Human Metabolome Database Version 3.5

Showing metabocard for Hydrogen carbonate (HMDB00595)

Record Information
Version 3.5
Creation Date 2005-11-16 08:48:42 -0700
Update Date 2013-05-29 13:27:55 -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 | PDB | 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 Reference
Blood Detected and Quantified
24900.0 +/- 1790.0 uM Adult (>18 years old) Both Normal
  • Geigy Scient...
Blood Detected and Quantified
24700.0 +/- 1200.0 uM Adult (>18 years old) Male Normal
  • Geigy Scient...
Blood Detected and Quantified
23100.0 +/- 1500.0 uM Adult (>18 years old) Female Comment Normal
  • Geigy Scient...
Blood Detected and Quantified
20000.0 (15500.0-22500.0) uM Newborn (0-30 days old) Both Normal
  • Geigy Scient...
Blood Detected and Quantified
25500.00 (24000.00-27000.00) uM Adult (>18 years old) Both Normal
Cellular Cytoplasm Detected and Quantified
11200 +/- 150 uM Adult (>18 years old) Not Specified Normal
  • Geigy Scient...
Cerebrospinal Fluid (CSF) Detected and Quantified
10000 +/- 1000 uM Adult (>18 years old) Both Normal
Cerebrospinal Fluid (CSF) Detected and Quantified
7600 +/- 1600 uM Adult (>18 years old) Both Normal
Abnormal Concentrations
Biofluid Status Value Age Sex Condition Reference
Blood Detected and Quantified 13600.00 uM Adult (>18 years old) Both Diabetic ketoacidosis
Blood Detected and Quantified 12000.00 (10000.00-14000.00) uM Children (1-13 year old) Both Hawkinsinuria
Associated Disorders and Diseases
Disease References
Hawkinsinuria
      Associated OMIM IDs
      DrugBank ID Not Available
      DrugBank Metabolite 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
      1. Medinas DB, Cerchiaro G, Trindade DF, Augusto O: The carbonate radical and related oxidants derived from bicarbonate buffer. IUBMB Life. 2007 Apr-May;59(4-5):255-62. Pubmed: 17505962 Link_out
      2. Casey JR: Why bicarbonate? Biochem Cell Biol. 2006 Dec;84(6):930-9. Pubmed: 17215880 Link_out

      Enzymes
      Name: Bile salt-activated lipase
      Reactions: Not Available
      Gene Name: CEL
      Uniprot ID: P19835 Link_out
      Protein Sequence: FASTA
      Gene Sequence: FASTA
      Name: Inositol polyphosphate 5-phosphatase OCRL-1
      Reactions: Not Available
      Gene Name: OCRL
      Uniprot ID: Q01968 Link_out
      Protein Sequence: FASTA
      Gene Sequence: FASTA
      Name: Lactotransferrin
      Reactions: Not Available
      Gene Name: LTF
      Uniprot ID: P02788 Link_out
      Protein Sequence: FASTA
      Gene Sequence: FASTA
      Name: Serotransferrin
      Reactions: Not Available
      Gene Name: TF
      Uniprot ID: P02787 Link_out
      Protein Sequence: FASTA
      Gene Sequence: FASTA
      Name: Cystic fibrosis transmembrane conductance regulator
      Reactions: Not Available
      Gene Name: CFTR
      Uniprot ID: P13569 Link_out
      Protein Sequence: FASTA
      Gene Sequence: FASTA
      Name: Carbonic anhydrase 4
      Reactions: Not Available
      Gene Name: CA4
      Uniprot ID: P22748 Link_out
      Protein Sequence: FASTA
      Gene Sequence: FASTA
      Name: Chloride anion exchanger
      Reactions: Not Available
      Gene Name: SLC26A3
      Uniprot ID: P40879 Link_out
      Protein Sequence: FASTA
      Gene Sequence: FASTA
      Name: Adenylate cyclase type 10
      Reactions: Not Available
      Gene Name: ADCY10
      Uniprot ID: Q96PN6 Link_out
      Protein Sequence: FASTA
      Gene Sequence: FASTA
      Name: Solute carrier family 26 member 9
      Reactions: Not Available
      Gene Name: SLC26A9
      Uniprot ID: Q7LBE3 Link_out
      Protein Sequence: FASTA
      Gene Sequence: FASTA
      Name: Anion exchange transporter
      Reactions: Not Available
      Gene Name: SLC26A7
      Uniprot ID: Q8TE54 Link_out
      Protein Sequence: FASTA
      Gene Sequence: FASTA
      Name: Bestrophin-1
      Reactions: Not Available
      Gene Name: BEST1
      Uniprot ID: O76090 Link_out
      Protein Sequence: FASTA
      Gene Sequence: FASTA
      Name: Bestrophin-2
      Reactions: Not Available
      Gene Name: BEST2
      Uniprot ID: Q8NFU1 Link_out
      Protein Sequence: FASTA
      Gene Sequence: FASTA
      Name: Bestrophin-3
      Reactions: Not Available
      Gene Name: BEST3
      Uniprot ID: Q8N1M1 Link_out
      Protein Sequence: FASTA
      Gene Sequence: FASTA
      Name: Bestrophin-4
      Reactions: Not Available
      Gene Name: BEST4
      Uniprot ID: Q8NFU0 Link_out
      Protein Sequence: FASTA
      Gene Sequence: FASTA
      Name: Solute carrier family 26 member 10
      Reactions: Not Available
      Gene Name: SLC26A10
      Uniprot ID: Q8NG04 Link_out
      Protein Sequence: FASTA
      Gene Sequence: FASTA
      Name: Prestin
      Reactions: Not Available
      Gene Name: SLC26A5
      Uniprot ID: P58743 Link_out
      Protein Sequence: FASTA
      Gene Sequence: FASTA
      Name: Sodium/hydrogen exchanger 10
      Reactions: Not Available
      Gene Name: SLC9A10
      Uniprot ID: Q4G0N8 Link_out
      Protein Sequence: FASTA
      Gene Sequence: FASTA
      Transporters
      Name: Electrogenic sodium bicarbonate cotransporter 1
      Reactions: Not Available
      Gene Name: SLC4A4
      Uniprot ID: Q9Y6R1 Link_out
      Protein Sequence: FASTA
      Gene Sequence: FASTA
      Name: Sodium-driven chloride bicarbonate exchanger
      Reactions: Not Available
      Gene Name: SLC4A10
      Uniprot ID: Q6U841 Link_out
      Protein Sequence: FASTA
      Gene Sequence: FASTA
      Name: Sodium bicarbonate cotransporter 3
      Reactions: Not Available
      Gene Name: SLC4A7
      Uniprot ID: Q9Y6M7 Link_out
      Protein Sequence: FASTA
      Gene Sequence: FASTA
      Name: Electrogenic sodium bicarbonate cotransporter 4
      Reactions: Not Available
      Gene Name: SLC4A5
      Uniprot ID: Q9BY07 Link_out
      Protein Sequence: FASTA
      Gene Sequence: FASTA