Showing metabocard for Hydrogen carbonate (MMDBc0000120)

Record Information
Version1.0
StatusDetected and Quantified
Creation Date2020-10-27 23:36:36 UTC
Update Date2024-04-30 19:31:07 UTC
Metabolite IDMMDBc0000120
Metabolite Identification
Common NameHydrogen carbonate
DescriptionBicarbonate, or hydrogen carbonate, is a simple single carbon molecule that plays surprisingly important roles in diverse biological processes. Among these are photosynthesis, the Krebs cycle, whole-body and cellular pH regulation, and volume regulation. Since bicarbonate is charged it is not permeable to lipid bilayers. Mammalian membranes thus contain bicarbonate transport proteins to facilitate the specific transmembrane movement of HCO3(-). Bicarbonate ion is an anion that consists of one central carbon atom surrounded by three oxygen atoms in a trigonal planar arrangement, with a hydrogen atom attached to one of the oxygens. The bicarbonate ion carries a negative one formal charge and is the conjugate base of carbonic acid, H2CO3. The carbonate radical is an elusive and strong one-electron oxidant. Bicarbonate in equilibrium with carbon dioxide constitutes the main physiological buffer. The bicarbonate-carbon dioxide pair stimulates the oxidation, peroxidation and nitration of several biological targets. The demonstration that the carbonate radical existed as an independent species in aqueous solutions at physiological pH and temperature renewed the interest in the pathophysiological roles of this radical and related species. The carbonate radical has been proposed to be a key mediator of the oxidative damage resulting from peroxynitrite production, xanthine oxidase turnover and superoxide dismutase1 peroxidase activity. The carbonate radical has also been proposed to be responsible for the stimulatory effects of the bicarbonate-carbon dioxide pair on oxidations mediated by hydrogen peroxide/transition metal ions. The ultimate precursor of the carbonate radical anion being bicarbonate, carbon dioxide, peroxymonocarbonate or complexes of transition metal ions with bicarbonate-derived species remains a matter of debate. The carbonate radical mediates some of the pathogenic effects of peroxynitrite. The carbonate radical as the oxidant produced from superoxide dismutase (EC 1.15.1.1, SOD1) peroxidase activity. Peroxymonocarbonate is a biological oxidant, whose existence is in equilibrium with hydrogen peroxide and bicarbonate (PMID: 17505962 , 17215880 ). Hydrogen carbonate is found to be associated with hawkinsinuria, which is an inborn error of metabolism.
Structure
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for #<Metabolite:0x00007fdb13ba7840>


  Mrv1652309042000042D          

  4  3  0  0  0  0            999 V2000
    1.2375    0.7145    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    0.0000    0.0000 C   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  1  0  0  0  0
  2  3  2  0  0  0  0
  4  2  1  0  0  0  0
M  END
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3D MOL for #<Metabolite:0x00007fdb13ba7840>

HMDB0000595
     RDKit          3D
Hydrogen carbonate
  6  5  0  0  0  0  0  0  0  0999 V2000
   -0.0452    1.5038   -0.2260 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0037    0.3238    0.1954 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1954   -0.3366    0.4100 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2237   -0.2538    0.4228 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7060   -0.6317   -0.4206 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7266   -0.6056   -0.3817 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 #<Metabolite:0x00007fdb13ba7840>


  Mrv1652309042000042D          

  4  3  0  0  0  0            999 V2000
    1.2375    0.7145    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    0.0000    0.0000 C   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  1  0  0  0  0
  2  3  2  0  0  0  0
  4  2  1  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0000120

> <DATABASE_NAME>
MIME

> <SMILES>
OC(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/CH2O3/c2-1(3)4/h(H2,2,3,4)

> <INCHI_KEY>
BVKZGUZCCUSVTD-UHFFFAOYSA-N

> <FORMULA>
CH2O3

> <MOLECULAR_WEIGHT>
62.0248

> <EXACT_MASS>
62.00039393

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
6

> <JCHEM_AVERAGE_POLARIZABILITY>
4.2300133967078954

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
carbonic acid

> <ALOGPS_LOGP>
0.60

> <JCHEM_LOGP>
0.25005136566666664

> <ALOGPS_LOGS>
0.57

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
10.638414228618222

> <JCHEM_PKA_STRONGEST_ACIDIC>
6.052541895520343

> <JCHEM_POLAR_SURFACE_AREA>
57.53

> <JCHEM_REFRACTIVITY>
9.4982

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.31e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
carbonic acid

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for #<Metabolite:0x00007fdb13ba7840>

HMDB0000595
     RDKit          3D
Hydrogen carbonate
  6  5  0  0  0  0  0  0  0  0999 V2000
   -0.0452    1.5038   -0.2260 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0037    0.3238    0.1954 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1954   -0.3366    0.4100 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2237   -0.2538    0.4228 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7060   -0.6317   -0.4206 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7266   -0.6056   -0.3817 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 #<Metabolite:0x00007fdb13ba7840>

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  O   UNK     0       2.310   1.334   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0       1.540   0.000   0.000  0.00  0.00           C+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                                                            
CONECT    2    1    3    4                                                  
CONECT    3    2                                                            
CONECT    4    2                                                            
MASTER        0    0    0    0    0    0    0    0    4    0    6    0
END
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3D PDB for #<Metabolite:0x00007fdb13ba7840>

COMPND    HMDB0000595
HETATM    1  O1  UNL     1      -0.045   1.504  -0.226  1.00  0.00           O  
HETATM    2  C1  UNL     1      -0.004   0.324   0.195  1.00  0.00           C  
HETATM    3  O2  UNL     1      -1.195  -0.337   0.410  1.00  0.00           O  
HETATM    4  O3  UNL     1       1.224  -0.254   0.423  1.00  0.00           O  
HETATM    5  H1  UNL     1      -1.706  -0.632  -0.421  1.00  0.00           H  
HETATM    6  H2  UNL     1       1.727  -0.606  -0.382  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 #<Metabolite:0x00007fdb13ba7840>

OC(O)=O
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INCHI for #<Metabolite:0x00007fdb13ba7840>

InChI=1S/CH2O3/c2-1(3)4/h(H2,2,3,4)
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Synonyms
ValueSource
[CO(OH)2]ChEBI
Dihydrogen carbonateChEBI
H2CO3ChEBI
KoehlensaeureChEBI
Dihydrogen carbonic acidGenerator
Hydrogen carbonic acidGenerator
CarbonateGenerator, HMDB
Acid OF airHMDB
Aerial acidHMDB
Bisodium carbonateHMDB
CalcinedHMDB
Carbonic acid sodium saltHMDB
ConsalHMDB
Crystol carbonateHMDB
Disodium carbonateHMDB
Mild alkaliHMDB
Na-XHMDB
OxyperHMDB
Sal sodaHMDB
Salt OF sodaHMDB
Scotch sodaHMDB
SodaHMDB
Soda ashHMDB
Sodium carbonateHMDB
Sodium carbonate anhydrousHMDB
Sodium carbonate hydratedHMDB
Sodium carbonate peroxyhydrateHMDB
Solvay sodaHMDB
Trona soda ashHMDB
Tronalight light soda ashHMDB
Acid, carbonicMeSH, HMDB
Carbonic acidMeSH, HMDB
Ions, bicarbonateMeSH
Carbonate, hydrogenMeSH
Carbonates, hydrogenMeSH
Bicarbonate ionMeSH
Hydrogen carbonatesMeSH
BicarbonatesMeSH
Bicarbonate ionsMeSH
Carbonic acid ionsMeSH
Ions, carbonic acidMeSH
Molecular FormulaCH2O3
Average Mass62.0248
Monoisotopic Mass62.00039393
IUPAC Namecarbonic acid
Traditional Namecarbonic acid
CAS Registry Number71-52-3
SMILES
OC(O)=O
InChI Identifier
InChI=1S/CH2O3/c2-1(3)4/h(H2,2,3,4)
InChI KeyBVKZGUZCCUSVTD-UHFFFAOYSA-N