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Showing metabocard for Dimethyl diselenide (HMDB0033208)

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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2012-09-11 17:55:15 UTC
Update Date2022-03-07 02:53:37 UTC
HMDB IDHMDB0033208
Secondary Accession Numbers
  • HMDB33208
Metabolite Identification
Common NameDimethyl diselenide
DescriptionDimethyl diselenide, also known as (CH3Se)2 or 1,2-dimethyldiselane, belongs to the class of organic compounds known as diselenides. These are organoselenium compounds with the general structure R-Se-Se-R' (R,R' = H or organic moiety). Dimethyl diselenide has been detected, but not quantified in, several different foods, such as onion-family vegetables, red onion, green onion, garden onion (var.), and welsh onions (Allium fistulosum). This could make dimethyl diselenide a potential biomarker for the consumption of these foods. Dimethyl diselenide is a secondary metabolite. Secondary metabolites are metabolically or physiologically non-essential metabolites that may serve a role as defense or signalling molecules. In some cases they are simply molecules that arise from the incomplete metabolism of other secondary metabolites. Based on a literature review a significant number of articles have been published on Dimethyl diselenide.
Structure
Data?1563862368
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0033208 (Dimethyl diselenide)


  Mrv0541 05061306592D          

  4  3  0  0  0  0            999 V2000
    1.6500    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8250    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    0.0000    0.0000 Se  0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 Se  0  0  0  0  0  0  0  0  0  0  0  0
  3  1  1  0  0  0  0
  4  2  1  0  0  0  0
  4  3  1  0  0  0  0
M  END
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3D MOL for HMDB0033208 (Dimethyl diselenide)

HMDB0033208
     RDKit          3D
Dimethyl diselenide
 10  9  0  0  0  0  0  0  0  0999 V2000
    2.2770   -0.0582    0.0175 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9108    0.8326   -1.0194 Se  0  0  0  0  0  2  0  0  0  0  0  0
   -0.9562    1.2127    0.4354 Se  0  0  0  0  0  2  0  0  0  0  0  0
   -2.2867   -0.1547    0.0035 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1880    0.2908    1.0592 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1449   -1.1520    0.0043 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2533    0.2192   -0.3958 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5123   -0.0172   -1.0867 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2041   -0.0209    0.6216 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8146   -1.1521    0.1550 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
  1  5  1  0
  1  6  1  0
  1  7  1  0
  4  8  1  0
  4  9  1  0
  4 10  1  0
M  END
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3D SDF for HMDB0033208 (Dimethyl diselenide)


  Mrv0541 05061306592D          

  4  3  0  0  0  0            999 V2000
    1.6500    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8250    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    0.0000    0.0000 Se  0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 Se  0  0  0  0  0  0  0  0  0  0  0  0
  3  1  1  0  0  0  0
  4  2  1  0  0  0  0
  4  3  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0033208

> <DATABASE_NAME>
hmdb

> <SMILES>
C[Se][Se]C

> <INCHI_IDENTIFIER>
InChI=1S/C2H6Se2/c1-3-4-2/h1-2H3

> <INCHI_KEY>
VLXBWPOEOIIREY-UHFFFAOYSA-N

> <FORMULA>
C2H6Se2

> <MOLECULAR_WEIGHT>
187.99

> <EXACT_MASS>
189.879993848

> <JCHEM_ACCEPTOR_COUNT>
0

> <JCHEM_AVERAGE_POLARIZABILITY>
8.489595266220796

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(methyldiselanyl)methane

> <ALOGPS_LOGP>
-0.06

> <JCHEM_LOGP>
0.3468

> <ALOGPS_LOGS>
-0.42

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_POLAR_SURFACE_AREA>
0

> <JCHEM_REFRACTIVITY>
37.79

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
7.22e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
dimethyl diselenide

> <JCHEM_VEBER_RULE>
1

$$$$
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3D-SDF for HMDB0033208 (Dimethyl diselenide)

HMDB0033208
     RDKit          3D
Dimethyl diselenide
 10  9  0  0  0  0  0  0  0  0999 V2000
    2.2770   -0.0582    0.0175 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9108    0.8326   -1.0194 Se  0  0  0  0  0  2  0  0  0  0  0  0
   -0.9562    1.2127    0.4354 Se  0  0  0  0  0  2  0  0  0  0  0  0
   -2.2867   -0.1547    0.0035 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1880    0.2908    1.0592 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1449   -1.1520    0.0043 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2533    0.2192   -0.3958 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5123   -0.0172   -1.0867 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2041   -0.0209    0.6216 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8146   -1.1521    0.1550 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
  1  5  1  0
  1  6  1  0
  1  7  1  0
  4  8  1  0
  4  9  1  0
  4 10  1  0
M  END
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PDB for HMDB0033208 (Dimethyl diselenide)

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       3.080   0.000   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -1.540   0.000   0.000  0.00  0.00           C+0
HETATM    3 Se   UNK     0       1.540   0.000   0.000  0.00  0.00          Se+0
HETATM    4 Se   UNK     0       0.000   0.000   0.000  0.00  0.00          Se+0
CONECT    1    3                                                            
CONECT    2    4                                                            
CONECT    3    1    4                                                       
CONECT    4    2    3                                                       
MASTER        0    0    0    0    0    0    0    0    4    0    6    0
END
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3D PDB for HMDB0033208 (Dimethyl diselenide)

COMPND    HMDB0033208
HETATM    1  C1  UNL     1       2.277  -0.058   0.017  1.00  0.00           C  
HETATM    2 SE1  UNL     1       0.911   0.833  -1.019  1.00  0.00          SE  
HETATM    3 SE2  UNL     1      -0.956   1.213   0.435  1.00  0.00          SE  
HETATM    4  C2  UNL     1      -2.287  -0.155   0.003  1.00  0.00           C  
HETATM    5  H1  UNL     1       2.188   0.291   1.059  1.00  0.00           H  
HETATM    6  H2  UNL     1       2.145  -1.152   0.004  1.00  0.00           H  
HETATM    7  H3  UNL     1       3.253   0.219  -0.396  1.00  0.00           H  
HETATM    8  H4  UNL     1      -2.512  -0.017  -1.087  1.00  0.00           H  
HETATM    9  H5  UNL     1      -3.204  -0.021   0.622  1.00  0.00           H  
HETATM   10  H6  UNL     1      -1.815  -1.152   0.155  1.00  0.00           H  
CONECT    1    2    5    6    7
CONECT    2    3
CONECT    3    4
CONECT    4    8    9   10
END
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SMILES for HMDB0033208 (Dimethyl diselenide)

C[Se][Se]C
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INCHI for HMDB0033208 (Dimethyl diselenide)

InChI=1S/C2H6Se2/c1-3-4-2/h1-2H3
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View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
ValueSource
(CH3Se)2ChEBI
(Methyldiselanyl)methaneChEBI
1,2-DimethyldiselaneChEBI
DimethyldiselenideChEBI
Diselenide, dimethylChEBI
DiselenobismethaneChEBI
Methyl diselenideChEBI
Methyl diselenide, 8ciHMDB
Chemical FormulaC2H6Se2
Average Molecular Weight187.99
Monoisotopic Molecular Weight189.879993848
IUPAC Name(methyldiselanyl)methane
Traditional Namedimethyl diselenide
CAS Registry Number7101-31-7
SMILES
C[Se][Se]C
InChI Identifier
InChI=1S/C2H6Se2/c1-3-4-2/h1-2H3
InChI KeyVLXBWPOEOIIREY-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as diselenides. These are organoselenium compounds with the general structure R-Se-Se-R' (R,R' = H or organic moiety).
KingdomOrganic compounds
Super ClassOrganometallic compounds
ClassOrganometalloid compounds
Sub ClassOrganoselenium compounds
Direct ParentDiselenides
Alternative Parents
Substituents
  • Diselenide group
  • Hydrocarbon derivative
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Ontology
Not AvailableNot Available
Physical Properties
StateNot Available
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water Solubility0.1 mg/mL at 25 °CNot Available
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
Water Solubility72.2 g/LALOGPS
logP-0.06ALOGPS
logP0.35ChemAxon
logS-0.42ALOGPS
Physiological Charge0ChemAxon
Hydrogen Acceptor Count0ChemAxon
Hydrogen Donor Count0ChemAxon
Polar Surface Area0 ŲChemAxon
Rotatable Bond Count1ChemAxon
Refractivity37.79 m³·mol⁻¹ChemAxon
Polarizability8.49 ųChemAxon
Number of Rings0ChemAxon
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]+123.62230932474
DeepCCS[M-H]-121.72730932474
DeepCCS[M-2H]-157.23130932474
DeepCCS[M+Na]+131.63830932474
AllCCS[M+H]+117.632859911
AllCCS[M+H-H2O]+114.332859911
AllCCS[M+NH4]+120.632859911
AllCCS[M+Na]+121.532859911
AllCCS[M-H]-201.632859911
AllCCS[M+Na-2H]-207.932859911
AllCCS[M+HCOO]-214.832859911

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
Dimethyl diselenideC[Se][Se]C568.2Standard polar33892256
Dimethyl diselenideC[Se][Se]C832.0Standard non polar33892256
Dimethyl diselenideC[Se][Se]C867.8Semi standard non polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - Dimethyl diselenide GC-MS (Non-derivatized) - 70eV, Positivesplash10-000f-9500000000-12d4ed89490a3eeb11412017-09-01Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Dimethyl diselenide GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Dimethyl diselenide 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 - Dimethyl diselenide 10V, Positive-QTOFsplash10-0006-0900000000-0de3f55f253811aa0ebe2016-08-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Dimethyl diselenide 20V, Positive-QTOFsplash10-0006-0900000000-ea321df13f87df5220d02016-08-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Dimethyl diselenide 40V, Positive-QTOFsplash10-0006-2900000000-af5f47251b86c8f200372016-08-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Dimethyl diselenide 10V, Negative-QTOFsplash10-000l-7900000000-6568b0595dc145aecc762016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Dimethyl diselenide 20V, Negative-QTOFsplash10-000i-1900000000-c4c1fdb2390ee247958c2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Dimethyl diselenide 40V, Negative-QTOFsplash10-000f-9700000000-a4b423bdf05b2a18496a2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Dimethyl diselenide 10V, Positive-QTOFsplash10-0006-0900000000-c2d864e5db5274bb97942021-09-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Dimethyl diselenide 20V, Positive-QTOFsplash10-0006-0900000000-c2d864e5db5274bb97942021-09-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Dimethyl diselenide 40V, Positive-QTOFsplash10-00di-0900000000-e11dab38a23a86b14f862021-09-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Dimethyl diselenide 10V, Negative-QTOFsplash10-000l-6900000000-f35bc4c49045402a54c02021-09-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Dimethyl diselenide 20V, Negative-QTOFsplash10-0006-9400000000-7a10692432d49e6d182c2021-09-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Dimethyl diselenide 40V, Negative-QTOFsplash10-000l-5900000000-695c3d11d44a0a07095e2021-09-25Wishart LabView Spectrum

NMR Spectra

Spectrum TypeDescriptionDeposition DateSourceView
Predicted 1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-09-25Wishart 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 IDFDB011221
KNApSAcK IDNot Available
Chemspider ID21967
KEGG Compound IDNot Available
BioCyc IDCPD-12006
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound23496
PDB IDNot Available
ChEBI ID176517
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. (). Yannai, Shmuel. (2004) Dictionary of food compounds with CD-ROM: Additives, flavors, and ingredients. Boca Raton: Chapman & Hall/CRC.. .