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Showing metabocard for Thiocyclam (HMDB0259009)

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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2021-09-11 20:54:28 UTC
Update Date2021-09-26 23:16:17 UTC
HMDB IDHMDB0259009
Secondary Accession NumbersNone
Metabolite Identification
Common NameThiocyclam
DescriptionThiocyclam, also known as evisect, belongs to the class of organic compounds known as trithianes. These are organic compounds containing a six-member aliphatic saturated heterocycle made up of three sulfur atoms and three carbon atoms. Based on a literature review a significant number of articles have been published on Thiocyclam. This compound has been identified in human blood as reported by (PMID: 31557052 ). Thiocyclam is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically Thiocyclam 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
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0259009 (Thiocyclam)


  Mrv1652309112122542D          

  9  9  0  0  0  0            999 V2000
    0.0000    2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    2.0625    0.0000 N   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
    0.7145    1.2375    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
    1.4289   -0.0000    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 S   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
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  2  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  4  9  1  0  0  0  0
M  END
Download

3D MOL for HMDB0259009 (Thiocyclam)

HMDB0259009
     RDKit          3D
Thiocyclam
 20 20  0  0  0  0  0  0  0  0999 V2000
   -1.2236    1.3792    0.5788 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5224    0.1138    0.6048 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5781   -0.9006    0.6359 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2573   -0.0136   -0.6119 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3082    1.0289   -0.7453 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3499    1.2347    0.7076 S   0  0  0  0  0  0  0  0  0  0  0  0
    2.8219   -0.6303    1.6000 S   0  0  0  0  0  0  0  0  0  0  0  0
    1.4302   -2.0581    0.8264 S   0  0  0  0  0  0  0  0  0  0  0  0
    0.8532   -1.3820   -0.7656 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5545    2.2522    0.5941 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8094    1.4321    1.5275 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9625    1.4127   -0.2529 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2274   -1.8942    0.9257 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1352   -0.8507   -0.3183 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3005   -0.5624    1.4292 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4656    0.1206   -1.4504 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8263    1.9714   -1.0444 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9925    0.7217   -1.5720 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7584   -1.2758   -1.3952 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1815   -2.0996   -1.2738 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  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  9  4  1  0
  1 10  1  0
  1 11  1  0
  1 12  1  0
  3 13  1  0
  3 14  1  0
  3 15  1  0
  4 16  1  0
  5 17  1  0
  5 18  1  0
  9 19  1  0
  9 20  1  0
M  END
Download

3D SDF for HMDB0259009 (Thiocyclam)


  Mrv1652309112122542D          

  9  9  0  0  0  0            999 V2000
    0.0000    2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    2.0625    0.0000 N   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
    0.7145    1.2375    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
    1.4289   -0.0000    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 S   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
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  2  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  4  9  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0259009

> <DATABASE_NAME>
hmdb

> <SMILES>
CN(C)C1CSSSC1

> <INCHI_IDENTIFIER>
InChI=1S/C5H11NS3/c1-6(2)5-3-7-9-8-4-5/h5H,3-4H2,1-2H3

> <INCHI_KEY>
DNVLJEWNNDHELH-UHFFFAOYSA-N

> <FORMULA>
C5H11NS3

> <MOLECULAR_WEIGHT>
181.33

> <EXACT_MASS>
181.00536288

> <JCHEM_ACCEPTOR_COUNT>
1

> <JCHEM_ATOM_COUNT>
20

> <JCHEM_AVERAGE_POLARIZABILITY>
18.5916103040057

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
N,N-dimethyl-1,2,3-trithian-5-amine

> <ALOGPS_LOGP>
1.34

> <JCHEM_LOGP>
1.3424894573333335

> <ALOGPS_LOGS>
-1.58

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA_STRONGEST_BASIC>
8.07245377906516

> <JCHEM_POLAR_SURFACE_AREA>
3.24

> <JCHEM_REFRACTIVITY>
48.7885

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
4.73e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
thiocyclam

> <JCHEM_VEBER_RULE>
1

$$$$
Download

3D-SDF for HMDB0259009 (Thiocyclam)

HMDB0259009
     RDKit          3D
Thiocyclam
 20 20  0  0  0  0  0  0  0  0999 V2000
   -1.2236    1.3792    0.5788 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5224    0.1138    0.6048 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5781   -0.9006    0.6359 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2573   -0.0136   -0.6119 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3082    1.0289   -0.7453 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3499    1.2347    0.7076 S   0  0  0  0  0  0  0  0  0  0  0  0
    2.8219   -0.6303    1.6000 S   0  0  0  0  0  0  0  0  0  0  0  0
    1.4302   -2.0581    0.8264 S   0  0  0  0  0  0  0  0  0  0  0  0
    0.8532   -1.3820   -0.7656 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5545    2.2522    0.5941 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8094    1.4321    1.5275 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9625    1.4127   -0.2529 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2274   -1.8942    0.9257 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1352   -0.8507   -0.3183 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3005   -0.5624    1.4292 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4656    0.1206   -1.4504 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8263    1.9714   -1.0444 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9925    0.7217   -1.5720 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7584   -1.2758   -1.3952 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1815   -2.0996   -1.2738 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  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  9  4  1  0
  1 10  1  0
  1 11  1  0
  1 12  1  0
  3 13  1  0
  3 14  1  0
  3 15  1  0
  4 16  1  0
  5 17  1  0
  5 18  1  0
  9 19  1  0
  9 20  1  0
M  END
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PDB for HMDB0259009 (Thiocyclam)

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       0.000   4.620   0.000  0.00  0.00           C+0
HETATM    2  N   UNK     0       1.334   3.850   0.000  0.00  0.00           N+0
HETATM    3  C   UNK     0       2.667   4.620   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
HETATM    6  S   UNK     0       2.667  -0.000   0.000  0.00  0.00           S+0
HETATM    7  S   UNK     0       1.334  -0.770   0.000  0.00  0.00           S+0
HETATM    8  S   UNK     0       0.000   0.000   0.000  0.00  0.00           S+0
HETATM    9  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3    4                                                  
CONECT    3    2                                                            
CONECT    4    2    5    9                                                  
CONECT    5    4    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8    4                                                       
MASTER        0    0    0    0    0    0    0    0    9    0   18    0
END
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3D PDB for HMDB0259009 (Thiocyclam)

COMPND    HMDB0259009
HETATM    1  C1  UNL     1      -1.224   1.379   0.579  1.00  0.00           C  
HETATM    2  N1  UNL     1      -0.522   0.114   0.605  1.00  0.00           N  
HETATM    3  C2  UNL     1      -1.578  -0.901   0.636  1.00  0.00           C  
HETATM    4  C3  UNL     1       0.257  -0.014  -0.612  1.00  0.00           C  
HETATM    5  C4  UNL     1       1.308   1.029  -0.745  1.00  0.00           C  
HETATM    6  S1  UNL     1       2.350   1.235   0.708  1.00  0.00           S  
HETATM    7  S2  UNL     1       2.822  -0.630   1.600  1.00  0.00           S  
HETATM    8  S3  UNL     1       1.430  -2.058   0.826  1.00  0.00           S  
HETATM    9  C5  UNL     1       0.853  -1.382  -0.766  1.00  0.00           C  
HETATM   10  H1  UNL     1      -0.554   2.252   0.594  1.00  0.00           H  
HETATM   11  H2  UNL     1      -1.809   1.432   1.527  1.00  0.00           H  
HETATM   12  H3  UNL     1      -1.962   1.413  -0.253  1.00  0.00           H  
HETATM   13  H4  UNL     1      -1.227  -1.894   0.926  1.00  0.00           H  
HETATM   14  H5  UNL     1      -2.135  -0.851  -0.318  1.00  0.00           H  
HETATM   15  H6  UNL     1      -2.301  -0.562   1.429  1.00  0.00           H  
HETATM   16  H7  UNL     1      -0.466   0.121  -1.450  1.00  0.00           H  
HETATM   17  H8  UNL     1       0.826   1.971  -1.044  1.00  0.00           H  
HETATM   18  H9  UNL     1       1.992   0.722  -1.572  1.00  0.00           H  
HETATM   19  H10 UNL     1       1.758  -1.276  -1.395  1.00  0.00           H  
HETATM   20  H11 UNL     1       0.182  -2.100  -1.274  1.00  0.00           H  
CONECT    1    2   10   11   12
CONECT    2    3    4
CONECT    3   13   14   15
CONECT    4    5    9   16
CONECT    5    6   17   18
CONECT    6    7
CONECT    7    8
CONECT    8    9
CONECT    9   19   20
END
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SMILES for HMDB0259009 (Thiocyclam)

CN(C)C1CSSSC1
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INCHI for HMDB0259009 (Thiocyclam)

InChI=1S/C5H11NS3/c1-6(2)5-3-7-9-8-4-5/h5H,3-4H2,1-2H3
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View in JSmolView Stereo Labels
Synonyms
ValueSource
5-(Dimethylamino)-1,2,3-trithianeChEBI
N,N-Dimethyl-1,2,3-trithian-5-ylamineChEBI
ThiocyclameChEBI
EvisectKegg
N,N-Dimethyl-1,2,3-trithian-5-yl amineHMDB
N,N-Dimethyl-1,2,3-trithian-5-yl amine hydrogen oxalateHMDB
Chemical FormulaC5H11NS3
Average Molecular Weight181.33
Monoisotopic Molecular Weight181.00536288
IUPAC NameN,N-dimethyl-1,2,3-trithian-5-amine
Traditional Namethiocyclam
CAS Registry NumberNot Available
SMILES
CN(C)C1CSSSC1
InChI Identifier
InChI=1S/C5H11NS3/c1-6(2)5-3-7-9-8-4-5/h5H,3-4H2,1-2H3
InChI KeyDNVLJEWNNDHELH-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as trithianes. These are organic compounds containing a six-member aliphatic saturated heterocycle made up of three sulfur atoms and three carbon atoms.
KingdomOrganic compounds
Super ClassOrganoheterocyclic compounds
ClassTrithianes
Sub ClassNot Available
Direct ParentTrithianes
Alternative Parents
Substituents
  • Trithiane
  • Organic trisulfide
  • Tertiary aliphatic amine
  • Tertiary amine
  • Organic nitrogen compound
  • Organopnictogen compound
  • Hydrocarbon derivative
  • Organonitrogen compound
  • Amine
  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic heteromonocyclic compounds
External Descriptors
Ontology
Physiological effectNot Available
Disposition
Biological locationSource
ProcessNot Available
RoleNot Available
Physical Properties
StateNot Available
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
logP1.34ALOGPS
logP1.34ChemAxon
logS-1.6ALOGPS
pKa (Strongest Basic)8.07ChemAxon
Physiological Charge1ChemAxon
Hydrogen Acceptor Count1ChemAxon
Hydrogen Donor Count0ChemAxon
Polar Surface Area3.24 ŲChemAxon
Rotatable Bond Count1ChemAxon
Refractivity48.79 m³·mol⁻¹ChemAxon
Polarizability18.59 ųChemAxon
Number of Rings1ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
DeepCCS[M+H]+136.36130932474
DeepCCS[M-H]-134.09930932474
DeepCCS[M-2H]-170.23130932474
DeepCCS[M+Na]+145.31330932474
AllCCS[M+H]+134.032859911
AllCCS[M+H-H2O]+129.832859911
AllCCS[M+NH4]+137.832859911
AllCCS[M+Na]+139.032859911
AllCCS[M-H]-137.232859911
AllCCS[M+Na-2H]-139.532859911
AllCCS[M+HCOO]-142.032859911

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
ThiocyclamCN(C)C1CSSSC12196.5Standard polar33892256
ThiocyclamCN(C)C1CSSSC11486.1Standard non polar33892256
ThiocyclamCN(C)C1CSSSC11508.9Semi standard non polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - Thiocyclam GC-MS (Non-derivatized) - 70eV, Positivesplash10-000f-9800000000-b56a6c1db12afc63b42c2021-09-24Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Thiocyclam GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart LabView Spectrum

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Experimental LC-MS/MSLC-MS/MS Spectrum - Thiocyclam 40V, Positive-QTOFsplash10-000i-0900000000-8af56486cafa579e3eaa2021-09-20HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Thiocyclam 30V, Positive-QTOFsplash10-000i-0900000000-f7e07b709d76afcf38572021-09-20HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Thiocyclam 10V, Positive-QTOFsplash10-001i-0900000000-07ed08fd99e35ab650a12021-09-20HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Thiocyclam 20V, Positive-QTOFsplash10-000i-0900000000-ea127cc7eba9fb6c64872021-09-20HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Thiocyclam 20V, Positive-QTOFsplash10-000i-0900000000-3a6f76dbbea7bafe04152021-09-20HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Thiocyclam 10V, Positive-QTOFsplash10-001i-0900000000-37478fc2ed30c4542cb12021-09-20HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Thiocyclam 30V, Positive-QTOFsplash10-000i-0900000000-40ef09ae20841dd5116b2021-09-20HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Thiocyclam 40V, Positive-QTOFsplash10-000i-0900000000-1fe1c0608e1f121f4e862021-09-20HMDB team, MONAView Spectrum
Biological Properties
Cellular LocationsNot Available
Biospecimen Locations
  • Blood
Tissue LocationsNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodDetected but not QuantifiedNot QuantifiedNot SpecifiedNot SpecifiedNormal details
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDNot Available
KNApSAcK IDNot Available
Chemspider ID33084
KEGG Compound IDC11473
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNereistoxin
METLIN IDNot Available
PubChem Compound35970
PDB IDNot Available
ChEBI ID4947
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General References
  1. 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 ]