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Showing metabocard for Selenite (HMDB0011119)

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IdentificationTaxonomyOntologyPhysical propertiesSpectraBiological propertiesConcentrationsLinksReferencesenzymes (3) Show 3 proteinsXML
enzymes (3) Show 3 proteins
Record Information
Version5.0
StatusDetected and Quantified
Creation Date2008-10-16 22:33:40 UTC
Update Date2023-02-21 17:17:27 UTC
HMDB IDHMDB0011119
Secondary Accession Numbers
  • HMDB11119
Metabolite Identification
Common NameSelenite
DescriptionThe selenite anion is a selenium oxoanion with the chemical formula SeO32−. A selenite (compound) is a compound that contains this ion. In slightly acid conditions, the hydrogenselenite ion, HSeO3−, is formed; in more acidic conditions selenous acid, H2SeO3, exists. Most selenite salts can be formed by heating the relevant metal oxide with selenium dioxide, e.g.:Na2O + SeO2 → Na2SeO3. Selenite is an inorganic form of selenium which may also be useful in cancer chemotherapy.(Wikipedia ).
Structure
Data?1676999847
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0011119 (Selenite)


  Mrv1652305171806002D          

  4  3  0  0  0  0            999 V2000
    0.8250    0.0000    0.0000 Se  0  0  0  0  0  4  0  0  0  0  0  0
    1.2375    0.7145    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375   -0.7145    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  3  1  1  0  0  0  0
  4  1  1  0  0  0  0
M  END
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3D MOL for HMDB0011119 (Selenite)

HMDB0011119
     RDKit          3D
Selenite
  6  5  0  0  0  0  0  0  0  0999 V2000
   -0.4126    1.9555   -0.4980 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1064    0.6707    0.4572 Se  0  0  0  0  0  4  0  0  0  0  0  0
   -1.4071   -0.5942    0.4067 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.5713    0.0036    0.2668 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2169   -1.1908   -0.3719 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5717   -0.8449   -0.2609 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  2  4  1  0
  3  5  1  0
  4  6  1  0
M  END
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3D SDF for HMDB0011119 (Selenite)


  Mrv1652305171806002D          

  4  3  0  0  0  0            999 V2000
    0.8250    0.0000    0.0000 Se  0  0  0  0  0  4  0  0  0  0  0  0
    1.2375    0.7145    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375   -0.7145    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  3  1  1  0  0  0  0
  4  1  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0011119

> <DATABASE_NAME>
hmdb

> <SMILES>
O[Se](O)=O

> <INCHI_IDENTIFIER>
InChI=1S/H2O3Se/c1-4(2)3/h(H2,1,2,3)

> <INCHI_KEY>
MCAHWIHFGHIESP-UHFFFAOYSA-N

> <FORMULA>
H2O3Se

> <MOLECULAR_WEIGHT>
128.97

> <EXACT_MASS>
129.916915758

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
6

> <JCHEM_AVERAGE_POLARIZABILITY>
5.839589010021143

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
selenous acid

> <JCHEM_LOGP>
-1.2765

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
6.80102999566398

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.1989700043360187

> <JCHEM_POLAR_SURFACE_AREA>
57.53

> <JCHEM_REFRACTIVITY>
19.686999999999998

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
selenious acid

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for HMDB0011119 (Selenite)

HMDB0011119
     RDKit          3D
Selenite
  6  5  0  0  0  0  0  0  0  0999 V2000
   -0.4126    1.9555   -0.4980 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1064    0.6707    0.4572 Se  0  0  0  0  0  4  0  0  0  0  0  0
   -1.4071   -0.5942    0.4067 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.5713    0.0036    0.2668 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2169   -1.1908   -0.3719 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5717   -0.8449   -0.2609 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  2  4  1  0
  3  5  1  0
  4  6  1  0
M  END
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PDB for HMDB0011119 (Selenite)

HEADER    PROTEIN                                 17-MAY-18   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   17-MAY-18         0                                  
HETATM    1 Se   UNK     0       1.540   0.000   0.000  0.00  0.00          Se+0
HETATM    2  O   UNK     0       2.310   1.334   0.000  0.00  0.00           O+0
HETATM    3  O   UNK     0       2.310  -1.334   0.000  0.00  0.00           O+0
HETATM    4  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
CONECT    1    2    3    4                                                  
CONECT    2    1                                                            
CONECT    3    1                                                            
CONECT    4    1                                                            
MASTER        0    0    0    0    0    0    0    0    4    0    6    0
END
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3D PDB for HMDB0011119 (Selenite)

COMPND    HMDB0011119
HETATM    1  O1  UNL     1      -0.413   1.956  -0.498  1.00  0.00           O  
HETATM    2 SE1  UNL     1      -0.106   0.671   0.457  1.00  0.00          SE  
HETATM    3  O2  UNL     1      -1.407  -0.594   0.407  1.00  0.00           O  
HETATM    4  O3  UNL     1       1.571   0.004   0.267  1.00  0.00           O  
HETATM    5  H1  UNL     1      -1.217  -1.191  -0.372  1.00  0.00           H  
HETATM    6  H2  UNL     1       1.572  -0.845  -0.261  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3    4
CONECT    3    5
CONECT    4    6
END
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SMILES for HMDB0011119 (Selenite)

O[Se](O)=O
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INCHI for HMDB0011119 (Selenite)

InChI=1S/H2O3Se/c1-4(2)3/h(H2,1,2,3)
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View in JSmolView Stereo Labels
Synonyms
ValueSource
[seo(OH)2]ChEBI
Selenige saeureChEBI
Selenious acidChEBI
SeleniteMeSH
Acid, seleniousMeSH, HMDB
Acid, selenousMeSH, HMDB
Selenous acidMeSH
Chemical FormulaH2O3Se
Average Molecular Weight128.97
Monoisotopic Molecular Weight129.916915758
IUPAC Nameselenous acid
Traditional Nameselenious acid
CAS Registry Number14124-67-5
SMILES
O[Se](O)=O
InChI Identifier
InChI=1S/H2O3Se/c1-4(2)3/h(H2,1,2,3)
InChI KeyMCAHWIHFGHIESP-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of inorganic compounds known as non-metal selenites. These are inorganic non-metallic compounds containing a selenite as its largest oxoanion.
KingdomInorganic compounds
Super ClassMixed metal/non-metal compounds
ClassOther mixed metal/non-metal oxoanionic compounds
Sub ClassNon-metal selenites
Direct ParentNon-metal selenites
Alternative Parents
Substituents
  • Non-metal selenite
  • Inorganic oxide
Molecular FrameworkNot Available
External Descriptors
Ontology
Not AvailableNot Available
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-1.3ChemAxon
pKa (Strongest Acidic)1.2ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count4ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area57.53 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity19.69 m³·mol⁻¹ChemAxon
Polarizability5.84 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
DeepCCS[M+H]+123.32430932474
DeepCCS[M-H]-121.17530932474
DeepCCS[M-2H]-157.13830932474
DeepCCS[M+Na]+131.54530932474
AllCCS[M+H]+135.032859911
AllCCS[M+H-H2O]+130.832859911
AllCCS[M+NH4]+138.932859911
AllCCS[M+Na]+140.032859911
AllCCS[M-H]-166.432859911
AllCCS[M+Na-2H]-173.132859911
AllCCS[M+HCOO]-180.532859911

Predicted Retention Times

Underivatized

Chromatographic MethodRetention TimeReference
AjsUoB = Accucore 150 Amide HILIC with 10mM Ammonium Formate, 0.1% Formic Acid205.6 seconds40023050
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid1117.2 seconds40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid420.8 seconds40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid166.9 seconds40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid326.7 seconds40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid154.0 seconds40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid326.5 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 Acid419.2 seconds40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)489.6 seconds40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid701.2 seconds40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid212.0 seconds40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid906.3 seconds40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid277.1 seconds40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid345.1 seconds40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate697.7 seconds40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA337.0 seconds40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water277.7 seconds40023050

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
SeleniteO[Se](O)=O1620.5Standard polar33892256
SeleniteO[Se](O)=O816.2Standard non polar33892256
SeleniteO[Se](O)=O941.1Semi standard non polar33892256
Spectra
Biological Properties
Cellular LocationsNot Available
Biospecimen Locations
  • Blood
Tissue LocationsNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodDetected and Quantified0.0013 (0.00-0.0063) uMAdult (>18 years old)FemaleNormal details
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDDB11127
Phenol Explorer Compound IDNot Available
FooDB IDNot Available
KNApSAcK IDNot Available
Chemspider IDNot Available
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkSelenite
METLIN IDNot Available
PubChem Compound1091
PDB IDNot Available
ChEBI IDNot Available
Food Biomarker OntologyNot Available
VMH IDSELNI
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General ReferencesNot Available

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. 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