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Showing metabocard for Superoxide (HMDB0002168)

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enzymes (4) Show 4 proteins
Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2006-05-22 14:17:39 UTC
Update Date2020-05-12 19:04:00 UTC
HMDB IDHMDB0002168
Secondary Accession Numbers
  • HMDB02168
Metabolite Identification
Common NameSuperoxide
DescriptionSuperoxide is the anionic form O2. It is important as the product of the one-electron reduction of dioxygen (oxygen gas), which occurs widely in nature. With one unpaired electron, the superoxide ion is a free radical. It is also paramagnetic. The biological toxicity of superoxide is due to its capacity to inactivate iron-sulfur cluster containing enzymes (which are critical in a wide variety of metabolic pathways), thereby liberating free iron in the cell, which can undergo fenton-chemistry and generate the highly reactive hydroxyl radical. In its HO2 form, superoxide can also initiate lipid peroxidation of polyunsaturated fatty acids. It also reacts with carbonyl compounds and halogenated carbons to create toxic peroxy radicals. As such, superoxide is a main cause of oxidative stress. Highly reactive compounds produced when oxygen is reduced by a single electron. In biological systems, they may be generated during the normal catalytic function of a number of enzymes and during the oxidation of hemoglobin to Methemoglobin. Because superoxide is toxic, nearly all organisms living in the presence of oxygen contain isoforms of the superoxide scavenging enzyme, superoxide dismutase, or SOD. SOD is an extremely efficient enzyme; it catalyzes the neutralization of superoxide nearly as fast as the two can diffuse together spontaneously in solution. Genetic inactivation ("knockout") of SOD produces deleterious phenotypes in organisms ranging from bacteria to mice. The latter species dies around 21 days after birth if the mitochondrial variant of SOD (Mn-SOD) is inactivated, and suffers from multiple pathologies, including reduced lifespan, liver cancer, muscle atrophy, cataracts and female infertility when the cytoplasmic (Cu, Zn -SOD) variant is inactivated. With one unpaired electron, the superoxide ion is a free radical and therefore paramagnetic. In living organisms, superoxide dismutase protects the cell from the deleterious effects of superoxides.
Structure
Data?1589310240
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0002168 (Superoxide)

5359597
  Mrv0541 02231219242D          

  2  1  0  0  0  0            999 V2000
    1.6500    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4750    0.0000    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
M  CHG  1   2  -1
M  RAD  1   1   2
M  END
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3D MOL for HMDB0002168 (Superoxide)

HMDB0002168
     RDKit          3D
Superoxide
  2  1  0  0  0  0  0  0  0  0999 V2000
    0.6608    0.0000    0.0000 O   0  0  0  0  0  1  0  0  0  0  0  0
   -0.6608    0.0000    0.0000 O   0  0  0  0  0  1  0  0  0  0  0  0
  1  2  1  0
M  CHG  1   2  -1
M  RAD  1   1   2
M  END
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3D SDF for HMDB0002168 (Superoxide)

5359597
  Mrv0541 02231219242D          

  2  1  0  0  0  0            999 V2000
    1.6500    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4750    0.0000    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
M  CHG  1   2  -1
M  RAD  1   1   2
M  END
> <DATABASE_ID>
HMDB0002168

> <DATABASE_NAME>
hmdb

> <SMILES>
[O][O-]

> <INCHI_IDENTIFIER>
InChI=1S/HO2/c1-2/h1H/p-1

> <INCHI_KEY>
OUUQCZGPVNCOIJ-UHFFFAOYSA-M

> <FORMULA>
O2

> <MOLECULAR_WEIGHT>
31.9988

> <EXACT_MASS>
31.989829244

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_AVERAGE_POLARIZABILITY>
1.6723109476406521

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
-1

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
oxidanidyloxidanyl

> <JCHEM_LOGP>
-0.3622170719999999

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA_STRONGEST_ACIDIC>
5.802463079075391

> <JCHEM_PKA_STRONGEST_BASIC>
-6.821802649212423

> <JCHEM_POLAR_SURFACE_AREA>
23.06

> <JCHEM_REFRACTIVITY>
2.8858

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
superoxide

> <JCHEM_VEBER_RULE>
1

$$$$
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3D-SDF for HMDB0002168 (Superoxide)

HMDB0002168
     RDKit          3D
Superoxide
  2  1  0  0  0  0  0  0  0  0999 V2000
    0.6608    0.0000    0.0000 O   0  0  0  0  0  1  0  0  0  0  0  0
   -0.6608    0.0000    0.0000 O   0  0  0  0  0  1  0  0  0  0  0  0
  1  2  1  0
M  CHG  1   2  -1
M  RAD  1   1   2
M  END
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PDB for HMDB0002168 (Superoxide)

HEADER    PROTEIN                                 23-FEB-12   NONE
TITLE     NULL                                                        
COMPND    MOLECULE: 5359597                                           
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   23-FEB-12         0                                  
HETATM    1  O   UNK     0       3.080   0.000   0.000  0.00  0.00           O+0
HETATM    2  O   UNK     0       4.620   0.000   0.000  0.00  0.00           O-1
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 HMDB0002168 (Superoxide)

COMPND    HMDB0002168
HETATM    1  O1  UNL     1       0.661   0.000   0.000  1.00  0.00           O  
HETATM    2  O2  UNL     1      -0.661   0.000   0.000  1.00  0.00           O1-
CONECT    1    2
END
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SMILES for HMDB0002168 (Superoxide)

[O][O-]
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INCHI for HMDB0002168 (Superoxide)

InChI=1S/HO2/c1-2/h1H/p-1
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View in JSmolView Stereo Labels
Synonyms
ValueSource
(O2)(.-)ChEBI
Dioxide(1-)ChEBI
HyperoxidChEBI
HyperoxideChEBI
O2(.-)ChEBI
O2(-)ChEBI
Superoxide anionChEBI
Superoxide anion radicalChEBI
Superoxide radicalChEBI
Superoxide radical anionChEBI
SuperoxydeChEBI
SuperoxidesMeSH
DioxidanidylHMDB
Chemical FormulaO2
Average Molecular Weight31.9988
Monoisotopic Molecular Weight31.989829244
IUPAC Nameoxidanidyloxidanyl
Traditional Namesuperoxide
CAS Registry Number11062-77-4
SMILES
[O][O-]
InChI Identifier
InChI=1S/HO2/c1-2/h1H/p-1
InChI KeyOUUQCZGPVNCOIJ-UHFFFAOYSA-M
Chemical Taxonomy
Description Belongs to the class of inorganic compounds known as non-metal superoxides. These are inorganic non-metallic compounds containing a superoxide as its largest oxoanion.
KingdomInorganic compounds
Super ClassHomogeneous non-metal compounds
ClassNon-metal oxoanionic compounds
Sub ClassNon-metal superoxides
Direct ParentNon-metal superoxides
Alternative Parents
Substituents
  • Non-metal superoxide
  • 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-0.36ChemAxon
pKa (Strongest Acidic)5.8ChemAxon
pKa (Strongest Basic)-6.8ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count2ChemAxon
Hydrogen Donor Count0ChemAxon
Polar Surface Area23.06 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity2.89 m³·mol⁻¹ChemAxon
Polarizability1.67 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]+109.71430932474
DeepCCS[M-H]-107.98630932474
DeepCCS[M-2H]-143.14930932474
DeepCCS[M+Na]+116.47130932474

Predicted Retention Times

Underivatized

Chromatographic MethodRetention TimeReference
Predicted by Siyang on May 30, 20228.879 minutes33406817
AjsUoB = Accucore 150 Amide HILIC with 10mM Ammonium Formate, 0.1% Formic Acid295.9 seconds40023050
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid1083.7 seconds40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid496.4 seconds40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid219.0 seconds40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid408.3 seconds40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid267.2 seconds40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid382.7 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 Acid495.8 seconds40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)685.2 seconds40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid795.5 seconds40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid270.2 seconds40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid875.7 seconds40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid344.2 seconds40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid416.3 seconds40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate757.1 seconds40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA425.1 seconds40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water317.1 seconds40023050

Predicted Kovats Retention Indices

Not Available
Spectra

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Superoxide 10V, Positive-QTOFsplash10-001i-9000000000-a9a93dd42f2cfa0b34c42015-09-15Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Superoxide 20V, Positive-QTOFsplash10-001i-9000000000-a9a93dd42f2cfa0b34c42015-09-15Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Superoxide 40V, Positive-QTOFsplash10-001i-9000000000-a9a93dd42f2cfa0b34c42015-09-15Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Superoxide 10V, Negative-QTOFsplash10-001i-9000000000-5e864878b295db1744732015-09-15Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Superoxide 20V, Negative-QTOFsplash10-001i-9000000000-5e864878b295db1744732015-09-15Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Superoxide 40V, Negative-QTOFsplash10-001i-9000000000-5e864878b295db1744732015-09-15Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Superoxide 10V, Negative-QTOFsplash10-001i-9000000000-a5bd793545bcb46f03852021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Superoxide 20V, Negative-QTOFsplash10-001i-9000000000-a5bd793545bcb46f03852021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Superoxide 40V, Negative-QTOFsplash10-001i-9000000000-a5bd793545bcb46f03852021-09-22Wishart LabView Spectrum
Biological Properties
Cellular Locations
  • Cytoplasm
  • Extracellular
  • Mitochondria
  • Nucleus
  • Peroxisome
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 IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB022880
KNApSAcK IDNot Available
Chemspider ID4514331
KEGG Compound IDC00704
BioCyc IDSUPER-OXIDE
BiGG ID35743
Wikipedia LinkSuperoxide
METLIN IDNot Available
PubChem Compound5359597
PDB IDNot Available
ChEBI ID18421
Food Biomarker OntologyNot Available
VMH IDO2S
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. Catalase
General function:
Involved in catalase activity
Specific function:
Occurs in almost all aerobically respiring organisms and serves to protect cells from the toxic effects of hydrogen peroxide. Promotes growth of cells including T-cells, B-cells, myeloid leukemia cells, melanoma cells, mastocytoma cells and normal and transformed fibroblast cells.
Gene Name:
CAT
Uniprot ID:
P04040
Molecular weight:
59755.82
Reactions
3-Hydroxyanthranilic acid + Oxygen → Cinnabarinic acid + Superoxide + Hydrogen peroxide + Hydrogen Iondetails
Enzyme Details
2. Superoxide dismutase [Mn], mitochondrial
General function:
Involved in superoxide dismutase activity
Specific function:
Destroys superoxide anion radicals which are normally produced within the cells and which are toxic to biological systems.
Gene Name:
SOD2
Uniprot ID:
P04179
Molecular weight:
24750.015
Reactions
Superoxide + Hydrogen Ion → Oxygen + Hydrogen peroxidedetails
Enzyme Details
3. Superoxide dismutase [Cu-Zn]
General function:
Involved in metal ion binding
Specific function:
Destroys radicals which are normally produced within the cells and which are toxic to biological systems.
Gene Name:
SOD1
Uniprot ID:
P00441
Molecular weight:
15935.685
Reactions
Superoxide + Hydrogen Ion → Oxygen + Hydrogen peroxidedetails
Enzyme Details
4. Extracellular superoxide dismutase [Cu-Zn]
General function:
Involved in metal ion binding
Specific function:
Protect the extracellular space from toxic effect of reactive oxygen intermediates by converting superoxide radicals into hydrogen peroxide and oxygen.
Gene Name:
SOD3
Uniprot ID:
P08294
Molecular weight:
25850.675
Reactions
Superoxide + Hydrogen Ion → Oxygen + Hydrogen peroxidedetails