Hmdb loader

Showing metabocard for 1,2,4,5,7-Pentathiocane (HMDB0039431)

Jump To Section:
IdentificationTaxonomyOntologyPhysical propertiesSpectraBiological propertiesConcentrationsLinksReferencesXML
Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2012-09-12 00:53:40 UTC
Update Date2023-02-21 17:26:57 UTC
HMDB IDHMDB0039431
Secondary Accession Numbers
  • HMDB39431
Metabolite Identification
Common Name1,2,4,5,7-Pentathiocane
Description1,2,4,5,7-Pentathiocane belongs to the class of organic compounds known as organic disulfides. These are organosulfur compounds with the general formula RSSR' (R,R' = alkyl, aryl). 1,2,4,5,7-Pentathiocane has been detected, but not quantified in, several different foods, such as common mushrooms (Agaricus bisporus), green vegetables, mushrooms, oyster mushrooms (Pleurotus ostreatus), and pulses. This could make 1,2,4,5,7-pentathiocane a potential biomarker for the consumption of these foods. Based on a literature review very few articles have been published on 1,2,4,5,7-Pentathiocane.
Structure
Data?1677000417
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0039431 (1,2,4,5,7-Pentathiocane)


  Mrv0541 05061311082D          

  8  8  0  0  0  0            999 V2000
    1.7581    1.1747    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2337    1.1747    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9959   -0.6654    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9959    1.4904    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
    2.0738    0.4125    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0821    0.4125    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
    1.7581   -0.3497    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
    0.2337   -0.3497    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
  4  1  1  0  0  0  0
  4  2  1  0  0  0  0
  5  1  1  0  0  0  0
  6  2  1  0  0  0  0
  7  3  1  0  0  0  0
  7  5  1  0  0  0  0
  8  3  1  0  0  0  0
  8  6  1  0  0  0  0
M  END
Download

3D MOL for HMDB0039431 (1,2,4,5,7-Pentathiocane)

HMDB0039431
     RDKit          3D
1,2,4,5,7-Pentathiocane
 14 14  0  0  0  0  0  0  0  0999 V2000
   -2.0578    0.9636   -0.5562 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3567   -0.7667   -0.0579 S   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7819   -1.3751    0.6463 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2838   -1.9547   -0.6630 S   0  0  0  0  0  0  0  0  0  0  0  0
    2.1797   -1.1350   -0.7179 S   0  0  0  0  0  0  0  0  0  0  0  0
    2.4002    0.4215    0.1013 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0219    1.5362    0.0182 S   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4401    0.9890   -1.4038 S   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0045    1.5529    0.3953 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8646    1.3481   -1.1815 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0714   -2.1974    1.3503 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2775   -0.5652    1.2015 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6562    0.2497    1.1823 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3127    0.9331   -0.3150 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  8  1  1  0
  1  9  1  0
  1 10  1  0
  3 11  1  0
  3 12  1  0
  6 13  1  0
  6 14  1  0
M  END
Download

3D SDF for HMDB0039431 (1,2,4,5,7-Pentathiocane)


  Mrv0541 05061311082D          

  8  8  0  0  0  0            999 V2000
    1.7581    1.1747    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2337    1.1747    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9959   -0.6654    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9959    1.4904    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
    2.0738    0.4125    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0821    0.4125    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
    1.7581   -0.3497    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
    0.2337   -0.3497    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
  4  1  1  0  0  0  0
  4  2  1  0  0  0  0
  5  1  1  0  0  0  0
  6  2  1  0  0  0  0
  7  3  1  0  0  0  0
  7  5  1  0  0  0  0
  8  3  1  0  0  0  0
  8  6  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0039431

> <DATABASE_NAME>
hmdb

> <SMILES>
C1SCSSCSS1

> <INCHI_IDENTIFIER>
InChI=1S/C3H6S5/c1-4-2-6-8-3-7-5-1/h1-3H2

> <INCHI_KEY>
QFHGOPGLIADNQA-UHFFFAOYSA-N

> <FORMULA>
C3H6S5

> <MOLECULAR_WEIGHT>
202.405

> <EXACT_MASS>
201.907303642

> <JCHEM_ACCEPTOR_COUNT>
0

> <JCHEM_AVERAGE_POLARIZABILITY>
18.78177196230326

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
1,2,4,5,7-pentathiocane

> <ALOGPS_LOGP>
1.19

> <JCHEM_LOGP>
2.2732743933333333

> <ALOGPS_LOGS>
-2.66

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_POLAR_SURFACE_AREA>
0

> <JCHEM_REFRACTIVITY>
52.506800000000005

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
4.43e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
1,2,4,5,7-pentathiocane

> <JCHEM_VEBER_RULE>
1

$$$$
Download

3D-SDF for HMDB0039431 (1,2,4,5,7-Pentathiocane)

HMDB0039431
     RDKit          3D
1,2,4,5,7-Pentathiocane
 14 14  0  0  0  0  0  0  0  0999 V2000
   -2.0578    0.9636   -0.5562 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3567   -0.7667   -0.0579 S   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7819   -1.3751    0.6463 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2838   -1.9547   -0.6630 S   0  0  0  0  0  0  0  0  0  0  0  0
    2.1797   -1.1350   -0.7179 S   0  0  0  0  0  0  0  0  0  0  0  0
    2.4002    0.4215    0.1013 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0219    1.5362    0.0182 S   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4401    0.9890   -1.4038 S   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0045    1.5529    0.3953 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8646    1.3481   -1.1815 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0714   -2.1974    1.3503 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2775   -0.5652    1.2015 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6562    0.2497    1.1823 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3127    0.9331   -0.3150 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  8  1  1  0
  1  9  1  0
  1 10  1  0
  3 11  1  0
  3 12  1  0
  6 13  1  0
  6 14  1  0
M  END
Download

PDB for HMDB0039431 (1,2,4,5,7-Pentathiocane)

HEADER    PROTEIN                                 06-MAY-13   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   06-MAY-13         0                                  
HETATM    1  C   UNK     0       3.282   2.193   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.436   2.193   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       1.859  -1.242   0.000  0.00  0.00           C+0
HETATM    4  S   UNK     0       1.859   2.782   0.000  0.00  0.00           S+0
HETATM    5  S   UNK     0       3.871   0.770   0.000  0.00  0.00           S+0
HETATM    6  S   UNK     0      -0.153   0.770   0.000  0.00  0.00           S+0
HETATM    7  S   UNK     0       3.282  -0.653   0.000  0.00  0.00           S+0
HETATM    8  S   UNK     0       0.436  -0.653   0.000  0.00  0.00           S+0
CONECT    1    4    5                                                       
CONECT    2    4    6                                                       
CONECT    3    7    8                                                       
CONECT    4    1    2                                                       
CONECT    5    1    7                                                       
CONECT    6    2    8                                                       
CONECT    7    3    5                                                       
CONECT    8    3    6                                                       
MASTER        0    0    0    0    0    0    0    0    8    0   16    0
END
Download

3D PDB for HMDB0039431 (1,2,4,5,7-Pentathiocane)

COMPND    HMDB0039431
HETATM    1  C1  UNL     1      -2.058   0.964  -0.556  1.00  0.00           C  
HETATM    2  S1  UNL     1      -2.357  -0.767  -0.058  1.00  0.00           S  
HETATM    3  C2  UNL     1      -0.782  -1.375   0.646  1.00  0.00           C  
HETATM    4  S2  UNL     1       0.284  -1.955  -0.663  1.00  0.00           S  
HETATM    5  S3  UNL     1       2.180  -1.135  -0.718  1.00  0.00           S  
HETATM    6  C3  UNL     1       2.400   0.422   0.101  1.00  0.00           C  
HETATM    7  S4  UNL     1       1.022   1.536   0.018  1.00  0.00           S  
HETATM    8  S5  UNL     1      -0.440   0.989  -1.404  1.00  0.00           S  
HETATM    9  H1  UNL     1      -2.004   1.553   0.395  1.00  0.00           H  
HETATM   10  H2  UNL     1      -2.865   1.348  -1.181  1.00  0.00           H  
HETATM   11  H3  UNL     1      -1.071  -2.197   1.350  1.00  0.00           H  
HETATM   12  H4  UNL     1      -0.277  -0.565   1.202  1.00  0.00           H  
HETATM   13  H5  UNL     1       2.656   0.250   1.182  1.00  0.00           H  
HETATM   14  H6  UNL     1       3.313   0.933  -0.315  1.00  0.00           H  
CONECT    1    2    8    9   10
CONECT    2    3
CONECT    3    4   11   12
CONECT    4    5
CONECT    5    6
CONECT    6    7   13   14
CONECT    7    8
END
Download

SMILES for HMDB0039431 (1,2,4,5,7-Pentathiocane)

C1SCSSCSS1
Download

INCHI for HMDB0039431 (1,2,4,5,7-Pentathiocane)

InChI=1S/C3H6S5/c1-4-2-6-8-3-7-5-1/h1-3H2
Download
View in JSmolView Stereo Labels
Synonyms
ValueSource
1,2,4,5,7-PentathiacyclooctaneHMDB
1,2,4,5,7-PentathiaoctaneHMDB
Chemical FormulaC3H6S5
Average Molecular Weight202.405
Monoisotopic Molecular Weight201.907303642
IUPAC Name1,2,4,5,7-pentathiocane
Traditional Name1,2,4,5,7-pentathiocane
CAS Registry Number81531-39-7
SMILES
C1SCSSCSS1
InChI Identifier
InChI=1S/C3H6S5/c1-4-2-6-8-3-7-5-1/h1-3H2
InChI KeyQFHGOPGLIADNQA-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as organic disulfides. These are organosulfur compounds with the general formula RSSR' (R,R' = alkyl, aryl).
KingdomOrganic compounds
Super ClassOrganosulfur compounds
ClassOrganic disulfides
Sub ClassNot Available
Direct ParentOrganic disulfides
Alternative Parents
Substituents
  • Organic disulfide
  • Organoheterocyclic compound
  • Dialkylthioether
  • Thioether
  • Hydrocarbon derivative
  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic heteromonocyclic compounds
External DescriptorsNot Available
Ontology
Physiological effectNot Available
Disposition
Biological locationRoute of exposureSource
ProcessNot Available
Role
Biological role
Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting Point102 - 104 °CNot Available
Boiling PointNot AvailableNot Available
Water Solubility381.6 mg/L @ 25 °C (est)The Good Scents Company Information System
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
Water Solubility0.44 g/LALOGPS
logP1.19ALOGPS
logP2.27ChemAxon
logS-2.7ALOGPS
Physiological Charge0ChemAxon
Hydrogen Acceptor Count0ChemAxon
Hydrogen Donor Count0ChemAxon
Polar Surface Area0 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity52.51 m³·mol⁻¹ChemAxon
Polarizability18.78 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
DarkChem[M+H]+140.25531661259
DarkChem[M-H]-132.95331661259
DeepCCS[M+H]+136.00630932474
DeepCCS[M-H]-133.90230932474
DeepCCS[M-2H]-169.53630932474
DeepCCS[M+Na]+144.33430932474
AllCCS[M+H]+134.132859911
AllCCS[M+H-H2O]+130.132859911
AllCCS[M+NH4]+137.932859911
AllCCS[M+Na]+139.032859911
AllCCS[M-H]-128.732859911
AllCCS[M+Na-2H]-131.232859911
AllCCS[M+HCOO]-133.932859911

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
1,2,4,5,7-PentathiocaneC1SCSSCSS12911.9Standard polar33892256
1,2,4,5,7-PentathiocaneC1SCSSCSS11731.1Standard non polar33892256
1,2,4,5,7-PentathiocaneC1SCSSCSS11685.6Semi standard non polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - 1,2,4,5,7-Pentathiocane GC-MS (Non-derivatized) - 70eV, Positivesplash10-00dm-9810000000-78da0ca6235ad2b330dc2017-09-01Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 1,2,4,5,7-Pentathiocane GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart LabView Spectrum

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 1,2,4,5,7-Pentathiocane 10V, Positive-QTOFsplash10-0udi-1090000000-aca19efcd40993f4d3b42015-04-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 1,2,4,5,7-Pentathiocane 20V, Positive-QTOFsplash10-0udi-3890000000-bdcea2f0d7450204e1012015-04-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 1,2,4,5,7-Pentathiocane 40V, Positive-QTOFsplash10-004i-9200000000-06db36492a6ceb5ffe322015-04-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 1,2,4,5,7-Pentathiocane 10V, Negative-QTOFsplash10-0udi-4960000000-e89830430ebf515dd46b2015-04-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 1,2,4,5,7-Pentathiocane 20V, Negative-QTOFsplash10-0udl-7900000000-3064d066738f3ab47a2e2015-04-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 1,2,4,5,7-Pentathiocane 40V, Negative-QTOFsplash10-004i-9300000000-f11b1db44586fc38ad842015-04-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 1,2,4,5,7-Pentathiocane 10V, Positive-QTOFsplash10-0udi-0090000000-62d30d79f2698efd87232021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 1,2,4,5,7-Pentathiocane 20V, Positive-QTOFsplash10-0udi-5190000000-d0d032f389aed9a238512021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 1,2,4,5,7-Pentathiocane 40V, Positive-QTOFsplash10-0002-9000000000-5abf974285d6f887a8f12021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 1,2,4,5,7-Pentathiocane 10V, Negative-QTOFsplash10-004i-9000000000-a9f5eeff369a7ca8b2d42021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 1,2,4,5,7-Pentathiocane 20V, Negative-QTOFsplash10-0fb9-9280000000-17cebdc9b09802de228b2021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 1,2,4,5,7-Pentathiocane 40V, Negative-QTOFsplash10-0fb9-9080000000-9c1349a134de24872c932021-09-24Wishart LabView Spectrum

IR Spectra

Spectrum TypeDescriptionDeposition DateSourceView
Predicted IR SpectrumIR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M+H]+)2023-02-04FELIX labView Spectrum
Predicted IR SpectrumIR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M+Na]+)2023-02-04FELIX labView Spectrum
Biological Properties
Cellular Locations
  • Cytoplasm
  • Extracellular
Biospecimen LocationsNot Available
Tissue LocationsNot Available
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB019026
KNApSAcK IDC00057568
Chemspider ID455997
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound522753
PDB IDNot Available
ChEBI IDNot Available
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDrw1877321
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General References
  1. (). Yannai, Shmuel. (2004) Dictionary of food compounds with CD-ROM: Additives, flavors, and ingredients. Boca Raton: Chapman & Hall/CRC.. .