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Showing metabocard for Methaneselenol (HMDB0060488)

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enzymes (5) Show 5 proteins
Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2013-05-17 01:24:25 UTC
Update Date2022-03-07 03:17:45 UTC
HMDB IDHMDB0060488
Secondary Accession Numbers
  • HMDB60488
Metabolite Identification
Common NameMethaneselenol
DescriptionMethaneselenol, commonly referred to as methylselenol, is an organoselenium compound that is a selenium analogue of methanol. It consists of a methyl group covalently bound to a selenol group. Methylselenol is a naturally produced metabolite of selenium (Se), an essential trace element (PMID: 25258323 ). Inorganic selenium is mainly represented by selenate and selenite, whereas the organic selenium forms are represented by the selenoamino acids: selenomethionine (SeMet), selenocysteine (SeCys) and selenium methylselenocysteine (MSC) (PMID: 25258323 ). SeMet and MSC can be found in vegetables such as garlic and onions. Selenite is reduced in the presence of glutathione to selenide (H2Se). SeMet and selenocysteine (SeCys2) are also primarily converted to selenide and incorporated into selenoproteins or selenosugars. On the other hand, MSC (a natural metabolite) and the antineoplastic drug methylselenic acid (MSA) are converted to methylselenol by the enzyme beta-lyase (PMID: 25258323 ). Both selenide and methylselenol are highly reactive and both can interconvert through methylation/demethylation activities. Methylselenol is thought to be most significant in the anticancer activity of Se compounds (PMID: 30241340 ). Redox active Se compounds such as methylselenol have gained significant attention in the past decade as potential cancer therapeutic agents. Methylselenol is known for its action to selectively kill transformed cells through mechanisms that include increased formation of reactive oxygen species, induction of DNA damage, triggering of apoptosis, and inhibition of angiogenesis. Methylselenol also regulates the expression of ligands that trigger immune activation through the lymphocyte receptor NKG2D. The expression of NKG2D ligands is induced by stress-associated pathways that occur early during malignant transformation and enable the recognition and elimination of tumors by activating the lymphocyte receptor NKG2D (PMID: 25258323 ). This suggests that the application of selenium compounds that are metabolized to CH3SeH could improve NKG2D-based immune therapy for cancer treatment.
Structure
Data?1563866067
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0060488 (Methaneselenol)


  Mrv0541 05161318242D          

  2  1  0  0  0  0            999 V2000
    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  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  0  0  0  0
M  END
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3D MOL for HMDB0060488 (Methaneselenol)

HMDB0060488
     RDKit          3D
Methaneselenol
  6  5  0  0  0  0  0  0  0  0999 V2000
   -0.6021    0.0171   -0.0076 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1653   -0.7455   -0.0650 Se  0  0  0  0  0  2  0  0  0  0  0  0
   -1.3016   -0.7151   -0.4621 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9088    0.1520    1.0497 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5921    0.9712   -0.5634 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2393    0.3202    0.0485 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  1  3  1  0
  1  4  1  0
  1  5  1  0
  2  6  1  0
M  END
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3D SDF for HMDB0060488 (Methaneselenol)


  Mrv0541 05161318242D          

  2  1  0  0  0  0            999 V2000
    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  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0060488

> <DATABASE_NAME>
hmdb

> <SMILES>
C[SeH]

> <INCHI_IDENTIFIER>
InChI=1S/CH4Se/c1-2/h2H,1H3

> <INCHI_KEY>
APKHDKJWSHYLEU-UHFFFAOYSA-N

> <FORMULA>
CH4Se

> <MOLECULAR_WEIGHT>
95.0

> <EXACT_MASS>
95.947821956

> <JCHEM_ACCEPTOR_COUNT>
1

> <JCHEM_AVERAGE_POLARIZABILITY>
4.757287886859288

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
methaneselenol

> <ALOGPS_LOGP>
-0.82

> <JCHEM_LOGP>
0.06430000000000008

> <ALOGPS_LOGS>
0.12

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_POLAR_SURFACE_AREA>
0

> <JCHEM_REFRACTIVITY>
19.464000000000002

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.26e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
methaneselenol

> <JCHEM_VEBER_RULE>
1

$$$$
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3D-SDF for HMDB0060488 (Methaneselenol)

HMDB0060488
     RDKit          3D
Methaneselenol
  6  5  0  0  0  0  0  0  0  0999 V2000
   -0.6021    0.0171   -0.0076 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1653   -0.7455   -0.0650 Se  0  0  0  0  0  2  0  0  0  0  0  0
   -1.3016   -0.7151   -0.4621 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9088    0.1520    1.0497 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5921    0.9712   -0.5634 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2393    0.3202    0.0485 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  1  3  1  0
  1  4  1  0
  1  5  1  0
  2  6  1  0
M  END
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PDB for HMDB0060488 (Methaneselenol)

HEADER    PROTEIN                                 16-MAY-13   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   16-MAY-13         0                                  
HETATM    1  C   UNK     0       1.540   0.000   0.000  0.00  0.00           C+0
HETATM    2 Se   UNK     0       0.000   0.000   0.000  0.00  0.00          Se+0
CONECT    1    2                                                            
CONECT    2    1                                                            
MASTER        0    0    0    0    0    0    0    0    2    0    2    0
END
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3D PDB for HMDB0060488 (Methaneselenol)

COMPND    HMDB0060488
HETATM    1  C1  UNL     1      -0.602   0.017  -0.008  1.00  0.00           C  
HETATM    2 SE1  UNL     1       1.165  -0.745  -0.065  1.00  0.00          SE  
HETATM    3  H1  UNL     1      -1.302  -0.715  -0.462  1.00  0.00           H  
HETATM    4  H2  UNL     1      -0.909   0.152   1.050  1.00  0.00           H  
HETATM    5  H3  UNL     1      -0.592   0.971  -0.563  1.00  0.00           H  
HETATM    6  H4  UNL     1       2.239   0.320   0.048  1.00  0.00           H  
CONECT    1    2    3    4    5
CONECT    2    6
END
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SMILES for HMDB0060488 (Methaneselenol)

C[SeH]
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INCHI for HMDB0060488 (Methaneselenol)

InChI=1S/CH4Se/c1-2/h2H,1H3
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View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
ValueSource
MethylselenolKegg
MethaneselenolChEBI
Chemical FormulaCH4Se
Average Molecular Weight95.0
Monoisotopic Molecular Weight95.947821956
IUPAC Namemethaneselenol
Traditional Namemethaneselenol
CAS Registry NumberNot Available
SMILES
C[SeH]
InChI Identifier
InChI=1S/CH4Se/c1-2/h2H,1H3
InChI KeyAPKHDKJWSHYLEU-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as selenols. These are organic compounds that contains the functional group with the connectivity R-Se-H.
KingdomOrganic compounds
Super ClassOrganometallic compounds
ClassOrganometalloid compounds
Sub ClassOrganoselenium compounds
Direct ParentSelenols
Alternative Parents
Substituents
  • Hydrocarbon derivative
  • Selenol
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Ontology
Physiological effectNot Available
DispositionNot Available
Process
Naturally occurring process
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 Solubility126 g/LALOGPS
logP-0.82ALOGPS
logP0.064ChemAxon
logS0.12ALOGPS
Physiological Charge0ChemAxon
Hydrogen Acceptor Count1ChemAxon
Hydrogen Donor Count1ChemAxon
Polar Surface Area0 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity19.46 m³·mol⁻¹ChemAxon
Polarizability4.76 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]+119.7230932474
DeepCCS[M-H]-117.87430932474
DeepCCS[M-2H]-153.18930932474
DeepCCS[M+Na]+127.05630932474
AllCCS[M+H]+135.332859911
AllCCS[M+H-H2O]+131.032859911
AllCCS[M+NH4]+139.332859911
AllCCS[M+Na]+140.432859911
AllCCS[M-H]-274.132859911
AllCCS[M+Na-2H]-284.732859911
AllCCS[M+HCOO]-296.232859911

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
MethaneselenolC[SeH]822.5Standard polar33892256
MethaneselenolC[SeH]411.9Standard non polar33892256
MethaneselenolC[SeH]540.4Semi standard non polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - Methaneselenol GC-MS (Non-derivatized) - 70eV, Positivesplash10-0005-9000000000-0ad8c1eee45c56fe8f2b2016-09-22Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Methaneselenol 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 - Methaneselenol 10V, Positive-QTOFsplash10-0002-9000000000-e4d95352b945b461c6922016-09-14Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Methaneselenol 20V, Positive-QTOFsplash10-0002-9000000000-e4d95352b945b461c6922016-09-14Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Methaneselenol 40V, Positive-QTOFsplash10-0002-9000000000-e4d95352b945b461c6922016-09-14Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Methaneselenol 10V, Negative-QTOFsplash10-0006-9000000000-714d406c305f53bf1f7b2016-09-14Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Methaneselenol 20V, Negative-QTOFsplash10-0006-9000000000-714d406c305f53bf1f7b2016-09-14Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Methaneselenol 40V, Negative-QTOFsplash10-0006-9000000000-714d406c305f53bf1f7b2016-09-14Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Methaneselenol 10V, Positive-QTOFsplash10-0002-9000000000-186d833c2a1d3a4b8f2b2021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Methaneselenol 20V, Positive-QTOFsplash10-0002-9000000000-186d833c2a1d3a4b8f2b2021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Methaneselenol 40V, Positive-QTOFsplash10-0002-9000000000-186d833c2a1d3a4b8f2b2021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Methaneselenol 10V, Negative-QTOFsplash10-0006-9000000000-f9689d19a8a4fb34dc2c2021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Methaneselenol 20V, Negative-QTOFsplash10-0006-9000000000-f9689d19a8a4fb34dc2c2021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Methaneselenol 40V, Negative-QTOFsplash10-0006-9000000000-f9689d19a8a4fb34dc2c2021-10-12Wishart LabView Spectrum

NMR Spectra

Spectrum TypeDescriptionDeposition DateSourceView
Predicted 1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 100 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, 1000 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, 200 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, 300 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, 400 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, 500 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, 600 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, 700 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, 800 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C 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 IDDBMET01461
Phenol Explorer Compound IDNot Available
FooDB IDNot Available
KNApSAcK IDNot Available
Chemspider IDNot Available
KEGG Compound IDC05703
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkSelenol
METLIN IDNot Available
PubChem Compound440764
PDB IDNot Available
ChEBI ID64685
Food Biomarker OntologyNot Available
VMH IDM02469
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General References
  1. Magrane M: UniProt Knowledgebase: a hub of integrated protein data. Database (Oxford). 2011 Mar 29;2011:bar009. doi: 10.1093/database/bar009. Print 2011. [PubMed:21447597 ]
  2. Hagemann-Jensen M, Uhlenbrock F, Kehlet S, Andresen L, Gabel-Jensen C, Ellgaard L, Gammelgaard B, Skov S: The selenium metabolite methylselenol regulates the expression of ligands that trigger immune activation through the lymphocyte receptor NKG2D. J Biol Chem. 2014 Nov 7;289(45):31576-90. doi: 10.1074/jbc.M114.591537. Epub 2014 Sep 25. [PubMed:25258323 ]
  3. Khalkar P, Diaz-Argelich N, Antonio Palop J, Sanmartin C, Fernandes AP: Novel Methylselenoesters Induce Programed Cell Death via Entosis in Pancreatic Cancer Cells. Int J Mol Sci. 2018 Sep 20;19(10). pii: ijms19102849. doi: 10.3390/ijms19102849. [PubMed:30241340 ]

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
NADPH + Hydrogen Ion + Methylselenic acid → NADP + Water + Methaneselenoldetails
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
NADPH + Hydrogen Ion + Methylselenic acid → NADP + Water + Methaneselenoldetails
Enzyme Details
3. Cystathionine gamma-lyase
General function:
Involved in pyridoxal phosphate binding
Specific function:
Catalyzes the last step in the trans-sulfuration pathway from methionine to cysteine. Has broad substrate specificity. Converts cystathionine to cysteine, ammonia and 2-oxobutanoate. Converts two cysteine molecules to lanthionine and hydrogen sulfide. Can also accept homocysteine as substrate. Specificity depends on the levels of the endogenous substrates. Generates the endogenous signaling molecule hydrogen sulfide (H2S), and so contributes to the regulation of blood pressure. Acts as a cysteine-protein sulfhydrase by mediating sulfhydration of target proteins: sulfhydration consists of converting -SH groups into -SSH on specific cysteine residues of target proteins such as GAPDH, PTPN1 and NF-kappa-B subunit RELA, thereby regulating their function.
Gene Name:
CTH
Uniprot ID:
P32929
Molecular weight:
41259.91
Reactions
Selenomethionine + Water → Methaneselenol + Ammonia + 2-Ketobutyric aciddetails
Enzyme Details
4. 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
Se-Methylselenocysteine + Water → Pyruvic acid + Ammonia + Methaneselenoldetails
Enzyme Details
5. 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
NADPH + Hydrogen Ion + Methylselenic acid → NADP + Water + Methaneselenoldetails