Showing metabocard for Oxygen (MMDBc0029799)

Record Information
Version1.0
StatusDetected and Quantified
Creation Date2021-11-17 23:42:08 UTC
Update Date2024-10-07 03:06:24 UTC
Metabolite IDMMDBc0029799
Metabolite Identification
Common NameOxygen
DescriptionOxygen is the third most abundant element in the universe after hydrogen and helium and the most abundant element by mass in the Earth's crust. Diatomic oxygen gas constitutes 20.9% of the volume of air. All major classes of structural molecules in living organisms, such as proteins, carbohydrates, and fats, contain oxygen, as do the major inorganic compounds that comprise animal shells, teeth, and bone. Oxygen in the form of O2 is produced from water by cyanobacteria, algae and plants during photosynthesis and is used in cellular respiration for all living organisms. Green algae and cyanobacteria in marine environments provide about 70% of the free oxygen produced on earth and the rest is produced by terrestrial plants. Produced O2- can react with other radicals, such as NO, or spontaneously dismutate to produce hydrogen peroxide (H2O2). In cells, the latter reaction is an important pathway for normal O2- breakdown and is usually catalyzed by the enzyme superoxide dismutase (SOD). Once formed, H2O2 can undergo various reactions, both enzymatic and nonenzymatic. The antioxidant enzymes catalase and glutathione peroxidase act to limit ROS accumulation within cells by breaking down H2O2 to H2O. Metabolism of H2O2 can also produce other, more damaging ROS. For example, the endogenous enzyme myeloperoxidase uses H2O2 as a substrate to form the highly reactive compound hypochlorous acid. Alternatively, H2O2 can undergo Fenton or Haber-Weiss chemistry, reacting with Fe2+/Fe3+ ions to form toxic hydroxyl radicals (-.OH). (PMID: 17027622 , 15765131 )
Structure
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for #<Metabolite:0x0000559d051818a0>

977
  Mrv1652309042000222D          

  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  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
M  END
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3D MOL for #<Metabolite:0x0000559d051818a0>

HMDB0001377
     RDKit          3D
Oxygen
  2  1  0  0  0  0  0  0  0  0999 V2000
    0.5733    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5733    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
M  END
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3D SDF for #<Metabolite:0x0000559d051818a0>

977
  Mrv1652309042000222D          

  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  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0029799

> <DATABASE_NAME>
MIME

> <SMILES>
O=O

> <INCHI_IDENTIFIER>
InChI=1S/O2/c1-2

> <INCHI_KEY>
MYMOFIZGZYHOMD-UHFFFAOYSA-N

> <FORMULA>
O2

> <MOLECULAR_WEIGHT>
31.9988

> <EXACT_MASS>
31.989829244

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_ATOM_COUNT>
2

> <JCHEM_AVERAGE_POLARIZABILITY>
1.528255145499405

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
dioxygen

> <JCHEM_LOGP>
-0.27723172999999995

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_POLAR_SURFACE_AREA>
34.14

> <JCHEM_REFRACTIVITY>
2.8858

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
singlet oxygen

> <JCHEM_VEBER_RULE>
1

$$$$
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3D-SDF for #<Metabolite:0x0000559d051818a0>

HMDB0001377
     RDKit          3D
Oxygen
  2  1  0  0  0  0  0  0  0  0999 V2000
    0.5733    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5733    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
M  END
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PDB for #<Metabolite:0x0000559d051818a0>

HEADER    PROTEIN                                 04-SEP-20   NONE
TITLE     NULL                                                        
COMPND    MOLECULE: 977                                               
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   04-SEP-20         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+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 #<Metabolite:0x0000559d051818a0>

COMPND    HMDB0001377
HETATM    1  O1  UNL     1       0.573   0.000   0.000  1.00  0.00           O  
HETATM    2  O2  UNL     1      -0.573   0.000   0.000  1.00  0.00           O  
CONECT    1    2    2
END
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SMILES for #<Metabolite:0x0000559d051818a0>

O=O
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INCHI for #<Metabolite:0x0000559d051818a0>

InChI=1S/O2/c1-2
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Synonyms
ValueSource
[OO]ChEBI
DioxygeneChEBI
DisauerstoffChEBI
e 948ChEBI
e-948ChEBI
e948ChEBI
Molecular oxygenChEBI
O2ChEBI
OXYGEN moleculeChEBI
DioxygenHMDB
Oxygen-16HMDB
Oxygen 16HMDB
Molecular FormulaO2
Average Mass31.9988
Monoisotopic Mass31.989829244
IUPAC Namedioxygen
Traditional Namesinglet oxygen
CAS Registry Number7782-44-7
SMILES
O=O
InChI Identifier
InChI=1S/O2/c1-2
InChI KeyMYMOFIZGZYHOMD-UHFFFAOYSA-N