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Identification Taxonomy Ontology Physical properties Spectra Biological properties Concentrations Links References enzymes (6) Show 6 proteins XML

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Record Information

Version

5.0

Status

Expected but not Quantified

Creation Date

2008-10-16 22:28:01 UTC

Update Date

2020-06-26 02:34:23 UTC

HMDB ID

HMDB0011110

Secondary Accession Numbers

HMDB11110

Metabolite Identification

Common Name

Hydrogen selenide

Description

Hydrogen 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

MOL 3D MOL SDF 3D SDF PDB 3D PDB SMILES InChI

View in JSmol View NMR Assignments View Stereo Labels

Synonyms

Value	Source
Selenide	Kegg
[SeH2]	ChEBI
H2Se	ChEBI
Hydroselenic acid	ChEBI
Hydroselenate	Generator
Dihydrogen monoselenide	HMDB
Dihydrogen selenide	HMDB
Selane	HMDB, MeSH
Selenium dihydride	HMDB
Selenium hydride	HMDB
Selenium hydride (seh2)	HMDB
Hydrogen selenide, 75Se-labeled	MeSH

Chemical Formula

H₂Se

Average Molecular Weight

80.98

Monoisotopic Molecular Weight

81.932171892

IUPAC Name

hydrogen selenide

Traditional Name

hydrogen selenide

CAS Registry Number

7783-07-5

SMILES

[SeH2]

InChI Identifier

InChI=1S/H2Se/h1H2

InChI Key

SPVXKVOXSXTJOY-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'.

Kingdom

Inorganic compounds

Super Class

Homogeneous non-metal compounds

Class

Homogeneous other non-metal compounds

Sub Class

Not Available

Direct Parent

Homogeneous other non-metal compounds

Alternative Parents

Inorganic selenides

Substituents

Homogeneous other non metal
Inorganic selenide

Molecular Framework

Not Available

External Descriptors

selenium hydride (CHEBI:16503 )
mononuclear parent hydride (CHEBI:16503 )
a small molecule (CPD-678 )

Ontology

Not Available

Physical Properties

State

Solid

Experimental Molecular Properties

Property	Value	Reference
Melting Point	Not Available	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	Not Available	Not Available
LogP	Not Available	Not Available

Experimental Chromatographic Properties

Not Available

Predicted Molecular Properties

Property	Value	Source
logP	-0.5	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	1	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	0 Å²	ChemAxon
Rotatable Bond Count	0	ChemAxon
Refractivity	14.71 m³·mol⁻¹	ChemAxon
Polarizability	2.81 Å³	ChemAxon
Number of Rings	0	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	Yes	ChemAxon
MDDR-like Rule	No	ChemAxon

Predicted Chromatographic Properties

Predicted Collision Cross Sections

Predictor	Adduct Type	CCS Value (Å²)	Reference
DeepCCS	[M+H]+	113.205	30932474
DeepCCS	[M-H]-	111.426	30932474
DeepCCS	[M-2H]-	146.661	30932474
DeepCCS	[M+Na]+	120.156	30932474
AllCCS	[M+H]+	138.7	32859911
AllCCS	[M+H-H2O]+	134.5	32859911
AllCCS	[M+NH4]+	142.7	32859911
AllCCS	[M+Na]+	143.9	32859911
AllCCS	[M-H]-	349.9	32859911
AllCCS	[M+Na-2H]-	362.2	32859911
AllCCS	[M+HCOO]-	375.5	32859911

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
Hydrogen selenide	[SeH2]	256.2	Standard polar	33892256
Hydrogen selenide	[SeH2]	277.2	Standard non polar	33892256
Hydrogen selenide	[SeH2]	260.0	Semi standard non polar	33892256

Spectra

MS/MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Hydrogen selenide 10V, Positive-QTOF	splash10-001i-9000000000-d9ac578ecd68e91829fb	2015-09-15	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Hydrogen selenide 20V, Positive-QTOF	splash10-001i-9000000000-d9ac578ecd68e91829fb	2015-09-15	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Hydrogen selenide 40V, Positive-QTOF	splash10-001i-9000000000-d9ac578ecd68e91829fb	2015-09-15	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Hydrogen selenide 10V, Negative-QTOF	splash10-001i-9000000000-b0759ba90e57e47d8446	2015-09-15	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Hydrogen selenide 20V, Negative-QTOF	splash10-001i-9000000000-b0759ba90e57e47d8446	2015-09-15	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Hydrogen selenide 40V, Negative-QTOF	splash10-001i-9000000000-b0759ba90e57e47d8446	2015-09-15	Wishart Lab	View Spectrum

NMR Spectra

Spectrum Type	Description	Deposition Date	Source	View
Predicted 1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Not Available

Tissue Locations

Not Available

Pathways

Name	SMPDB/PathBank	KEGG
Selenocompound metabolism	Not Available

Normal Concentrations

Not Available

Abnormal Concentrations

Not Available

Associated Disorders and Diseases

Disease References

None

Associated OMIM IDs

None

External Links

DrugBank ID

DBMET01458

Phenol Explorer Compound ID

Not Available

FooDB ID

FDB027892

KNApSAcK ID

Not Available

Chemspider ID

518

KEGG Compound ID

C01528

BioCyc ID

CPD-678

BiGG ID

Not Available

Wikipedia Link

Hydrogen selenide

METLIN ID

Not Available

PubChem Compound

533

PDB ID

ChEBI ID

16503

Food Biomarker Ontology

Not Available

VMH ID

SELN

MarkerDB ID

Not Available

Good Scents ID

Not Available

References

Synthesis Reference

Not Available

Material Safety Data Sheet (MSDS)

Not Available

General References

Sayato Y, Nakamuro K, Hasegawa T: [Selenium methylation and toxicity mechanism of selenocystine]. Yakugaku Zasshi. 1997 Nov;117(10-11):665-72. [PubMed:9414580 ]
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 Ion	details

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 Ion	details

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 + Phosphate	details

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 + Phosphate	details

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 + acceptor	details
Selenocysteine + Reduced acceptor → Hydrogen selenide + L-Alanine + Acceptor	details

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 Ion	details

Showing metabocard for Hydrogen selenide (HMDB0011110)

MOL for HMDB0011110 (Hydrogen selenide)

3D MOL for HMDB0011110 (Hydrogen selenide)

3D SDF for HMDB0011110 (Hydrogen selenide)

3D-SDF for HMDB0011110 (Hydrogen selenide)

PDB for HMDB0011110 (Hydrogen selenide)

3D PDB for HMDB0011110 (Hydrogen selenide)

SMILES for HMDB0011110 (Hydrogen selenide)

INCHI for HMDB0011110 (Hydrogen selenide)

Structure for HMDB0011110 (Hydrogen selenide)

3D Structure for HMDB0011110 (Hydrogen selenide)

Predicted Collision Cross Sections

Predicted Kovats Retention Indices

Underivatized

MS/MS Spectra

NMR Spectra

Enzymes

Reactions

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