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Showing metabocard for Pyrrolidine dithiocarbamate (HMDB0256998)

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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2021-09-11 17:38:57 UTC
Update Date2021-09-26 23:13:04 UTC
HMDB IDHMDB0256998
Secondary Accession NumbersNone
Metabolite Identification
Common NamePyrrolidine dithiocarbamate
Descriptionpyrrolidine dithiocarbamate, also known as 1-pyrrolidinecarbodithioic acid or tetramethylenedithiocarbamate, belongs to the class of organic compounds known as pyrrolidines. Pyrrolidines are compounds containing a pyrrolidine ring, which is a five-membered saturated aliphatic heterocycle with one nitrogen atom and four carbon atoms. Based on a literature review a significant number of articles have been published on pyrrolidine dithiocarbamate. This compound has been identified in human blood as reported by (PMID: 31557052 ). Pyrrolidine dithiocarbamate is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically Pyrrolidine dithiocarbamate 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 HMDB0256998 (Pyrrolidine dithiocarbamate)


  Mrv1652309112119392D          

  8  8  0  0  0  0            999 V2000
    0.9803   -0.1553    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1553   -0.1553    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0997    0.6294    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5678    1.1143    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.2352    0.6294    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5678    1.9393    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1467    2.3518    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
    1.2822    2.3518    0.0000 S   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  1  0  0  0  0
  4  5  1  0  0  0  0
  1  5  1  0  0  0  0
  4  6  1  0  0  0  0
  6  7  2  0  0  0  0
  6  8  1  0  0  0  0
M  END
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3D MOL for HMDB0256998 (Pyrrolidine dithiocarbamate)

HMDB0256998
     RDKit          3D
Pyrrolidine dithiocarbamate
 17 17  0  0  0  0  0  0  0  0999 V2000
    2.5573    1.6542   -1.2605 S   0  0  0  0  0  0  0  0  0  0  0  0
    1.9163    0.7720   -0.0273 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9492    0.4082    1.3800 S   0  0  0  0  0  0  0  0  0  0  0  0
    0.5803    0.3108   -0.0760 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0472   -0.4665    0.9671 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4744   -0.6536    0.6049 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6532   -0.0202   -0.7564 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3383    0.5509   -1.1691 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5562   -0.8459    1.1330 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4510   -1.4685    1.0284 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1188    0.0289    1.9423 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7322   -1.7326    0.5268 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1102   -0.2103    1.3764 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4439    0.7546   -0.6708 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9595   -0.7728   -1.5312 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0720    0.0414   -2.0785 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4422    1.6495   -1.3892 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  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  4  1  0
  3  9  1  0
  5 10  1  0
  5 11  1  0
  6 12  1  0
  6 13  1  0
  7 14  1  0
  7 15  1  0
  8 16  1  0
  8 17  1  0
M  END
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3D SDF for HMDB0256998 (Pyrrolidine dithiocarbamate)


  Mrv1652309112119392D          

  8  8  0  0  0  0            999 V2000
    0.9803   -0.1553    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1553   -0.1553    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0997    0.6294    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5678    1.1143    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.2352    0.6294    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5678    1.9393    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1467    2.3518    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
    1.2822    2.3518    0.0000 S   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  1  0  0  0  0
  4  5  1  0  0  0  0
  1  5  1  0  0  0  0
  4  6  1  0  0  0  0
  6  7  2  0  0  0  0
  6  8  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0256998

> <DATABASE_NAME>
hmdb

> <SMILES>
SC(=S)N1CCCC1

> <INCHI_IDENTIFIER>
InChI=1S/C5H9NS2/c7-5(8)6-3-1-2-4-6/h1-4H2,(H,7,8)

> <INCHI_KEY>
VSWDORGPIHIGNW-UHFFFAOYSA-N

> <FORMULA>
C5H9NS2

> <MOLECULAR_WEIGHT>
147.25

> <EXACT_MASS>
147.017641642

> <JCHEM_ACCEPTOR_COUNT>
0

> <JCHEM_ATOM_COUNT>
17

> <JCHEM_AVERAGE_POLARIZABILITY>
15.617636016772188

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
pyrrolidine-1-carbodithioic acid

> <ALOGPS_LOGP>
2.44

> <JCHEM_LOGP>
1.6996422873333332

> <ALOGPS_LOGS>
-2.86

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.9998467935469488

> <JCHEM_POLAR_SURFACE_AREA>
3.24

> <JCHEM_REFRACTIVITY>
43.0595

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.03e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
pyrrolidine dithiocarbamate

> <JCHEM_VEBER_RULE>
1

$$$$
Download

3D-SDF for HMDB0256998 (Pyrrolidine dithiocarbamate)

HMDB0256998
     RDKit          3D
Pyrrolidine dithiocarbamate
 17 17  0  0  0  0  0  0  0  0999 V2000
    2.5573    1.6542   -1.2605 S   0  0  0  0  0  0  0  0  0  0  0  0
    1.9163    0.7720   -0.0273 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9492    0.4082    1.3800 S   0  0  0  0  0  0  0  0  0  0  0  0
    0.5803    0.3108   -0.0760 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0472   -0.4665    0.9671 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4744   -0.6536    0.6049 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6532   -0.0202   -0.7564 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3383    0.5509   -1.1691 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5562   -0.8459    1.1330 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4510   -1.4685    1.0284 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1188    0.0289    1.9423 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7322   -1.7326    0.5268 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1102   -0.2103    1.3764 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4439    0.7546   -0.6708 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9595   -0.7728   -1.5312 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0720    0.0414   -2.0785 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4422    1.6495   -1.3892 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  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  4  1  0
  3  9  1  0
  5 10  1  0
  5 11  1  0
  6 12  1  0
  6 13  1  0
  7 14  1  0
  7 15  1  0
  8 16  1  0
  8 17  1  0
M  END
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PDB for HMDB0256998 (Pyrrolidine dithiocarbamate)

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       1.830  -0.290   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.290  -0.290   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -0.186   1.175   0.000  0.00  0.00           C+0
HETATM    4  N   UNK     0       1.060   2.080   0.000  0.00  0.00           N+0
HETATM    5  C   UNK     0       2.306   1.175   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       1.060   3.620   0.000  0.00  0.00           C+0
HETATM    7  S   UNK     0      -0.274   4.390   0.000  0.00  0.00           S+0
HETATM    8  S   UNK     0       2.393   4.390   0.000  0.00  0.00           S+0
CONECT    1    2    5                                                       
CONECT    2    1    3                                                       
CONECT    3    2    4                                                       
CONECT    4    3    5    6                                                  
CONECT    5    4    1                                                       
CONECT    6    4    7    8                                                  
CONECT    7    6                                                            
CONECT    8    6                                                            
MASTER        0    0    0    0    0    0    0    0    8    0   16    0
END
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3D PDB for HMDB0256998 (Pyrrolidine dithiocarbamate)

COMPND    HMDB0256998
HETATM    1  S1  UNL     1       2.557   1.654  -1.260  1.00  0.00           S  
HETATM    2  C1  UNL     1       1.916   0.772  -0.027  1.00  0.00           C  
HETATM    3  S2  UNL     1       2.949   0.408   1.380  1.00  0.00           S  
HETATM    4  N1  UNL     1       0.580   0.311  -0.076  1.00  0.00           N  
HETATM    5  C2  UNL     1      -0.047  -0.467   0.967  1.00  0.00           C  
HETATM    6  C3  UNL     1      -1.474  -0.654   0.605  1.00  0.00           C  
HETATM    7  C4  UNL     1      -1.653  -0.020  -0.756  1.00  0.00           C  
HETATM    8  C5  UNL     1      -0.338   0.551  -1.169  1.00  0.00           C  
HETATM    9  H1  UNL     1       3.556  -0.846   1.133  1.00  0.00           H  
HETATM   10  H2  UNL     1       0.451  -1.468   1.028  1.00  0.00           H  
HETATM   11  H3  UNL     1       0.119   0.029   1.942  1.00  0.00           H  
HETATM   12  H4  UNL     1      -1.732  -1.733   0.527  1.00  0.00           H  
HETATM   13  H5  UNL     1      -2.110  -0.210   1.376  1.00  0.00           H  
HETATM   14  H6  UNL     1      -2.444   0.755  -0.671  1.00  0.00           H  
HETATM   15  H7  UNL     1      -1.960  -0.773  -1.531  1.00  0.00           H  
HETATM   16  H8  UNL     1       0.072   0.041  -2.079  1.00  0.00           H  
HETATM   17  H9  UNL     1      -0.442   1.650  -1.389  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3    4
CONECT    3    9
CONECT    4    5    8
CONECT    5    6   10   11
CONECT    6    7   12   13
CONECT    7    8   14   15
CONECT    8   16   17
END
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SMILES for HMDB0256998 (Pyrrolidine dithiocarbamate)

SC(=S)N1CCCC1
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INCHI for HMDB0256998 (Pyrrolidine dithiocarbamate)

InChI=1S/C5H9NS2/c7-5(8)6-3-1-2-4-6/h1-4H2,(H,7,8)
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View in JSmolView Stereo Labels
Synonyms
ValueSource
1-Pyrrolidinecarbodithioic acidChEBI
Pyrrolidine dithiocarbamic acidChEBI
Pyrrolidine-N-carbodithioic acidChEBI
Tetramethylenedithiocarbamic acidChEBI
1-PyrrolidinecarbodithioateGenerator
Pyrrolidine-N-carbodithioateGenerator
TetramethylenedithiocarbamateGenerator
PyrrolidinedithiocarbamateMeSH
Ammonium pyrrolidine dithiocarbamateMeSH
Ammonium tetramethylene dithiocarbamateMeSH
Pyrrolidine dithiocarbamic acid, ammonium saltMeSH
Pyrrolidine dithiocarbamic acid, sodium saltMeSH
Chemical FormulaC5H9NS2
Average Molecular Weight147.25
Monoisotopic Molecular Weight147.017641642
IUPAC Namepyrrolidine-1-carbodithioic acid
Traditional Namepyrrolidine dithiocarbamate
CAS Registry NumberNot Available
SMILES
SC(=S)N1CCCC1
InChI Identifier
InChI=1S/C5H9NS2/c7-5(8)6-3-1-2-4-6/h1-4H2,(H,7,8)
InChI KeyVSWDORGPIHIGNW-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as pyrrolidines. Pyrrolidines are compounds containing a pyrrolidine ring, which is a five-membered saturated aliphatic heterocycle with one nitrogen atom and four carbon atoms.
KingdomOrganic compounds
Super ClassOrganoheterocyclic compounds
ClassPyrrolidines
Sub ClassNot Available
Direct ParentPyrrolidines
Alternative Parents
Substituents
  • Pyrrolidine
  • Azacycle
  • Organic nitrogen compound
  • Organopnictogen compound
  • Hydrocarbon derivative
  • Organosulfur compound
  • Organonitrogen compound
  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic heteromonocyclic compounds
External Descriptors
Ontology
Physiological effectNot Available
Disposition
Biological location
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
logP2.44ALOGPS
logP1.7ChemAxon
logS-2.9ALOGPS
pKa (Strongest Acidic)2ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count0ChemAxon
Hydrogen Donor Count1ChemAxon
Polar Surface Area3.24 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity43.06 m³·mol⁻¹ChemAxon
Polarizability15.62 ųChemAxon
Number of Rings1ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
DeepCCS[M+H]+131.08130932474
DeepCCS[M-H]-128.86830932474
DeepCCS[M-2H]-164.94130932474
DeepCCS[M+Na]+139.86330932474
AllCCS[M+H]+128.932859911
AllCCS[M+H-H2O]+124.432859911
AllCCS[M+NH4]+133.132859911
AllCCS[M+Na]+134.332859911
AllCCS[M-H]-131.432859911
AllCCS[M+Na-2H]-134.132859911
AllCCS[M+HCOO]-137.232859911

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
Pyrrolidine dithiocarbamateSC(=S)N1CCCC12200.8Standard polar33892256
Pyrrolidine dithiocarbamateSC(=S)N1CCCC11368.9Standard non polar33892256
Pyrrolidine dithiocarbamateSC(=S)N1CCCC11742.3Semi standard non polar33892256

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
Pyrrolidine dithiocarbamate,1TMS,isomer #1C[Si](C)(C)SC(=S)N1CCCC11581.7Semi standard non polar33892256
Pyrrolidine dithiocarbamate,1TMS,isomer #1C[Si](C)(C)SC(=S)N1CCCC11510.0Standard non polar33892256
Pyrrolidine dithiocarbamate,1TMS,isomer #1C[Si](C)(C)SC(=S)N1CCCC12027.9Standard polar33892256
Pyrrolidine dithiocarbamate,1TBDMS,isomer #1CC(C)(C)[Si](C)(C)SC(=S)N1CCCC11808.3Semi standard non polar33892256
Pyrrolidine dithiocarbamate,1TBDMS,isomer #1CC(C)(C)[Si](C)(C)SC(=S)N1CCCC11776.4Standard non polar33892256
Pyrrolidine dithiocarbamate,1TBDMS,isomer #1CC(C)(C)[Si](C)(C)SC(=S)N1CCCC12197.1Standard polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - Pyrrolidine dithiocarbamate GC-MS (Non-derivatized) - 70eV, Positivesplash10-01t9-9300000000-1f875eb055c2591d589d2021-09-23Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Pyrrolidine dithiocarbamate GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart LabView 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 ID58828
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkPyrrolidine_dithiocarbamate
METLIN IDNot Available
PubChem CompoundNot Available
PDB IDNot Available
ChEBI ID78782
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 ]