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Showing metabocard for Dimethyl selenide (HMDB0033212)

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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2012-09-11 17:55:32 UTC
Update Date2022-03-07 02:53:37 UTC
HMDB IDHMDB0033212
Secondary Accession Numbers
  • HMDB33212
Metabolite Identification
Common NameDimethyl selenide
DescriptionDimethyl selenide, also known as (CH3)2Se or selenium dimethyl, belongs to the class of organic compounds known as selenoethers. These are organic compounds containing a selenoether group, with the general formula RseR' ( where R, R' are not H atoms). Dimethyl selenide is a drug. Dimethyl selenide has been detected, but not quantified in, several different foods, such as mustard spinaches (Brassica perviridis), sweet rowanberries (Grataegosorbus mitschurinii), agaves (Agave), chinese bayberries (Myrica rubra), and cinnamons (Cinnamomum). This could make dimethyl selenide a potential biomarker for the consumption of these foods. Dimethyl selenide is a primary metabolite. Primary metabolites are metabolically or physiologically essential metabolites. They are directly involved in an organism’s growth, development or reproduction. Based on a literature review a significant number of articles have been published on Dimethyl selenide.
Structure
Data?1563862369
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0033212 (Dimethyl selenide)

  Mrv0541 05061306592D          

  3  2  0  0  0  0            999 V2000
   -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 C   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
  3  2  1  0  0  0  0
M  END
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3D MOL for HMDB0033212 (Dimethyl selenide)

HMDB0033212
     RDKit          3D
Dimethyl selenide
  9  8  0  0  0  0  0  0  0  0999 V2000
    1.4807   -0.0187   -0.2648 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0941   -0.2359    1.0266 Se  0  0  0  0  0  2  0  0  0  0  0  0
   -1.5902   -0.0759    0.0802 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3865    1.0494    0.1178 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9433   -0.8181    0.4037 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4892    0.2518   -0.4732 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5531    0.6664   -0.7354 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3624    0.2260    0.7915 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8882   -1.0451   -0.4092 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  1  4  1  0
  1  5  1  0
  1  6  1  0
  3  7  1  0
  3  8  1  0
  3  9  1  0
M  END
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3D SDF for HMDB0033212 (Dimethyl selenide)

  Mrv0541 05061306592D          

  3  2  0  0  0  0            999 V2000
   -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 C   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
  3  2  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0033212

> <DATABASE_NAME>
hmdb

> <SMILES>
C[Se]C

> <INCHI_IDENTIFIER>
InChI=1S/C2H6Se/c1-3-2/h1-2H3

> <INCHI_KEY>
RVIXKDRPFPUUOO-UHFFFAOYSA-N

> <FORMULA>
C2H6Se

> <MOLECULAR_WEIGHT>
109.03

> <EXACT_MASS>
109.96347202

> <JCHEM_ACCEPTOR_COUNT>
0

> <JCHEM_AVERAGE_POLARIZABILITY>
6.681577872472303

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(methylselanyl)methane

> <ALOGPS_LOGP>
0.09

> <JCHEM_LOGP>
0.6333000000000002

> <ALOGPS_LOGS>
-0.19

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_POLAR_SURFACE_AREA>
0

> <JCHEM_REFRACTIVITY>
24.2131

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
7.10e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
dimethylselenide

> <JCHEM_VEBER_RULE>
1

$$$$
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3D-SDF for HMDB0033212 (Dimethyl selenide)

HMDB0033212
     RDKit          3D
Dimethyl selenide
  9  8  0  0  0  0  0  0  0  0999 V2000
    1.4807   -0.0187   -0.2648 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0941   -0.2359    1.0266 Se  0  0  0  0  0  2  0  0  0  0  0  0
   -1.5902   -0.0759    0.0802 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3865    1.0494    0.1178 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9433   -0.8181    0.4037 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4892    0.2518   -0.4732 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5531    0.6664   -0.7354 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3624    0.2260    0.7915 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8882   -1.0451   -0.4092 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  1  4  1  0
  1  5  1  0
  1  6  1  0
  3  7  1  0
  3  8  1  0
  3  9  1  0
M  END
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PDB for HMDB0033212 (Dimethyl selenide)

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      -1.540   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       0.000   0.000   0.000  0.00  0.00          Se+0
CONECT    1    3                                                            
CONECT    2    3                                                            
CONECT    3    1    2                                                       
MASTER        0    0    0    0    0    0    0    0    3    0    4    0
END
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3D PDB for HMDB0033212 (Dimethyl selenide)

COMPND    HMDB0033212
HETATM    1  C1  UNL     1       1.481  -0.019  -0.265  1.00  0.00           C  
HETATM    2 SE1  UNL     1       0.094  -0.236   1.027  1.00  0.00          SE  
HETATM    3  C2  UNL     1      -1.590  -0.076   0.080  1.00  0.00           C  
HETATM    4  H1  UNL     1       1.386   1.049   0.118  1.00  0.00           H  
HETATM    5  H2  UNL     1       1.943  -0.818   0.404  1.00  0.00           H  
HETATM    6  H3  UNL     1       2.489   0.252  -0.473  1.00  0.00           H  
HETATM    7  H4  UNL     1      -1.553   0.666  -0.735  1.00  0.00           H  
HETATM    8  H5  UNL     1      -2.362   0.226   0.792  1.00  0.00           H  
HETATM    9  H6  UNL     1      -1.888  -1.045  -0.409  1.00  0.00           H  
CONECT    1    2    4    5    6
CONECT    2    3
CONECT    3    7    8    9
END
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SMILES for HMDB0033212 (Dimethyl selenide)

C[Se]C
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INCHI for HMDB0033212 (Dimethyl selenide)

InChI=1S/C2H6Se/c1-3-2/h1-2H3
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View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
ValueSource
(CH3)2SeChEBI
DimethylseleniumChEBI
Methyl selenideChEBI
Methyl seleniumChEBI
Selenium dimethylChEBI
SelenobismethaneChEBI
(Methylselanyl)methaneHMDB
Dimethyl-selenideHMDB
DimethylselenideHMDB
Methane, selenobis- (9ci)HMDB
Methyl selenide (8ci)HMDB
Methyl selenide, 8ciHMDB
Selenobis-methaneHMDB
Selenobismethane, 9ciHMDB
DMe-selenideMeSH, HMDB
Dimethylselenide, 75Se-labeledMeSH, HMDB
Chemical FormulaC2H6Se
Average Molecular Weight109.03
Monoisotopic Molecular Weight109.96347202
IUPAC Name(methylselanyl)methane
Traditional Namedimethylselenide
CAS Registry Number593-79-3
SMILES
C[Se]C
InChI Identifier
InChI=1S/C2H6Se/c1-3-2/h1-2H3
InChI KeyRVIXKDRPFPUUOO-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as selenoethers. These are organic compounds containing a selenoether group, with the general formula RseR' ( where R, R' are not H atoms).
KingdomOrganic compounds
Super ClassOrganometallic compounds
ClassOrganometalloid compounds
Sub ClassOrganoselenium compounds
Direct ParentSelenoethers
Alternative Parents
Substituents
  • Selenoether
  • Hydrocarbon derivative
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Ontology
Physiological effectNot Available
Disposition
Biological locationRoute of exposureSource
ProcessNot Available
Role
Biological role
Physical Properties
StateLiquid
Experimental Molecular Properties
PropertyValueReference
Melting Point-87.2 °CNot Available
Boiling PointNot AvailableNot Available
Water Solubility24.4 mg/mL at 25 °CNot Available
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
Predicted Chromatographic Properties
Spectra
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 IDDBMET01462
Phenol Explorer Compound IDNot Available
FooDB IDFDB011225
KNApSAcK IDC00033776
Chemspider ID11158
KEGG Compound IDC02535
BioCyc IDCPD-12005
BiGG IDNot Available
Wikipedia LinkDimethyl selenide
METLIN IDNot Available
PubChem Compound11648
PDB IDNot Available
ChEBI ID4610
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

Enzymes

Enzyme Details
1. Indolethylamine N-methyltransferase
General function:
Involved in methyltransferase activity
Specific function:
Functions as thioether S-methyltransferase and is active with a variety of thioethers and the corresponding selenium and tellurium compounds, including 3-methylthiopropionaldehyde, dimethyl selenide, dimethyl telluride, 2-methylthioethylamine, 2-methylthioethanol, methyl-n-propyl sulfide and diethyl sulfide. Plays an important role in the detoxification of selenium compounds (By similarity). Catalyzes the N-methylation of tryptamine and structurally related compounds.
Gene Name:
INMT
Uniprot ID:
O95050
Molecular weight:
28833.695
Reactions
S-Adenosylmethionine + Dimethyl selenide → S-Adenosylhomocysteine + Trimethylselenoniumdetails