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Human Metabolome Database Version 3.5

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Showing metabocard for Hydrogen carbonate (HMDB00595)

Record Information
Version 3.5
Creation Date 2005-11-16 08:48:42 -0700
Update Date 2013-04-19 17:12:54 -0600
HMDB ID HMDB00595
Secondary Accession Numbers None
Metabolite Identification
Common Name Hydrogen carbonate
Description Bicarbonate, 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 Link_out, 17215880 Link_out).
Structure Thumb
Download: MOL | SDF | SMILES | InChI
Display: 2D Structure | 3D Structure
Synonyms
  1. Bicarbonate
  2. Bicarbonate (HCO3-)
  3. Bicarbonate anion
  4. Bicarbonate ion
  5. Bicarbonate ion (HCO31-)
  6. Bicarbonate ions
  7. Carbonate
  8. Carbonate (HCO31-)
  9. Carbonate ion (HCO31-)
  10. Carbonic acid
  11. Hydrocarbonate(1-)
  12. Hydrogen carbonate
  13. Hydrogen carbonate (HCO3-)
  14. Hydrogen carbonate anion
  15. Hydrogen carbonate ion
  16. Hydrogen carbonate ion (HCO3-)
  17. Hydrogencarbonate
  18. Hydrogentrioxocarbonate
  19. Monohydrogen carbonate
Chemical Formula CHO3
Average Molecular Weight 61.0168
Monoisotopic Molecular Weight 60.992568898
IUPAC Name hydrogen carbonate
Traditional IUPAC Name bicarbonate
CAS Registry Number 71-52-3
SMILES OC([O-])=O
InChI Identifier InChI=1S/CH2O3/c2-1(3)4/h(H2,2,3,4)/p-1
InChI Key BVKZGUZCCUSVTD-UHFFFAOYSA-M
Chemical Taxonomy
Kingdom Organic Compounds
Super Class Organic Acids and Derivatives
Class Organic Carbonic Acids and Derivatives
Sub Class N/A
Other Descriptors
  • Aliphatic Acyclic Compounds
  • an anion(Cyc)
  • carbon oxoanion(ChEBI)
Substituents
  • N/A
Direct Parent Organic Carbonic Acids and Derivatives
Ontology
Status Detected and Quantified
Origin
  • Endogenous
Biofunction
  • Osmolyte, enzyme cofactor, signalling
Application Not Available
Cellular locations
  • Cytoplasm
  • Extracellular
  • Mitochondria
Physical Properties
State Solid
Experimental Properties
Property Value Reference
Melting Point 720 °C Not Available
Boiling Point Not Available Not Available
Water Solubility 12.8 mg/mL (cold water) MERCK INDEX (1996)
LogP Not Available Not Available
Predicted Properties
Property Value Source
Water Solubility 732 g/L ALOGPS
LogP -0.20 ALOGPS
LogP 0.25 ChemAxon
LogS 0.97 ALOGPS
pKa (strongest acidic) 6.05 ChemAxon
Hydrogen Acceptor Count 3 ChemAxon
Hydrogen Donor Count 1 ChemAxon
Polar Surface Area 60.36 A2 ChemAxon
Rotatable Bond Count 0 ChemAxon
Refractivity 20.34 ChemAxon
Polarizability 3.86 ChemAxon
Formal Charge -1 ChemAxon
Physiological Charge -1 ChemAxon
Spectra
Not Available
Biological Properties
Cellular Locations
  • Cytoplasm
  • Extracellular
  • Mitochondria
Biofluid Locations
  • Blood
  • Cellular Cytoplasm
  • Cerebrospinal Fluid (CSF)
Tissue Location Not Available
Pathways
Name SMPDB Link KEGG Link
Citric Acid Cycle SMP00057 map00020 Link_out
Urea Cycle SMP00059 map00330 Link_out
Threonine and 2-Oxobutanoate Degradation SMP00452 Not Available
Normal Concentrations
Biofluid Status Value Age Sex Condition Comments
Blood Detected and Quantified
Article_icon
24900.0 +/- 1790.0 uM Adult (>18 years old) Both Normal Not Available
Blood Detected and Quantified
Article_icon
24700.0 +/- 1200.0 uM Adult (>18 years old) Male Normal Not Available
Blood Detected and Quantified
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23100.0 +/- 1500.0 uM Adult (>18 years old) Female Normal Capillary blood plasma from 20 women
Blood Detected and Quantified
Article_icon
20000.0 (15500.0-22500.0) uM Newborn (0-30 days old) Both Normal Not Available
Cellular Cytoplasm Detected and Quantified
Article_icon
11200 +/- 150 uM Adult (>18 years old) Not Specified Normal Not Available
Cerebrospinal Fluid (CSF) Detected and Quantified
Article_icon
10000 +/- 1000 uM Adult (>18 years old) Both Normal Not Available
Cerebrospinal Fluid (CSF) Detected and Quantified
Article_icon
7600 +/- 1600 uM Adult (>18 years old) Both Normal Not Available
Abnormal Concentrations
Biofluid Status Value Age Sex Condition Comments
Blood Detected and Quantified
Article_icon
13600.00 uM Adult (>18 years old) Both Diabetic ketoacidosis Not Available
Blood Detected and Quantified
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25500.00 (24000.00-27000.00) uM Adult (>18 years old) Both Hawkinsinuria Not Available
Blood Detected and Quantified
Article_icon
12000.00 (10000.00-14000.00) uM Adult (>18 years old) Both Hawkinsinuria Not Available
Associated Disorders and Diseases
Disease References
Hawkinsinuria
    • http://www.metagene.de/program/d.prg?mp=HAWKINSINURIA
    Associated OMIM IDs
    DrugBank ID Not Available
    Phenol Explorer Compound ID Not Available
    Phenol Explorer Metabolite ID Not Available
    FoodDB ID FDB022134
    KNApSAcK ID Not Available
    Chemspider ID 749 Link_out
    KEGG Compound ID C00288 Link_out
    BioCyc ID HCO3 Link_out
    BiGG ID 34509 Link_out
    Wikipedia Link Bicarbonate Link_out
    NuGOwiki Link HMDB00595 Link_out
    Metagene Link HMDB00595 Link_out
    METLIN ID Not Available
    PubChem Compound 769 Link_out
    PDB ID BCT Link_out
    ChEBI ID 17544 Link_out
    References
    Synthesis Reference Nakajima, Fumiaki; Arima, Toshikazu; Kikuchi, Shintaro; Hirano, Hachiro. Production of alkaline hydrogen carbonate. Jpn. Kokai Tokkyo Koho (2005), 15 pp.
    Material Safety Data Sheet (MSDS) Download (PDF)
    General References Not Available
    Enzymes
    Name: Bile salt-activated lipase
    Reactions:
    • a steryl ester + H2O = a sterol + a fatty acid [RN:R02115]
    Gene Name: CEL
    Uniprot ID: P19835 Link_out
    Protein Sequence: FASTA
    Gene Sequence: FASTA
    Name: Inositol polyphosphate 5-phosphatase OCRL-1
    Reactions:
    • 1-phosphatidyl-1D-myo-inositol 4,5-bisphosphate + H2O = 1-phosphatidyl-1D-myo-inositol 4-phosphate + phosphate [RN:R04404]
    Gene Name: OCRL
    Uniprot ID: Q01968 Link_out
    Protein Sequence: FASTA
    Gene Sequence: FASTA
    Name: Lactotransferrin
    Reactions:
      Gene Name: LTF
      Uniprot ID: P02788 Link_out
      Protein Sequence: FASTA
      Gene Sequence: FASTA
      Name: Serotransferrin
      Reactions:
        Gene Name: TF
        Uniprot ID: P02787 Link_out
        Protein Sequence: FASTA
        Gene Sequence: FASTA
        Name: Cystic fibrosis transmembrane conductance regulator
        Reactions:
        • ATP + H2O = ADP + phosphate [RN:R00086]
        Gene Name: CFTR
        Uniprot ID: P13569 Link_out
        Protein Sequence: FASTA
        Gene Sequence: FASTA
        Name: Carbonic anhydrase 4
        Reactions:
        • H2CO3 = CO2 + H2O [RN:R00132]
        Gene Name: CA4
        Uniprot ID: P22748 Link_out
        Protein Sequence: FASTA
        Gene Sequence: FASTA
        Name: Chloride anion exchanger
        Reactions:
          Gene Name: SLC26A3
          Uniprot ID: P40879 Link_out
          Protein Sequence: FASTA
          Gene Sequence: FASTA
          Name: Adenylate cyclase type 10
          Reactions:
          • ATP = 3',5'-cyclic AMP + diphosphate [RN:R00089]
          Gene Name: ADCY10
          Uniprot ID: Q96PN6 Link_out
          Protein Sequence: FASTA
          Gene Sequence: FASTA
          Name: Solute carrier family 26 member 9
          Reactions:
            Gene Name: SLC26A9
            Uniprot ID: Q7LBE3 Link_out
            Protein Sequence: FASTA
            Gene Sequence: FASTA
            Name: Anion exchange transporter
            Reactions:
              Gene Name: SLC26A7
              Uniprot ID: Q8TE54 Link_out
              Protein Sequence: FASTA
              Gene Sequence: FASTA
              Name: Bestrophin-1
              Reactions:
                Gene Name: BEST1
                Uniprot ID: O76090 Link_out
                Protein Sequence: FASTA
                Gene Sequence: FASTA
                Name: Bestrophin-2
                Reactions:
                  Gene Name: BEST2
                  Uniprot ID: Q8NFU1 Link_out
                  Protein Sequence: FASTA
                  Gene Sequence: FASTA
                  Name: Bestrophin-3
                  Reactions:
                    Gene Name: BEST3
                    Uniprot ID: Q8N1M1 Link_out
                    Protein Sequence: FASTA
                    Gene Sequence: FASTA
                    Name: Bestrophin-4
                    Reactions:
                      Gene Name: BEST4
                      Uniprot ID: Q8NFU0 Link_out
                      Protein Sequence: FASTA
                      Gene Sequence: FASTA
                      Name: Solute carrier family 26 member 10
                      Reactions:
                        Gene Name: SLC26A10
                        Uniprot ID: Q8NG04 Link_out
                        Protein Sequence: FASTA
                        Gene Sequence: FASTA
                        Name: Prestin
                        Reactions:
                          Gene Name: SLC26A5
                          Uniprot ID: P58743 Link_out
                          Protein Sequence: FASTA
                          Gene Sequence: FASTA
                          Name: Sodium/hydrogen exchanger 10
                          Reactions:
                            Gene Name: SLC9A10
                            Uniprot ID: Q4G0N8 Link_out
                            Protein Sequence: FASTA
                            Gene Sequence: FASTA
                            Transporters
                            Name: Electrogenic sodium bicarbonate cotransporter 1
                            Reactions:
                              Gene Name: SLC4A4
                              Uniprot ID: Q9Y6R1 Link_out
                              Protein Sequence: FASTA
                              Gene Sequence: FASTA
                              Name: Sodium-driven chloride bicarbonate exchanger
                              Reactions:
                                Gene Name: SLC4A10
                                Uniprot ID: Q6U841 Link_out
                                Protein Sequence: FASTA
                                Gene Sequence: FASTA
                                Name: Sodium bicarbonate cotransporter 3
                                Reactions:
                                  Gene Name: SLC4A7
                                  Uniprot ID: Q9Y6M7 Link_out
                                  Protein Sequence: FASTA
                                  Gene Sequence: FASTA
                                  Name: Electrogenic sodium bicarbonate cotransporter 4
                                  Reactions:
                                    Gene Name: SLC4A5
                                    Uniprot ID: Q9BY07 Link_out
                                    Protein Sequence: FASTA
                                    Gene Sequence: FASTA