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Showing metabocard for Oxalic acid (HMDB0002329)

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Record Information
Version5.0
StatusDetected and Quantified
Creation Date2006-05-22 14:17:48 UTC
Update Date2023-02-21 17:16:20 UTC
HMDB IDHMDB0002329
Secondary Accession Numbers
  • HMDB02329
Metabolite Identification
Common NameOxalic acid
DescriptionOxalic acid is a strong dicarboxylic acid occurring in many plants and vegetables. It is produced in the body by metabolism of glyoxylic acid or ascorbic acid. It is not metabolized but excreted in the urine. It is used as an analytical reagent and general reducing agent (Pubchem). Oxalic acid (IUPAC name: ethanedioic acid, formula H2C2O4) is a dicarboxylic acid with structure (HOOC)-(COOH). Because of the joining of two carboxyl groups, this is one of the strongest organic acids. It is also a reducing agent. The anions of oxalic acid as well as its salts and esters are known as oxalates (Wikipedia ). Bodily oxalic acid may also be synthesized via the metabolism of either glyoxylic acid or unused ascorbic acid (vitamin C), which is a serious health consideration for long term megadosers of vitamin C supplements. 80% of kidney stones are formed from calcium oxalate. Some Aspergillus species produce oxalic acid, which reacts with blood or tissue calcium to precipitate calcium oxalate. There is some preliminary evidence that the administration of probiotics can affect oxalic acid excretion rates (and presumably oxalic acid levels as well) (Wikipedia ). Oxalic acid is found to be associated with fumarase deficiency and primary hyperoxaluria I, which are inborn errors of metabolism. Oxalic acid is a marker for yeast overgrowth from Aspergillus, Penicillum and/or Candida. Can also be elevated due to exposures from vitamin C or ethylene glycol poisoning. Oxalate is elevated in the urine of children with autism. (PMID: 21911305 ). Oxalic acid has also been identified as a uremic toxin according to the European Uremic Toxin Working Group (PMID: 22626821 ).
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0002329 (Oxalic acid)

  Mrv0541 02231217162D          

  6  5  0  0  0  0            999 V2000
    0.8250    1.4289    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0625    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
  2  4  1  0  0  0  0
  4  5  1  0  0  0  0
  4  6  2  0  0  0  0
M  END
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3D MOL for HMDB0002329 (Oxalic acid)

HMDB0002329
     RDKit          3D
Oxalic acid
  8  7  0  0  0  0  0  0  0  0999 V2000
   -0.9001   -0.9019   -1.4683 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7712   -0.2195   -0.4280 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8812    0.3943    0.1098 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5154   -0.0699    0.2085 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6127    0.6164    1.2443 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6510   -0.6760   -0.3099 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7853    1.2076    0.7004 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5587   -0.3510   -0.0568 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
  4  5  2  0
  4  6  1  0
  3  7  1  0
  6  8  1  0
M  END
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3D SDF for HMDB0002329 (Oxalic acid)

  Mrv0541 02231217162D          

  6  5  0  0  0  0            999 V2000
    0.8250    1.4289    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0625    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
  2  4  1  0  0  0  0
  4  5  1  0  0  0  0
  4  6  2  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0002329

> <DATABASE_NAME>
hmdb

> <SMILES>
OC(=O)C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C2H2O4/c3-1(4)2(5)6/h(H,3,4)(H,5,6)

> <INCHI_KEY>
MUBZPKHOEPUJKR-UHFFFAOYSA-N

> <FORMULA>
C2H2O4

> <MOLECULAR_WEIGHT>
90.0349

> <EXACT_MASS>
89.995308552

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_AVERAGE_POLARIZABILITY>
6.229225106776085

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
oxalic acid

> <ALOGPS_LOGP>
-0.51

> <JCHEM_LOGP>
-0.2637515693333333

> <ALOGPS_LOGS>
-0.14

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
4.110222978861222

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.3639908147001307

> <JCHEM_POLAR_SURFACE_AREA>
74.6

> <JCHEM_REFRACTIVITY>
14.4386

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
6.57e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
oxalic acid

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for HMDB0002329 (Oxalic acid)

HMDB0002329
     RDKit          3D
Oxalic acid
  8  7  0  0  0  0  0  0  0  0999 V2000
   -0.9001   -0.9019   -1.4683 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7712   -0.2195   -0.4280 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8812    0.3943    0.1098 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5154   -0.0699    0.2085 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6127    0.6164    1.2443 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6510   -0.6760   -0.3099 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7853    1.2076    0.7004 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5587   -0.3510   -0.0568 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
  4  5  2  0
  4  6  1  0
  3  7  1  0
  6  8  1  0
M  END
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PDB for HMDB0002329 (Oxalic acid)

HEADER    PROTEIN                                 23-FEB-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   23-FEB-12         0                                  
HETATM    1  O   UNK     0       1.540   2.667   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0       2.310   1.334   0.000  0.00  0.00           C+0
HETATM    3  O   UNK     0       3.850   1.334   0.000  0.00  0.00           O+0
HETATM    4  C   UNK     0       1.540   0.000   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0       2.310  -1.334   0.000  0.00  0.00           O+0
HETATM    6  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    5    6                                                  
CONECT    5    4                                                            
CONECT    6    4                                                            
MASTER        0    0    0    0    0    0    0    0    6    0   10    0
END
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3D PDB for HMDB0002329 (Oxalic acid)

COMPND    HMDB0002329
HETATM    1  O1  UNL     1      -0.900  -0.902  -1.468  1.00  0.00           O  
HETATM    2  C1  UNL     1      -0.771  -0.220  -0.428  1.00  0.00           C  
HETATM    3  O2  UNL     1      -1.881   0.394   0.110  1.00  0.00           O  
HETATM    4  C2  UNL     1       0.515  -0.070   0.209  1.00  0.00           C  
HETATM    5  O3  UNL     1       0.613   0.616   1.244  1.00  0.00           O  
HETATM    6  O4  UNL     1       1.651  -0.676  -0.310  1.00  0.00           O  
HETATM    7  H1  UNL     1      -1.785   1.208   0.700  1.00  0.00           H  
HETATM    8  H2  UNL     1       2.559  -0.351  -0.057  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3    4
CONECT    3    7
CONECT    4    5    5    6
CONECT    6    8
END
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SMILES for HMDB0002329 (Oxalic acid)

OC(=O)C(O)=O
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INCHI for HMDB0002329 (Oxalic acid)

InChI=1S/C2H2O4/c3-1(4)2(5)6/h(H,3,4)(H,5,6)
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View in JSmolView Stereo Labels
Synonyms
Chemical FormulaC2H2O4
Average Molecular Weight90.0349
Monoisotopic Molecular Weight89.995308552
IUPAC Nameoxalic acid
Traditional Nameoxalic acid
CAS Registry Number144-62-7
SMILES
OC(=O)C(O)=O
InChI Identifier
InChI=1S/C2H2O4/c3-1(4)2(5)6/h(H,3,4)(H,5,6)
InChI KeyMUBZPKHOEPUJKR-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as dicarboxylic acids and derivatives. These are organic compounds containing exactly two carboxylic acid groups.
KingdomOrganic compounds
Super ClassOrganic acids and derivatives
ClassCarboxylic acids and derivatives
Sub ClassDicarboxylic acids and derivatives
Direct ParentDicarboxylic acids and derivatives
Alternative Parents
Substituents
  • Dicarboxylic acid or derivatives
  • Carboxylic acid
  • Organic oxygen compound
  • Organic oxide
  • Hydrocarbon derivative
  • Organooxygen compound
  • Carbonyl group
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Ontology
Physiological effect
Health effect
Disposition
Biological locationSource
Process
Naturally occurring process
Role
Biological roleIndustrial application
Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting Point189.5 °CNot Available
Boiling PointNot AvailableNot Available
Water Solubility220 mg/mL at 25 °CNot Available
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
Predicted Chromatographic Properties
Spectra
Biological Properties
Cellular Locations
  • Extracellular
  • Peroxisome
Biospecimen Locations
  • Blood
  • Feces
  • Saliva
  • Sweat
  • Urine
Tissue Locations
  • Bladder
  • Epidermis
  • Eye Lens
  • Fibroblasts
  • Intestine
  • Kidney
  • Liver
  • Pancreas
  • Placenta
  • Testis
Pathways
Normal Concentrations
Abnormal Concentrations
Associated Disorders and Diseases
Disease References
Hemodialysis
  1. Ogawa Y, Machida N, Jahana M, Gakiya M, Chinen Y, Oda M, Morozumi M, Sugaya K: Major factors modulating the serum oxalic acid level in hemodialysis patients. Front Biosci. 2004 Sep 1;9:2901-8. [PubMed:15353324 ]
Uremia
  1. Duranton F, Cohen G, De Smet R, Rodriguez M, Jankowski J, Vanholder R, Argiles A: Normal and pathologic concentrations of uremic toxins. J Am Soc Nephrol. 2012 Jul;23(7):1258-70. doi: 10.1681/ASN.2011121175. Epub 2012 May 24. [PubMed:22626821 ]
  2. Psychogios N, Hau DD, Peng J, Guo AC, Mandal R, Bouatra S, Sinelnikov I, Krishnamurthy R, Eisner R, Gautam B, Young N, Xia J, Knox C, Dong E, Huang P, Hollander Z, Pedersen TL, Smith SR, Bamforth F, Greiner R, McManus B, Newman JW, Goodfriend T, Wishart DS: The human serum metabolome. PLoS One. 2011 Feb 16;6(2):e16957. doi: 10.1371/journal.pone.0016957. [PubMed:21359215 ]
  3. Shoemaker JD, Elliott WH: Automated screening of urine samples for carbohydrates, organic and amino acids after treatment with urease. J Chromatogr. 1991 Jan 2;562(1-2):125-38. [PubMed:2026685 ]
  4. Hoppe B, Kemper MJ, Hvizd MG, Sailer DE, Langman CB: Simultaneous determination of oxalate, citrate and sulfate in children's plasma with ion chromatography. Kidney Int. 1998 May;53(5):1348-52. [PubMed:9573551 ]
  5. Bouatra S, Aziat F, Mandal R, Guo AC, Wilson MR, Knox C, Bjorndahl TC, Krishnamurthy R, Saleem F, Liu P, Dame ZT, Poelzer J, Huynh J, Yallou FS, Psychogios N, Dong E, Bogumil R, Roehring C, Wishart DS: The human urine metabolome. PLoS One. 2013 Sep 4;8(9):e73076. doi: 10.1371/journal.pone.0073076. eCollection 2013. [PubMed:24023812 ]
  6. Ogawa Y, Machida N, Jahana M, Gakiya M, Chinen Y, Oda M, Morozumi M, Sugaya K: Major factors modulating the serum oxalic acid level in hemodialysis patients. Front Biosci. 2004 Sep 1;9:2901-8. [PubMed:15353324 ]
  7. Vanholder R, De Smet R, Glorieux G, Argiles A, Baurmeister U, Brunet P, Clark W, Cohen G, De Deyn PP, Deppisch R, Descamps-Latscha B, Henle T, Jorres A, Lemke HD, Massy ZA, Passlick-Deetjen J, Rodriguez M, Stegmayr B, Stenvinkel P, Tetta C, Wanner C, Zidek W: Review on uremic toxins: classification, concentration, and interindividual variability. Kidney Int. 2003 May;63(5):1934-43. doi: 10.1046/j.1523-1755.2003.00924.x. [PubMed:12675874 ]
  8. (). Merck Manual of Diagnosis and Therapy. . . [ISBN:978-0-911910-19-3 ]
  9. (). David F. Putnam Composition and Concentrative Properties of Human Urine. NASA Contractor Report. July 1971. .
  10. (). Geigy Scientific Tables, 8th Rev edition, pp. 130. Edited by C. Lentner, West Cadwell, N.J.: Medical education Div., Ciba-Geigy Corp. Basel, Switzerland c1981-1992.. .
  11. (). Geigy Scientific Tables, 8th Rev edition, pp. 165-177. Edited by C. Lentner, West Cadwell, N.J.: Medical education Div., Ciba-Geigy Corp., Basel, Switzerland c1981-1992.. .
Primary hyperoxaluria I
  1. Holmgren G, Hornstrom T, Johansson S, Samuelson G: Primary hyperoxaluria (glycolic acid variant): a clinical and genetical investigation of eight cases. Ups J Med Sci. 1978;83(1):65-70. [PubMed:705974 ]
Fumarase deficiency
  1. Bastug O, Kardas F, Ozturk MA, Halis H, Memur S, Korkmaz L, Tag Z, Gunes T: A rare cause of opistotonus; fumaric aciduria: The first case presentation in Turkey. Turk Pediatri Ars. 2014 Mar 1;49(1):74-6. doi: 10.5152/tpa.2014.442. eCollection 2014 Mar. [PubMed:26078636 ]
Glycolic aciduria
  1. Coulter-Mackie MB, White CT, Lange D, et al. (2002). Primary Hyperoxaluria Type 1. 2002 Jun 19 [Updated 2014 Jul 17]. In: Adam MP, Ardinger HH, Pagon RA, et al., editors. GeneReviews® [Internet]. Seattle (WA): University of Washington, Seattle; 1993-2017. Available from: https://www.ncbi.nlm.nih.gov/books/NBK1283/. University of Washington, Seattle.
Associated OMIM IDs
DrugBank IDDB03902
Phenol Explorer Compound IDNot Available
FooDB IDFDB031074
KNApSAcK IDC00001198
Chemspider ID946
KEGG Compound IDC00209
BioCyc IDOXALATE
BiGG ID34265
Wikipedia LinkOxalic_acid
METLIN ID113
PubChem Compound971
PDB IDNot Available
ChEBI ID16995
Food Biomarker OntologyNot Available
VMH IDOXA
MarkerDB IDMDB00000389
Good Scents IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General References

Enzymes

Enzyme Details
1. Proto-oncogene tyrosine-protein kinase Src
General function:
Involved in protein kinase activity
Specific function:
ATP + a [protein]-L-tyrosine = ADP + a [protein]-L-tyrosine phosphate
Gene Name:
SRC
Uniprot ID:
P12931
Molecular weight:
59834.3
References
  1. Overington JP, Al-Lazikani B, Hopkins AL: How many drug targets are there? Nat Rev Drug Discov. 2006 Dec;5(12):993-6. [PubMed:17139284 ]
  2. Imming P, Sinning C, Meyer A: Drugs, their targets and the nature and number of drug targets. Nat Rev Drug Discov. 2006 Oct;5(10):821-34. [PubMed:17016423 ]
  3. Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE: The Protein Data Bank. Nucleic Acids Res. 2000 Jan 1;28(1):235-42. [PubMed:10592235 ]

Transporters

Enzyme Details
1. Solute carrier organic anion transporter family member 2B1
General function:
Involved in transporter activity
Specific function:
Mediates the Na(+)-independent transport of organic anions such as taurocholate, the prostaglandins PGD2, PGE1, PGE2, leukotriene C4, thromboxane B2 and iloprost
Gene Name:
SLCO2B1
Uniprot ID:
O94956
Molecular weight:
76697.9
References
  1. Kobayashi D, Nozawa T, Imai K, Nezu J, Tsuji A, Tamai I: Involvement of human organic anion transporting polypeptide OATP-B (SLC21A9) in pH-dependent transport across intestinal apical membrane. J Pharmacol Exp Ther. 2003 Aug;306(2):703-8. Epub 2003 Apr 30. [PubMed:12724351 ]