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Showing metabocard for Iodide (HMDB0012238)

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IdentificationTaxonomyOntologyPhysical propertiesSpectraBiological propertiesConcentrationsLinksReferencesenzymes (5) Show 5 proteinsXML
enzymes (5) Show 5 proteins
Record Information
Version5.0
StatusDetected and Quantified
Creation Date2009-04-06 16:21:33 UTC
Update Date2020-02-26 21:37:11 UTC
HMDB IDHMDB0012238
Secondary Accession Numbers
  • HMDB12238
Metabolite Identification
Common NameIodide
DescriptionIodide can function as an antioxidant as it is a reducing species that can detoxify reactive oxygen species such as hydrogen peroxide. Over three billion years ago, blue-green algae were the most primitive oxygenic photosynthetic organisms and are the ancestors of multicellular eukaryotic algae (1). Algae that contain the highest amount of iodine (1-3 % of dry weight) and peroxidase enzymes, were the first living cells to produce poisonous oxygen in the atmosphere. Therefore algal cells required a protective antioxidant action of their molecular components, in which iodides, through peroxidase enzymes, seem to have had this specific role. In fact, iodides are greatly present and available in the sea, where algal phytoplankton, the basis of marine food-chain, acts as a biological accumulator of iodides, selenium, (and n-3 fatty acids) :; Antioxidant biochemical mechanism of iodides, probably one of the most ancient mechanisms of defense from poisonous reactive oxygen species:; An iodide ion is an iodine atom with a -1 charge. Compounds with iodine in formal oxidation state -1 are called iodides. This can include ionic compounds such as caesium iodide or covalent compounds such as phosphorus triiodide. This is the same naming scheme as is seen with chlorides and bromides. The chemical test for an iodide compound is to acidify the aqueous compound by adding some drops of acid, to dispel any carbonate ions present, then adding lead(II) nitrate, yielding a bright yellow precipitate of lead iodide. Most ionic iodides are soluble, with the exception of yellow silver iodide and yellow lead iodide. Aqueous solutions of iodide dissolve iodine better than pure water due to the formation of complex ions:.
Structure
Data?1582753031
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0012238 (Iodide)


  Mrv1652309042000352D          

  1  0  0  0  0  0            999 V2000
   19.5814  -17.2259    0.0000 I   0  5  0  0  0  0  0  0  0  0  0  0
M  CHG  1   1  -1
M  END
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3D MOL for HMDB0012238 (Iodide)

HMDB0012238
     RDKit          3D
Iodide
  1  0  0  0  0  0  0  0  0  0999 V2000
    0.0000    0.0000    0.0000 I   0  0  0  0  0 15  0  0  0  0  0  0
M  CHG  1   1  -1
M  END
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3D SDF for HMDB0012238 (Iodide)


  Mrv1652309042000352D          

  1  0  0  0  0  0            999 V2000
   19.5814  -17.2259    0.0000 I   0  5  0  0  0  0  0  0  0  0  0  0
M  CHG  1   1  -1
M  END
> <DATABASE_ID>
HMDB0012238

> <DATABASE_NAME>
hmdb

> <SMILES>
[I-]

> <INCHI_IDENTIFIER>
InChI=1S/HI/h1H/p-1

> <INCHI_KEY>
XMBWDFGMSWQBCA-UHFFFAOYSA-M

> <FORMULA>
I

> <MOLECULAR_WEIGHT>
126.9045

> <EXACT_MASS>
126.90446842

> <JCHEM_ACCEPTOR_COUNT>
0

> <JCHEM_ATOM_COUNT>
1

> <JCHEM_AVERAGE_POLARIZABILITY>
5.07487188

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
-1

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
iodide

> <JCHEM_LOGP>
1.02055578

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA_STRONGEST_ACIDIC>
-8.999999999999996

> <JCHEM_POLAR_SURFACE_AREA>
0.0

> <JCHEM_REFRACTIVITY>
13.9462

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
iodide

> <JCHEM_VEBER_RULE>
1

$$$$
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3D-SDF for HMDB0012238 (Iodide)

HMDB0012238
     RDKit          3D
Iodide
  1  0  0  0  0  0  0  0  0  0999 V2000
    0.0000    0.0000    0.0000 I   0  0  0  0  0 15  0  0  0  0  0  0
M  CHG  1   1  -1
M  END
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PDB for HMDB0012238 (Iodide)

HEADER    PROTEIN                                 04-SEP-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   04-SEP-20         0                                  
HETATM    1  I   UNK     0      36.552 -32.155   0.000  0.00  0.00           I-1
MASTER        0    0    0    0    0    0    0    0    1    0    0    0
END
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3D PDB for HMDB0012238 (Iodide)

COMPND    HMDB0012238
HETATM    1  I1  UNL     1       0.000   0.000   0.000  1.00  0.00           I1-
END
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SMILES for HMDB0012238 (Iodide)

[I-]
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INCHI for HMDB0012238 (Iodide)

InChI=1S/HI/h1H/p-1
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View in JSmolView Stereo Labels
Synonyms
ValueSource
I(-)ChEBI
IODIDE ionChEBI
Iodine anionChEBI
Iodide anionHMDB
Iodide saltHMDB
Iodide(1-)HMDB
IodinaneHMDB
Iodine ionHMDB
Lambda(3)-iodaneHMDB
TrihydridoiodineHMDB
IodolipolMeSH
Oils, iodizedMeSH
Oil, iodizedMeSH
Iodized oilMeSH
Iodized oilsMeSH
Chemical FormulaI
Average Molecular Weight126.9045
Monoisotopic Molecular Weight126.90446842
IUPAC Nameiodide
Traditional Nameiodide
CAS Registry Number20461-54-5
SMILES
[I-]
InChI Identifier
InChI=1S/HI/h1H/p-1
InChI KeyXMBWDFGMSWQBCA-UHFFFAOYSA-M
Chemical Taxonomy
Description Belongs to the class of inorganic compounds known as homogeneous halogens. These are inorganic non-metallic compounds in which the largest atom is a nobel gas.
KingdomInorganic compounds
Super ClassHomogeneous non-metal compounds
ClassHomogeneous halogens
Sub ClassNot Available
Direct ParentHomogeneous halogens
Alternative ParentsNot Available
Substituents
  • Homogeneous halogen
Molecular FrameworkNot Available
External Descriptors
Ontology
Physiological effectNot Available
Disposition
Biological locationRoute of exposureSource
Process
Naturally occurring process
Role
Industrial application
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
logP1.02ChemAxon
pKa (Strongest Acidic)-9ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count0ChemAxon
Hydrogen Donor Count0ChemAxon
Polar Surface Area0 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity13.95 m³·mol⁻¹ChemAxon
Polarizability5.07 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]+116.53430932474
DeepCCS[M-H]-114.68430932474
DeepCCS[M-2H]-149.97630932474
DeepCCS[M+Na]+123.79230932474
AllCCS[M+H]+129.032859911
AllCCS[M+H-H2O]+125.432859911
AllCCS[M+NH4]+132.432859911
AllCCS[M+Na]+133.432859911
AllCCS[M-H]-176.432859911
AllCCS[M+Na-2H]-188.232859911
AllCCS[M+HCOO]-201.032859911

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
Iodide[I-]874.9Standard polar33892256
Iodide[I-]355.2Standard non polar33892256
Iodide[I-]253.2Semi standard non polar33892256
Spectra

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Iodide 10V, Positive-QTOFsplash10-004i-0900000000-6dd6bb8e07c4fae8055b2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Iodide 20V, Positive-QTOFsplash10-004i-0900000000-6dd6bb8e07c4fae8055b2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Iodide 40V, Positive-QTOFsplash10-004i-0900000000-6dd6bb8e07c4fae8055b2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Iodide 10V, Negative-QTOFsplash10-004i-0900000000-004a30645c893513e9ed2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Iodide 20V, Negative-QTOFsplash10-004i-0900000000-004a30645c893513e9ed2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Iodide 40V, Negative-QTOFsplash10-004i-0900000000-004a30645c893513e9ed2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Iodide 10V, Negative-QTOFsplash10-004i-0900000000-0dba40d354fa6a5575e02021-09-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Iodide 20V, Negative-QTOFsplash10-004i-0900000000-0dba40d354fa6a5575e02021-09-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Iodide 40V, Negative-QTOFsplash10-004i-0900000000-0dba40d354fa6a5575e02021-09-23Wishart LabView Spectrum
Biological Properties
Cellular LocationsNot Available
Biospecimen Locations
  • Blood
  • Urine
Tissue LocationsNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodExpected but not QuantifiedNot QuantifiedNot AvailableNot Available
Normal
      Not Available
 details
UrineDetected and Quantified0.53 (0.20-1.65) umol/mmol creatinineChildren (1-13 years old)BothNormal
    • Geigy Scientific ...
 details
UrineDetected and Quantified0.42 +/- 0.189 umol/mmol creatinineAdolescent (13-18 years old)MaleNormal
    • Geigy Scientific ...
 details
UrineDetected and Quantified0.36 +/- 0.199 umol/mmol creatinineAdolescent (13-18 years old)FemaleNormal
    • Geigy Scientific ...
 details
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDDB12754
Phenol Explorer Compound IDNot Available
FooDB IDFDB028881
KNApSAcK IDC00046784
Chemspider ID28015
KEGG Compound IDC00708
BioCyc IDCPD-387
BiGG ID35753
Wikipedia LinkIodide
METLIN IDNot Available
PubChem Compound30165
PDB IDIOD
ChEBI ID16382
Food Biomarker OntologyNot Available
VMH IDI
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Download (PDF)
General ReferencesNot Available

Enzymes

Enzyme Details
1. Thyroid peroxidase
General function:
Involved in calcium ion binding
Specific function:
Iodination and coupling of the hormonogenic tyrosines in thyroglobulin to yield the thyroid hormones T(3) and T(4).
Gene Name:
TPO
Uniprot ID:
P07202
Molecular weight:
102961.63
Enzyme Details
2. Type I iodothyronine deiodinase
General function:
Involved in thyroxine 5'-deiodinase activity
Specific function:
Responsible for the deiodination of T4 (3,5,3',5'-tetraiodothyronine) into T3 (3,5,3'-triiodothyronine) and of T3 into T2 (3,3'-diiodothyronine). Plays a role in providing a source of plasma T3 by deiodination of T4 in peripheral tissues such as liver and kidney.
Gene Name:
DIO1
Uniprot ID:
P49895
Molecular weight:
28924.21
Enzyme Details
3. Type II iodothyronine deiodinase
General function:
Involved in thyroxine 5'-deiodinase activity
Specific function:
Responsible for the deiodination of T4 (3,5,3',5'-tetraiodothyronine) into T3 (3,5,3'-triiodothyronine). Essential for providing the brain with appropriate levels of T3 during the critical period of development.
Gene Name:
DIO2
Uniprot ID:
Q92813
Molecular weight:
30551.48
Enzyme Details
4. Iodotyrosine dehalogenase 1
General function:
Involved in oxidoreductase activity
Specific function:
Catalyzes the oxidative NADPH-dependent deiodination of monoiodotyrosine (L-MIT) or diiodotyrosine (L-DIT). Acts during the hydrolysis of thyroglobulin to liberate iodide, which can then reenter the hormone-producing pathways. Acts more efficiently on monoiodotyrosine than on diiodotyrosine.
Gene Name:
IYD
Uniprot ID:
Q6PHW0
Molecular weight:
33781.22
Enzyme Details
5. Type III iodothyronine deiodinase
General function:
Involved in thyroxine 5'-deiodinase activity
Specific function:
Responsible for the deiodination of T4 (3,5,3',5'-tetraiodothyronine) into RT3 (3,3',5'-triiodothyronine) and of T3 (3,5,3'-triiodothyronine) into T2 (3,3'-diiodothyronine). RT3 and T2 are inactive metabolites. May play a role in preventing premature exposure of developing fetal tissues to adult levels of thyroid hormones. Can regulate circulating fetal thyroid hormone concentrations throughout gestation. Essential role for regulation of thyroid hormone inactivation during embryological development.
Gene Name:
DIO3
Uniprot ID:
P55073
Molecular weight:
33947.175