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Showing metabocard for Trimethylselenonium (HMDB0042052)

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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2012-09-13 11:56:11 UTC
Update Date2019-07-23 06:35:25 UTC
HMDB IDHMDB0042052
Secondary Accession Numbers
  • HMDB42052
Metabolite Identification
Common NameTrimethylselenonium
DescriptionTrimethylselenonium 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). Trimethylselenonium is a drug. Trimethylselenonium has been detected, but not quantified in, a few different foods, such as anatidaes (Anatidae), chickens (Gallus gallus), and domestic pigs (Sus scrofa domestica). This could make trimethylselenonium a potential biomarker for the consumption of these foods. Trimethylselenonium 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 Trimethylselenonium.
Structure
Data?1563863725
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0042052 (Trimethylselenonium)


  Mrv1652304062013092D          

  4  3  0  0  0  0            999 V2000
   -0.4125   -0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4125    0.7145    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  3  0  0  0  0  0  0  0  0  0  0
  4  1  1  0  0  0  0
  4  2  1  0  0  0  0
  4  3  1  0  0  0  0
M  CHG  1   4   1
M  END
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3D MOL for HMDB0042052 (Trimethylselenonium)

HMDB0042052
     RDKit          3D
Trimethylselenonium
 13 12  0  0  0  0  0  0  0  0999 V2000
   -1.5313   -1.0220    0.1135 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0058    0.0804    0.4925 Se  0  0  0  0  0  3  0  0  0  0  0  0
    1.6673   -0.8080    0.1551 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1102    1.8370   -0.2536 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0540   -1.2112    1.0947 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2294   -2.0172   -0.3030 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2808   -0.5231   -0.5309 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4925   -0.2049    0.5496 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8348   -1.0712   -0.8987 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6643   -1.7620    0.7242 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0676    2.5779    0.5787 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6159    2.0351   -1.0672 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1311    2.0891   -0.6548 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  2  4  1  0
  1  5  1  0
  1  6  1  0
  1  7  1  0
  3  8  1  0
  3  9  1  0
  3 10  1  0
  4 11  1  0
  4 12  1  0
  4 13  1  0
M  CHG  1   2   1
M  END
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3D SDF for HMDB0042052 (Trimethylselenonium)


  Mrv1652304062013092D          

  4  3  0  0  0  0            999 V2000
   -0.4125   -0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4125    0.7145    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  3  0  0  0  0  0  0  0  0  0  0
  4  1  1  0  0  0  0
  4  2  1  0  0  0  0
  4  3  1  0  0  0  0
M  CHG  1   4   1
M  END
> <DATABASE_ID>
HMDB0042052

> <DATABASE_NAME>
hmdb

> <SMILES>
C[Se+](C)C

> <INCHI_IDENTIFIER>
InChI=1S/C3H9Se/c1-4(2)3/h1-3H3/q+1

> <INCHI_KEY>
BWJVPBNHAHLFAZ-UHFFFAOYSA-N

> <FORMULA>
C3H9Se

> <MOLECULAR_WEIGHT>
124.06

> <EXACT_MASS>
124.986947116

> <JCHEM_ACCEPTOR_COUNT>
1

> <JCHEM_ATOM_COUNT>
13

> <JCHEM_AVERAGE_POLARIZABILITY>
9.417720463922974

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
1

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
trimethylselanium

> <ALOGPS_LOGP>
1.56

> <JCHEM_LOGP>
0.8763000000000001

> <ALOGPS_LOGS>
-1.17

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_POLAR_SURFACE_AREA>
0.0

> <JCHEM_REFRACTIVITY>
29.7622

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.08e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
trimethylselenonium

> <JCHEM_VEBER_RULE>
1

$$$$
Download

3D-SDF for HMDB0042052 (Trimethylselenonium)

HMDB0042052
     RDKit          3D
Trimethylselenonium
 13 12  0  0  0  0  0  0  0  0999 V2000
   -1.5313   -1.0220    0.1135 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0058    0.0804    0.4925 Se  0  0  0  0  0  3  0  0  0  0  0  0
    1.6673   -0.8080    0.1551 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1102    1.8370   -0.2536 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0540   -1.2112    1.0947 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2294   -2.0172   -0.3030 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2808   -0.5231   -0.5309 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4925   -0.2049    0.5496 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8348   -1.0712   -0.8987 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6643   -1.7620    0.7242 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0676    2.5779    0.5787 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6159    2.0351   -1.0672 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1311    2.0891   -0.6548 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  2  4  1  0
  1  5  1  0
  1  6  1  0
  1  7  1  0
  3  8  1  0
  3  9  1  0
  3 10  1  0
  4 11  1  0
  4 12  1  0
  4 13  1  0
M  CHG  1   2   1
M  END
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PDB for HMDB0042052 (Trimethylselenonium)

HEADER    PROTEIN                                 06-APR-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   06-APR-20         0                                  
HETATM    1  C   UNK     0      -0.770  -1.334   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -0.770   1.334   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       1.540   0.000   0.000  0.00  0.00           C+0
HETATM    4 Se   UNK     0       0.000   0.000   0.000  0.00  0.00          Se+1
CONECT    1    4                                                            
CONECT    2    4                                                            
CONECT    3    4                                                            
CONECT    4    1    2    3                                                  
MASTER        0    0    0    0    0    0    0    0    4    0    6    0
END
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3D PDB for HMDB0042052 (Trimethylselenonium)

COMPND    HMDB0042052
HETATM    1  C1  UNL     1      -1.531  -1.022   0.113  1.00  0.00           C  
HETATM    2 SE1  UNL     1      -0.006   0.080   0.493  1.00  0.00          SE1+
HETATM    3  C2  UNL     1       1.667  -0.808   0.155  1.00  0.00           C  
HETATM    4  C3  UNL     1      -0.110   1.837  -0.254  1.00  0.00           C  
HETATM    5  H1  UNL     1      -2.054  -1.211   1.095  1.00  0.00           H  
HETATM    6  H2  UNL     1      -1.229  -2.017  -0.303  1.00  0.00           H  
HETATM    7  H3  UNL     1      -2.281  -0.523  -0.531  1.00  0.00           H  
HETATM    8  H4  UNL     1       2.492  -0.205   0.550  1.00  0.00           H  
HETATM    9  H5  UNL     1       1.835  -1.071  -0.899  1.00  0.00           H  
HETATM   10  H6  UNL     1       1.664  -1.762   0.724  1.00  0.00           H  
HETATM   11  H7  UNL     1       0.068   2.578   0.579  1.00  0.00           H  
HETATM   12  H8  UNL     1       0.616   2.035  -1.067  1.00  0.00           H  
HETATM   13  H9  UNL     1      -1.131   2.089  -0.655  1.00  0.00           H  
CONECT    1    2    5    6    7
CONECT    2    3    4
CONECT    3    8    9   10
CONECT    4   11   12   13
END
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SMILES for HMDB0042052 (Trimethylselenonium)

C[Se+](C)C
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INCHI for HMDB0042052 (Trimethylselenonium)

InChI=1S/C3H9Se/c1-4(2)3/h1-3H3/q+1
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View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
ValueSource
(CH3)3Se(+)ChEBI
Me3Se(+)ChEBI
Trimethylselenonium ionChEBI
Trimethylselenonium nitrate, (75)se-labeledHMDB
Trimethylselenonium chlorideHMDB
Trimethylselenonium iodide, (75)se-labeledHMDB
Chemical FormulaC3H9Se
Average Molecular Weight124.06
Monoisotopic Molecular Weight124.986947116
IUPAC Nametrimethylselanium
Traditional Nametrimethylselenonium
CAS Registry Number25930-79-4
SMILES
C[Se+](C)C
InChI Identifier
InChI=1S/C3H9Se/c1-4(2)3/h1-3H3/q+1
InChI KeyBWJVPBNHAHLFAZ-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
  • Organic cation
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Ontology
Physiological effectNot Available
Disposition
Source
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
Water Solubility10.8 g/LALOGPS
logP1.56ALOGPS
logP0.88ChemAxon
logS-1.2ALOGPS
Physiological Charge1ChemAxon
Hydrogen Acceptor Count1ChemAxon
Hydrogen Donor Count0ChemAxon
Polar Surface Area0 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity29.76 m³·mol⁻¹ChemAxon
Polarizability9.42 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]+122.3430932474
DeepCCS[M-H]-120.37930932474
DeepCCS[M-2H]-156.0430932474
DeepCCS[M+Na]+130.54930932474
AllCCS[M+H]+108.332859911
AllCCS[M+H-H2O]+104.532859911
AllCCS[M+NH4]+111.732859911
AllCCS[M+Na]+112.732859911
AllCCS[M-H]-178.232859911
AllCCS[M+Na-2H]-184.732859911
AllCCS[M+HCOO]-191.932859911

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
TrimethylselenoniumC[Se+](C)C572.4Standard polar33892256
TrimethylselenoniumC[Se+](C)C524.5Standard non polar33892256
TrimethylselenoniumC[Se+](C)C540.4Semi standard non polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - Trimethylselenonium GC-MS (Non-derivatized) - 70eV, Positivesplash10-0ab9-0900000000-c2316c0d70c4617e1e332017-09-01Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Trimethylselenonium 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 - Trimethylselenonium 10V, Positive-QTOFsplash10-00di-0900000000-cd46f21f38328bb1dc1e2017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Trimethylselenonium 20V, Positive-QTOFsplash10-00di-0900000000-bf2c6cafb1a989213d972017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Trimethylselenonium 40V, Positive-QTOFsplash10-00di-1900000000-aec03fcc37951090839d2017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Trimethylselenonium 10V, Positive-QTOFsplash10-00di-0900000000-f3ff6a1c0530e6d248ad2021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Trimethylselenonium 20V, Positive-QTOFsplash10-0a4i-0900000000-ab00b30d51975ba4f1142021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Trimethylselenonium 40V, Positive-QTOFsplash10-0a4i-0900000000-e5f6bb9bef71f031d8fa2021-09-22Wishart LabView Spectrum

NMR Spectra

Spectrum TypeDescriptionDeposition DateSourceView
Predicted 1D NMR13C NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Biological Properties
Cellular LocationsNot Available
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 IDDBMET01463
Phenol Explorer Compound IDNot Available
FooDB IDFDB111694
KNApSAcK IDNot Available
Chemspider ID82691
KEGG Compound IDC18872
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound91580
PDB IDNot Available
ChEBI ID77058
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. Nahapetian AT, Young VR, Janghorbani M: Measurement of trimethylselenonium ion in human urine. Anal Biochem. 1984 Jul;140(1):56-62. [PubMed:6486416 ]
  2. Kuehnelt D, Juresa D, Kienzl N, Francesconi KA: Marked individual variability in the levels of trimethylselenonium ion in human urine determined by HPLC/ICPMS and HPLC/vapor generation/ICPMS. Anal Bioanal Chem. 2006 Dec;386(7-8):2207-12. Epub 2006 Oct 24. [PubMed:17061074 ]
  3. Anan Y, Ohbo A, Tani Y, Hatakeyama Y, Yawata A, Ogra Y: Distribution and metabolism of selenite and selenomethionine in the Japanese quail. Metallomics. 2012 May;4(5):457-62. doi: 10.1039/c2mt20013a. Epub 2012 Apr 23. [PubMed:22526144 ]
  4. Ganther HE, Kraus RJ, Foster SJ: Trimethylselenonium ion. Methods Enzymol. 1987;143:195-201. [PubMed:3309552 ]
  5. Sun XF, Ting BT, Janghorbani M: Excretion of trimethylselenonium ion in human urine. Anal Biochem. 1987 Dec;167(2):304-11. [PubMed:3442325 ]
  6. Blotcky AJ, Hansen GT, Opelanio-Buencamino LR, Rack EP: Determination of trimethylselenonium ion in urine by ion-exchange chromatography and molecular neutron activation analysis. Anal Chem. 1985 Aug;57(9):1937-41. [PubMed:4037348 ]
  7. Palmer IS, Gunsalus RP, Halverson AW, Olson OE: Trimethylselenonium ion as a general excretory product from selenium metabolism in the rat. Biochim Biophys Acta. 1970 May 12;208(2):260-6. [PubMed:5420976 ]
  8. Hasunuma R, Ogawa T, Fujise Y, Kawanishi Y: Analysis of selenium metabolites in urine samples of minke whale (Balaenoptera Acutorostrata) using ion exchange chromatography. Comp Biochem Physiol C. 1993 Jan;104(1):87-9. [PubMed:8097456 ]

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