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Showing metabocard for selenide (HMDB0304483)

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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2021-09-24 10:07:25 UTC
Update Date2021-09-24 10:07:25 UTC
HMDB IDHMDB0304483
Secondary Accession NumbersNone
Metabolite Identification
Common Nameselenide
DescriptionSelenium, also known as se(2-) or selenide ion, is a member of the class of compounds known as homogeneous other non-metal compounds. Homogeneous other non-metal compounds are inorganic non-metallic compounds in which the largest atom belongs to the class of 'other nonmetals'. Selenium can be found in a number of food items such as root vegetables, oxheart cabbage, persimmon, and irish moss, which makes selenium a potential biomarker for the consumption of these food products. Selenium exists in E.coli (prokaryote) and yeast (eukaryote). Selenium salts are toxic in large amounts, but trace amounts are necessary for cellular function in many organisms, including all animals. Selenium is an ingredient in many multivitamins and other dietary supplements, including infant formula. It is a component of the antioxidant enzymes glutathione peroxidase and thioredoxin reductase (which indirectly reduce certain oxidized molecules in animals and some plants). It is also found in three deiodinase enzymes, which convert one thyroid hormone to another. Selenium requirements in plants differ by species, with some plants requiring relatively large amounts and others apparently requiring none .
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0304483 (selenide)

Structure #1
  Mrv0541 02241206192D          

  1  0  0  0  0  0            999 V2000
    0.0000    0.0000    0.0000 Se  0  6  0  0  0  0  0  0  0  0  0  0
M  CHG  1   1  -2
M  END
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3D MOL for HMDB0304483 (selenide)

HMDB0304483
     RDKit          3D
selenide
  1  0  0  0  0  0  0  0  0  0999 V2000
    0.0000    0.0000    0.0000 Se  0  0  0  0  0 15  0  0  0  0  0  0
M  CHG  1   1  -2
M  END
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3D SDF for HMDB0304483 (selenide)

Structure #1
  Mrv0541 02241206192D          

  1  0  0  0  0  0            999 V2000
    0.0000    0.0000    0.0000 Se  0  6  0  0  0  0  0  0  0  0  0  0
M  CHG  1   1  -2
M  END
> <DATABASE_ID>
HMDB0304483

> <DATABASE_NAME>
hmdb

> <SMILES>
[Se--]

> <INCHI_IDENTIFIER>
InChI=1S/Se/q-2

> <INCHI_KEY>
HMUBNCUQSSTAIB-UHFFFAOYSA-N

> <FORMULA>
Se

> <MOLECULAR_WEIGHT>
78.96

> <EXACT_MASS>
79.916521828

> <JCHEM_ACCEPTOR_COUNT>
0

> <JCHEM_AVERAGE_POLARIZABILITY>
1.7784

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
-2

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
selandiide

> <JCHEM_LOGP>
-0.5047

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_POLAR_SURFACE_AREA>
0

> <JCHEM_REFRACTIVITY>
13.1149

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
selandiide

> <JCHEM_VEBER_RULE>
1

$$$$
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3D-SDF for HMDB0304483 (selenide)

HMDB0304483
     RDKit          3D
selenide
  1  0  0  0  0  0  0  0  0  0999 V2000
    0.0000    0.0000    0.0000 Se  0  0  0  0  0 15  0  0  0  0  0  0
M  CHG  1   1  -2
M  END
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PDB for HMDB0304483 (selenide)

HEADER    PROTEIN                                 24-FEB-12   NONE
TITLE     NULL                                                        
COMPND    MOLECULE: Structure #1                                      
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-FEB-12         0                                  
HETATM    1 Se   UNK     0       0.000   0.000   0.000  0.00  0.00          Se-2
MASTER        0    0    0    0    0    0    0    0    1    0    0    0
END
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3D PDB for HMDB0304483 (selenide)

COMPND    HMDB0304483
HETATM    1 SE1  UNL     1       0.000   0.000   0.000  1.00  0.00          SE2-
END
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SMILES for HMDB0304483 (selenide)

[Se--]
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INCHI for HMDB0304483 (selenide)

InChI=1S/Se/q-2
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Synonyms
ValueSource
Se(2-)ChEBI
Chemical FormulaSe
Average Molecular Weight78.96
Monoisotopic Molecular Weight79.916521828
IUPAC Nameselandiide
Traditional Nameselandiide
CAS Registry NumberNot Available
SMILES
[Se--]
InChI Identifier
InChI=1S/Se/q-2
InChI KeyHMUBNCUQSSTAIB-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of inorganic compounds known as homogeneous other non-metal compounds. These are inorganic non-metallic compounds in which the largest atom belongs to the class of 'other non-metals'.
KingdomInorganic compounds
Super ClassHomogeneous non-metal compounds
ClassHomogeneous other non-metal compounds
Sub ClassNot Available
Direct ParentHomogeneous other non-metal compounds
Alternative ParentsNot Available
Substituents
  • Homogeneous other non metal
Molecular FrameworkNot Available
External Descriptors
Ontology
Not AvailableNot 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
logP-0.5ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count0ChemAxon
Hydrogen Donor Count0ChemAxon
Polar Surface Area0 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity13.11 m³·mol⁻¹ChemAxon
Polarizability1.78 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
AllCCS[M+H]+134.55932859911
AllCCS[M+H-H2O]+131.00532859911
AllCCS[M+Na]+138.83832859911
AllCCS[M+NH4]+137.87932859911
AllCCS[M-H]-186.54232859911
AllCCS[M+Na-2H]-198.53332859911
AllCCS[M+HCOO]-211.60732859911
DeepCCS[M+H]+112.41730932474
DeepCCS[M-H]-110.69330932474
DeepCCS[M-2H]-145.97330932474
DeepCCS[M+Na]+119.32730932474

Predicted Kovats Retention Indices

Not Available
Spectra

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - selenide 10V, Positive-QTOFsplash10-001i-9000000000-b0759ba90e57e47d84462015-09-15Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - selenide 20V, Positive-QTOFsplash10-001i-9000000000-b0759ba90e57e47d84462015-09-15Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - selenide 40V, Positive-QTOFsplash10-001i-9000000000-b0759ba90e57e47d84462015-09-15Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - selenide 10V, Negative-QTOFsplash10-004i-9000000000-7f9f44f14fd3479448b72015-09-15Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - selenide 20V, Negative-QTOFsplash10-004i-9000000000-7f9f44f14fd3479448b72015-09-15Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - selenide 40V, Negative-QTOFsplash10-004i-9000000000-7f9f44f14fd3479448b72015-09-15Wishart 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 IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB031170
KNApSAcK IDC00013092
Chemspider ID96846
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound107674
PDB IDNot Available
ChEBI ID15076
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 ReferencesNot Available