877.3	Standard non polar	33892256
5-(1H-Indol-3-ylmethyl)-3-methyl-2-thioxo-4-Imidazolidinone,1TBDMS,isomer #2	CN1C(=O)C(CC2=CN([Si](C)(C)C(C)(C)C)C3=CC=CC=C23)NC1=S	4016.9	Standard polar	33892256
5-(1H-Indol-3-ylmethyl)-3-methyl-2-thioxo-4-Imidazolidinone,2TBDMS,isomer #1	CN1C(=O)C(CC2=CN([Si](C)(C)C(C)(C)C)C3=CC=CC=C23)N([Si](C)(C)C(C)(C)C)C1=S	3057.7	Semi standard non polar	33892256
5-(1H-Indol-3-ylmethyl)-3-methyl-2-thioxo-4-Imidazolidinone,2TBDMS,isomer #1	CN1C(=O)C(CC2=CN([Si](C)(C)C(C)(C)C)C3=CC=CC=C23)N([Si](C)(C)C(C)(C)C)C1=S	3071.2	Standard non polar	33892256
5-(1H-Indol-3-ylmethyl)-3-methyl-2-thioxo-4-Imidazolidinone,2TBDMS,isomer #1	CN1C(=O)C(CC2=CN([Si](C)(C)C(C)(C)C)C3=CC=CC=C23)N([Si](C)(C)C(C)(C)C)C1=S	3363.5	Standard polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted GC-MS	Predicted GC-MS Spectrum - 5-(1H-Indol-3-ylmethyl)-3-methyl-2-thioxo-4-Imidazolidinone GC-MS (Non-derivatized) - 70eV, Positive	splash10-009x-7950000000-cc2aff166ef756220247	2021-09-23	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 5-(1H-Indol-3-ylmethyl)-3-methyl-2-thioxo-4-Imidazolidinone GC-MS (Non-derivatized) - 70eV, Positive	Not Available	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

2106293

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

Not Available

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-(1H-Indol-3-ylmethyl)-3-methyl-2-thioxo-4-Imidazolidinone (HMDB0255500)

MOL for HMDB0255500 (5-(1H-Indol-3-ylmethyl)-3-methyl-2-thioxo-4-Imidazolidinone)

3D MOL for HMDB0255500 (5-(1H-Indol-3-ylmethyl)-3-methyl-2-thioxo-4-Imidazolidinone)

3D SDF for HMDB0255500 (5-(1H-Indol-3-ylmethyl)-3-methyl-2-thioxo-4-Imidazolidinone)

3D-SDF for HMDB0255500 (5-(1H-Indol-3-ylmethyl)-3-methyl-2-thioxo-4-Imidazolidinone)

PDB for HMDB0255500 (5-(1H-Indol-3-ylmethyl)-3-methyl-2-thioxo-4-Imidazolidinone)

3D PDB for HMDB0255500 (5-(1H-Indol-3-ylmethyl)-3-methyl-2-thioxo-4-Imidazolidinone)

SMILES for HMDB0255500 (5-(1H-Indol-3-ylmethyl)-3-methyl-2-thioxo-4-Imidazolidinone)

INCHI for HMDB0255500 (5-(1H-Indol-3-ylmethyl)-3-methyl-2-thioxo-4-Imidazolidinone)

Structure for HMDB0255500 (5-(1H-Indol-3-ylmethyl)-3-methyl-2-thioxo-4-Imidazolidinone)

3D Structure for HMDB0255500 (5-(1H-Indol-3-ylmethyl)-3-methyl-2-thioxo-4-Imidazolidinone)

Predicted Collision Cross Sections

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra