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Showing metabocard for Methylene dithiocyanate (HMDB0254635)

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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2021-09-11 14:01:05 UTC
Update Date2021-09-26 23:08:45 UTC
HMDB IDHMDB0254635
Secondary Accession NumbersNone
Metabolite Identification
Common NameMethylene dithiocyanate
DescriptionMethylene thiocyanate, also known as methylenedirhodanid or CH2(SCN)2, belongs to the class of organic compounds known as dithioacetals. Dithioacetals are compounds containing a dithioacetal functional group with the general structure R2C(SR')2. Based on a literature review very few articles have been published on Methylene thiocyanate. This compound has been identified in human blood as reported by (PMID: 31557052 ). Methylene dithiocyanate is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically Methylene dithiocyanate 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 HMDB0254635 (Methylene dithiocyanate)


  Mrv0541 02241204362D          

  7  6  0  0  0  0            999 V2000
    1.7605   -1.0164    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.4750   -1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1895   -1.8414    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
    3.9039   -1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6184   -1.8414    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
    5.3329   -1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.0474   -1.0164    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  3  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
  5  6  1  0  0  0  0
  6  7  3  0  0  0  0
M  END
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3D MOL for HMDB0254635 (Methylene dithiocyanate)

HMDB0254635
     RDKit          3D
Methylene dithiocyanate
  9  8  0  0  0  0  0  0  0  0999 V2000
    3.5698    0.7481   -0.8925 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.5149    0.7372   -0.4147 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9098    0.7398    0.3123 S   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0003   -0.7785   -0.1034 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6323   -0.7539    0.6472 S   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6390    0.5220   -0.0554 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3049    1.3669   -0.4982 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.6107   -1.6106    0.3299 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0287   -0.9709   -1.1899 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  3  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  3  0
  4  8  1  0
  4  9  1  0
M  END
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3D SDF for HMDB0254635 (Methylene dithiocyanate)


  Mrv0541 02241204362D          

  7  6  0  0  0  0            999 V2000
    1.7605   -1.0164    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.4750   -1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1895   -1.8414    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
    3.9039   -1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6184   -1.8414    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
    5.3329   -1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.0474   -1.0164    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  3  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
  5  6  1  0  0  0  0
  6  7  3  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0254635

> <DATABASE_NAME>
hmdb

> <SMILES>
N#CSCSC#N

> <INCHI_IDENTIFIER>
InChI=1S/C3H2N2S2/c4-1-6-3-7-2-5/h3H2

> <INCHI_KEY>
JWZXKXIUSSIAMR-UHFFFAOYSA-N

> <FORMULA>
C3H2N2S2

> <MOLECULAR_WEIGHT>
130.191

> <EXACT_MASS>
129.965939454

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_AVERAGE_POLARIZABILITY>
11.84633545281082

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
{[(cyanosulfanyl)methyl]sulfanyl}carbonitrile

> <ALOGPS_LOGP>
0.39

> <JCHEM_LOGP>
1.155578425

> <ALOGPS_LOGS>
-1.38

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_POLAR_SURFACE_AREA>
47.58

> <JCHEM_REFRACTIVITY>
33.2205

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
5.44e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
methylene bisthiocyanate

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for HMDB0254635 (Methylene dithiocyanate)

HMDB0254635
     RDKit          3D
Methylene dithiocyanate
  9  8  0  0  0  0  0  0  0  0999 V2000
    3.5698    0.7481   -0.8925 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.5149    0.7372   -0.4147 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9098    0.7398    0.3123 S   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0003   -0.7785   -0.1034 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6323   -0.7539    0.6472 S   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6390    0.5220   -0.0554 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3049    1.3669   -0.4982 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.6107   -1.6106    0.3299 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0287   -0.9709   -1.1899 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  3  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  3  0
  4  8  1  0
  4  9  1  0
M  END
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PDB for HMDB0254635 (Methylene dithiocyanate)

HEADER    PROTEIN                                 24-FEB-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-FEB-12         0                                  
HETATM    1  N   UNK     0       3.286  -1.897   0.000  0.00  0.00           N+0
HETATM    2  C   UNK     0       4.620  -2.667   0.000  0.00  0.00           C+0
HETATM    3  S   UNK     0       5.954  -3.437   0.000  0.00  0.00           S+0
HETATM    4  C   UNK     0       7.287  -2.667   0.000  0.00  0.00           C+0
HETATM    5  S   UNK     0       8.621  -3.437   0.000  0.00  0.00           S+0
HETATM    6  C   UNK     0       9.955  -2.667   0.000  0.00  0.00           C+0
HETATM    7  N   UNK     0      11.288  -1.897   0.000  0.00  0.00           N+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6                                                            
MASTER        0    0    0    0    0    0    0    0    7    0   12    0
END
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3D PDB for HMDB0254635 (Methylene dithiocyanate)

COMPND    HMDB0254635
HETATM    1  N1  UNL     1       3.570   0.748  -0.892  1.00  0.00           N  
HETATM    2  C1  UNL     1       2.515   0.737  -0.415  1.00  0.00           C  
HETATM    3  S1  UNL     1       0.910   0.740   0.312  1.00  0.00           S  
HETATM    4  C2  UNL     1      -0.000  -0.779  -0.103  1.00  0.00           C  
HETATM    5  S2  UNL     1      -1.632  -0.754   0.647  1.00  0.00           S  
HETATM    6  C3  UNL     1      -2.639   0.522  -0.055  1.00  0.00           C  
HETATM    7  N2  UNL     1      -3.305   1.367  -0.498  1.00  0.00           N  
HETATM    8  H1  UNL     1       0.611  -1.611   0.330  1.00  0.00           H  
HETATM    9  H2  UNL     1      -0.029  -0.971  -1.190  1.00  0.00           H  
CONECT    1    2    2    2
CONECT    2    3
CONECT    3    4
CONECT    4    5    8    9
CONECT    5    6
CONECT    6    7    7    7
END
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SMILES for HMDB0254635 (Methylene dithiocyanate)

N#CSCSC#N
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INCHI for HMDB0254635 (Methylene dithiocyanate)

InChI=1S/C3H2N2S2/c4-1-6-3-7-2-5/h3H2
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View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
ValueSource
CH2(SCN)2ChEBI
DithiocyanatomethaneChEBI
Methylene dithiocyanateChEBI
MethylenedirhodanidChEBI
MethylenedirhodanideChEBI
N-948 BiocideChEBI
Thiocyanic acid, C,c'-methylene esterChEBI
Thiocyanic acid, methylene esterChEBI
Methylene dithiocyanic acidGenerator
Thiocyanate, C,c'-methylene esterGenerator
Thiocyanate, methylene esterGenerator
Methylene thiocyanic acidGenerator
Methylene bis(thiocyanate)MeSH
Chemical FormulaC3H2N2S2
Average Molecular Weight130.191
Monoisotopic Molecular Weight129.965939454
IUPAC Name{[(cyanosulfanyl)methyl]sulfanyl}carbonitrile
Traditional Namemethylene bisthiocyanate
CAS Registry NumberNot Available
SMILES
N#CSCSC#N
InChI Identifier
InChI=1S/C3H2N2S2/c4-1-6-3-7-2-5/h3H2
InChI KeyJWZXKXIUSSIAMR-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as dithioacetals. Dithioacetals are compounds containing a dithioacetal functional group with the general structure R2C(SR')2.
KingdomOrganic compounds
Super ClassOrganosulfur compounds
ClassThioacetals
Sub ClassDithioacetals
Direct ParentDithioacetals
Alternative Parents
Substituents
  • Thioacetal
  • Sulfenyl compound
  • Thiocyanate
  • Organic nitrogen compound
  • Organopnictogen compound
  • Hydrocarbon derivative
  • Organonitrogen compound
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External DescriptorsNot Available
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
logP0.39ALOGPS
logP1.16ChemAxon
logS-1.4ALOGPS
Physiological Charge0ChemAxon
Hydrogen Acceptor Count2ChemAxon
Hydrogen Donor Count0ChemAxon
Polar Surface Area47.58 ŲChemAxon
Rotatable Bond Count2ChemAxon
Refractivity33.22 m³·mol⁻¹ChemAxon
Polarizability11.85 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
DeepCCS[M+H]+125.62630932474
DeepCCS[M-H]-123.7430932474
DeepCCS[M-2H]-159.21230932474
DeepCCS[M+Na]+133.20130932474
AllCCS[M+H]+125.132859911
AllCCS[M+H-H2O]+121.232859911
AllCCS[M+NH4]+128.732859911
AllCCS[M+Na]+129.732859911
AllCCS[M-H]-129.632859911
AllCCS[M+Na-2H]-133.532859911
AllCCS[M+HCOO]-137.732859911

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
Methylene dithiocyanateN#CSCSC#N1767.9Standard polar33892256
Methylene dithiocyanateN#CSCSC#N1224.8Standard non polar33892256
Methylene dithiocyanateN#CSCSC#N1358.0Semi standard non polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - Methylene dithiocyanate GC-MS (Non-derivatized) - 70eV, Positivesplash10-00b9-9700000000-74f42ea0595be421e3992021-09-24Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Methylene dithiocyanate GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart LabView Spectrum
MSMass Spectrum (Electron Ionization)splash10-00dj-9000000000-26b07e3e0d9988fb36552014-09-20Not AvailableView Spectrum

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Methylene dithiocyanate 10V, Positive-QTOFsplash10-001i-0900000000-60d19c27d26cdb1c3ee32016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Methylene dithiocyanate 20V, Positive-QTOFsplash10-0ue9-0900000000-9e41cbdcab631626f8a22016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Methylene dithiocyanate 40V, Positive-QTOFsplash10-0ufr-4900000000-41fd085775dfaa5713242016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Methylene dithiocyanate 10V, Negative-QTOFsplash10-004i-0900000000-8b0071fe7a797cbdcf4f2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Methylene dithiocyanate 20V, Negative-QTOFsplash10-004i-1900000000-8e1219fdff9c7be951882016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Methylene dithiocyanate 40V, Negative-QTOFsplash10-004i-9000000000-ee2e4592354a79b827212016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Methylene dithiocyanate 10V, Positive-QTOFsplash10-00di-9000000000-d8809234fd836ceed0072021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Methylene dithiocyanate 20V, Positive-QTOFsplash10-00di-9000000000-d8809234fd836ceed0072021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Methylene dithiocyanate 40V, Positive-QTOFsplash10-00di-9000000000-e7d743502878a38df7df2021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Methylene dithiocyanate 10V, Negative-QTOFsplash10-004i-0900000000-0e7b6ff1c9c56fbc506e2021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Methylene dithiocyanate 20V, Negative-QTOFsplash10-0a4i-9100000000-121b6ded5805fdc1d81d2021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Methylene dithiocyanate 40V, Negative-QTOFsplash10-0a4i-9000000000-286b63d3516de7d14a122021-10-12Wishart LabView Spectrum

NMR Spectra

Spectrum TypeDescriptionDeposition DateSourceView
Predicted 1D NMR13C NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-10-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-10-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-10-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-10-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-10-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-10-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-10-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-10-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-10-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-10-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-10-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-10-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-10-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-10-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-10-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-10-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-10-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-10-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-10-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-10-25Wishart 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 ID21349
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound22772
PDB IDNot Available
ChEBI ID134614
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDrw1260861
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 ]