Showing metabocard for Hydrogen selenide (MMDBc0029902)

Record Information
Version1.0
StatusDetected and Quantified
Creation Date2021-11-17 23:46:12 UTC
Update Date2022-08-31 17:37:32 UTC
MiMeDB IDMMDBc0029902
Metabolite Identification
Common NameHydrogen selenide
DescriptionHydrogen selenide is a metabolite of selenium which could have potential antiangiogenic effect in the chemoprevention of cancer. The hydrogen selenide is a key intermediate in the selenium methylation metabolism of inorganic and organic selenium compounds. Accumulation of the hydrogen selenide resulting from inhibition of the selenium methylation metabolism, detoxification metabolic pathway of selenium, is found in animals following repeated administration of a toxic dose of selenocystine. The excess of the hydrogen selenide produced by inhibition of the selenium methylation metabolism contributes to the hepatotoxicity caused by selenocystine. (PMID: 9414580 , 11799926 )
Structure
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for #<Metabolite:0x000055b76a69c310>


  Mrv1652305221920242D          

  1  0  0  0  0  0            999 V2000
    0.0000    0.0000    0.0000 Se  0  0  0  0  0  0  0  0  0  0  0  0
M  END
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3D MOL for #<Metabolite:0x000055b76a69c310>

HMDB0011110
     RDKit          3D
Hydrogen selenide
  3  2  0  0  0  0  0  0  0  0999 V2000
   -0.0019    0.5887   -0.0000 Se  0  0  0  0  0  2  0  0  0  0  0  0
    1.2519   -0.2937    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2501   -0.2950   -0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  1  3  1  0
M  END
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3D SDF for #<Metabolite:0x000055b76a69c310>


  Mrv1652305221920242D          

  1  0  0  0  0  0            999 V2000
    0.0000    0.0000    0.0000 Se  0  0  0  0  0  0  0  0  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0029902

> <DATABASE_NAME>
MIME

> <SMILES>
[SeH2]

> <INCHI_IDENTIFIER>
InChI=1S/H2Se/h1H2

> <INCHI_KEY>
SPVXKVOXSXTJOY-UHFFFAOYSA-N

> <FORMULA>
H2Se

> <MOLECULAR_WEIGHT>
80.98

> <EXACT_MASS>
81.932171892

> <JCHEM_ACCEPTOR_COUNT>
1

> <JCHEM_ATOM_COUNT>
3

> <JCHEM_AVERAGE_POLARIZABILITY>
2.805576006751661

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
hydrogen selenide

> <JCHEM_LOGP>
-0.5047

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_POLAR_SURFACE_AREA>
0.0

> <JCHEM_REFRACTIVITY>
14.7149

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
hydrogen selenide

> <JCHEM_VEBER_RULE>
1

$$$$
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3D-SDF for #<Metabolite:0x000055b76a69c310>

HMDB0011110
     RDKit          3D
Hydrogen selenide
  3  2  0  0  0  0  0  0  0  0999 V2000
   -0.0019    0.5887   -0.0000 Se  0  0  0  0  0  2  0  0  0  0  0  0
    1.2519   -0.2937    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2501   -0.2950   -0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  1  3  1  0
M  END
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PDB for #<Metabolite:0x000055b76a69c310>

HEADER    PROTEIN                                 22-MAY-19   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   22-MAY-19         0                                  
HETATM    1 Se   UNK     0       0.000   0.000   0.000  0.00  0.00          Se+0
MASTER        0    0    0    0    0    0    0    0    1    0    0    0
END
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3D PDB for #<Metabolite:0x000055b76a69c310>

COMPND    HMDB0011110
HETATM    1 SE1  UNL     1      -0.002   0.589  -0.000  1.00  0.00          SE  
HETATM    2  H1  UNL     1       1.252  -0.294   0.000  1.00  0.00           H  
HETATM    3  H2  UNL     1      -1.250  -0.295  -0.000  1.00  0.00           H  
CONECT    1    2    3
END
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SMILES for #<Metabolite:0x000055b76a69c310>

[SeH2]
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INCHI for #<Metabolite:0x000055b76a69c310>

InChI=1S/H2Se/h1H2
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Synonyms
ValueSource
SelenideKegg
[SeH2]ChEBI
H2SeChEBI
Hydroselenic acidChEBI
HydroselenateGenerator
Dihydrogen monoselenideHMDB
Dihydrogen selenideHMDB
SelaneHMDB, MeSH
Selenium dihydrideHMDB
Selenium hydrideHMDB
Selenium hydride (seh2)HMDB
Hydrogen selenide, 75Se-labeledMeSH
Chemical FormulaH2Se
Average Molecular Weight80.98
Monoisotopic Molecular Weight81.932171892
IUPAC Namehydrogen selenide
Traditional Namehydrogen selenide
CAS Registry NumberNot Available
SMILES
[SeH2]
InChI Identifier
InChI=1S/H2Se/h1H2
InChI KeySPVXKVOXSXTJOY-UHFFFAOYSA-N