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Showing metabocard for Hydrogen selenide (HMDB0011110)

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IdentificationTaxonomyOntologyPhysical propertiesSpectraBiological propertiesConcentrationsLinksReferencesenzymes (6) Show 6 proteinsXML
enzymes (6) Show 6 proteins
Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2008-10-16 22:28:01 UTC
Update Date2020-06-26 02:34:23 UTC
HMDB IDHMDB0011110
Secondary Accession Numbers
  • HMDB11110
Metabolite Identification
Common NameHydrogen selenide
DescriptionHydrogen selenide, also known as selenide, 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'. Hydrogen selenide is a drug. Hydrogen selenide is possibly neutral. Hydrogen selenide exists in all living organisms, ranging from bacteria to humans. According to the Sonoda method, H2Se is generated from the reaction of H2O and CO on Se in the presence of Et3N. Within humans, hydrogen selenide participates in a number of enzymatic reactions. In particular, L-alanine and hydrogen selenide can be biosynthesized from selenocysteine; which is mediated by the enzyme selenocysteine lyase. In addition, hydrogen selenide can be converted into phosphoroselenoic acid; which is mediated by the enzyme selenide, water dikinase 2. In humans, hydrogen selenide is involved in selenoamino acid metabolism. Hydrogen selenide is a potentially toxic compound. Even at extremely low concentrations, this compound has a very irritating smell resembling that of decayed horseradish or 'leaking gas', but smells of rotten eggs at higher concentrations. H2Se is a colorless, flammable gas under standard conditions. H2Se + SO2 ⇌ 2 H2O + 2 Se + SIts decomposition is used to prepare the highly pure element.
Structure
Data?1593138863
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0011110 (Hydrogen selenide)


  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 HMDB0011110 (Hydrogen selenide)

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 HMDB0011110 (Hydrogen selenide)


  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>
HMDB0011110

> <DATABASE_NAME>
hmdb

> <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 HMDB0011110 (Hydrogen selenide)

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 HMDB0011110 (Hydrogen selenide)

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 HMDB0011110 (Hydrogen selenide)

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 HMDB0011110 (Hydrogen selenide)

[SeH2]
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INCHI for HMDB0011110 (Hydrogen selenide)

InChI=1S/H2Se/h1H2
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View in JSmolView NMR AssignmentsView Stereo Labels
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 Number7783-07-5
SMILES
[SeH2]
InChI Identifier
InChI=1S/H2Se/h1H2
InChI KeySPVXKVOXSXTJOY-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 Parents
Substituents
  • Homogeneous other non metal
  • Inorganic selenide
Molecular FrameworkNot Available
External Descriptors
Ontology
Physiological effect
Health effect
Disposition
Biological locationRoute of exposureSource
Process
Naturally occurring process
Role
Environmental role
Physical Properties
StateSolid
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 Charge-1ChemAxon
Hydrogen Acceptor Count1ChemAxon
Hydrogen Donor Count1ChemAxon
Polar Surface Area0 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity14.71 m³·mol⁻¹ChemAxon
Polarizability2.81 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]+113.20530932474
DeepCCS[M-H]-111.42630932474
DeepCCS[M-2H]-146.66130932474
DeepCCS[M+Na]+120.15630932474
AllCCS[M+H]+138.732859911
AllCCS[M+H-H2O]+134.532859911
AllCCS[M+NH4]+142.732859911
AllCCS[M+Na]+143.932859911
AllCCS[M-H]-349.932859911
AllCCS[M+Na-2H]-362.232859911
AllCCS[M+HCOO]-375.532859911

Predicted Retention Times

Underivatized

Chromatographic MethodRetention TimeReference
AjsUoB = Accucore 150 Amide HILIC with 10mM Ammonium Formate, 0.1% Formic Acid282.3 seconds40023050
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid1193.8 seconds40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid512.3 seconds40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid220.0 seconds40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid413.3 seconds40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid254.4 seconds40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid393.4 seconds40023050
BfG_NTS_RP1 =Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) with Water:ACN and 0.1% Formic Acid508.2 seconds40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)746.3 seconds40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid818.3 seconds40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid274.9 seconds40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid934.9 seconds40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid350.9 seconds40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid431.0 seconds40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate800.5 seconds40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA465.5 seconds40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water337.3 seconds40023050

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
Hydrogen selenide[SeH2]256.2Standard polar33892256
Hydrogen selenide[SeH2]277.2Standard non polar33892256
Hydrogen selenide[SeH2]260.0Semi standard non polar33892256
Spectra

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Hydrogen selenide 10V, Positive-QTOFsplash10-001i-9000000000-d9ac578ecd68e91829fb2015-09-15Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Hydrogen selenide 20V, Positive-QTOFsplash10-001i-9000000000-d9ac578ecd68e91829fb2015-09-15Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Hydrogen selenide 40V, Positive-QTOFsplash10-001i-9000000000-d9ac578ecd68e91829fb2015-09-15Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Hydrogen selenide 10V, Negative-QTOFsplash10-001i-9000000000-b0759ba90e57e47d84462015-09-15Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Hydrogen selenide 20V, Negative-QTOFsplash10-001i-9000000000-b0759ba90e57e47d84462015-09-15Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Hydrogen selenide 40V, Negative-QTOFsplash10-001i-9000000000-b0759ba90e57e47d84462015-09-15Wishart LabView Spectrum

NMR Spectra

Spectrum TypeDescriptionDeposition DateSourceView
Predicted 1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-09-29Wishart 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 IDDBMET01458
Phenol Explorer Compound IDNot Available
FooDB IDFDB027892
KNApSAcK IDNot Available
Chemspider ID518
KEGG Compound IDC01528
BioCyc IDCPD-678
BiGG IDNot Available
Wikipedia LinkHydrogen selenide
METLIN IDNot Available
PubChem Compound533
PDB IDSE
ChEBI ID16503
Food Biomarker OntologyNot Available
VMH IDSELN
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General References
  1. Sayato Y, Nakamuro K, Hasegawa T: [Selenium methylation and toxicity mechanism of selenocystine]. Yakugaku Zasshi. 1997 Nov;117(10-11):665-72. [PubMed:9414580 ]
  2. Lu J, Jiang C: Antiangiogenic activity of selenium in cancer chemoprevention: metabolite-specific effects. Nutr Cancer. 2001;40(1):64-73. [PubMed:11799926 ]

Enzymes

Enzyme Details
1. Thioredoxin reductase 1, cytoplasmic
General function:
Involved in oxidoreductase activity
Specific function:
Isoform 1 may possess glutaredoxin activity as well as thioredoxin reductase activity and induces actin and tubulin polymerization, leading to formation of cell membrane protrusions. Isoform 4 enhances the transcriptional activity of estrogen receptors alpha and beta while isoform 5 enhances the transcriptional activity of the beta receptor only. Isoform 5 also mediates cell death induced by a combination of interferon-beta and retinoic acid.
Gene Name:
TXNRD1
Uniprot ID:
Q16881
Molecular weight:
70905.58
Reactions
Hydrogen selenide + NADP + Water → Selenite + NADPH + Hydrogen Iondetails
Enzyme Details
2. Thioredoxin reductase 2, mitochondrial
General function:
Involved in oxidoreductase activity
Specific function:
Maintains thioredoxin in a reduced state. Implicated in the defenses against oxidative stress. May play a role in redox-regulated cell signaling.
Gene Name:
TXNRD2
Uniprot ID:
Q9NNW7
Molecular weight:
56506.275
Reactions
Hydrogen selenide + NADP + Water → Selenite + NADPH + Hydrogen Iondetails
Enzyme Details
3. Selenide, water dikinase 1
General function:
Involved in catalytic activity
Specific function:
Synthesizes selenophosphate from selenide and ATP.
Gene Name:
SEPHS1
Uniprot ID:
P49903
Molecular weight:
42910.325
Reactions
Adenosine triphosphate + Hydrogen selenide + Water → Adenosine monophosphate + Phosphoroselenoic acid + Phosphatedetails
Enzyme Details
4. Selenide, water dikinase 2
General function:
Involved in catalytic activity
Specific function:
Synthesizes selenophosphate from selenide and ATP.
Gene Name:
SEPHS2
Uniprot ID:
Q99611
Molecular weight:
47304.695
Reactions
Adenosine triphosphate + Hydrogen selenide + Water → Adenosine monophosphate + Phosphoroselenoic acid + Phosphatedetails
Enzyme Details
5. Selenocysteine lyase
General function:
Involved in metabolic process
Specific function:
Catalyzes the decomposition of L-selenocysteine to L-alanine and elemental selenium (By similarity).
Gene Name:
SCLY
Uniprot ID:
Q96I15
Molecular weight:
48793.15
Reactions
Selenocysteine + reduced acceptor → Hydrogen selenide + L-Alanine + acceptordetails
Selenocysteine + Reduced acceptor → Hydrogen selenide + L-Alanine + Acceptordetails
Enzyme Details
6. Thioredoxin reductase 3
General function:
Involved in oxidoreductase activity
Specific function:
Displays thioredoxin reductase, glutaredoxin and glutathione reductase activities. Catalyzes disulfide bond isomerization. Promotes disulfide bond formation between GPX4 and various sperm proteins and may play a role in sperm maturation by promoting formation of sperm structural components (By similarity).
Gene Name:
TXNRD3
Uniprot ID:
Q86VQ6
Molecular weight:
66600.92
Reactions
Hydrogen selenide + NADP + Water → Selenite + NADPH + Hydrogen Iondetails