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Showing NP-Card for Oxalate (NP0002618)

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Record Information
Version1.0
Created at2020-11-23 18:25:23 UTC
Updated at2021-08-19 23:59:13 UTC
NP-MRD IDNP0002618
Secondary Accession NumbersNone
Natural Product Identification
Common NameOxalate
Provided ByBMRBBMRB logo
DescriptionOxalic acid, also known as ethanedioic acid or ethandisaeure, belongs to the class of organic compounds known as dicarboxylic acids and derivatives. These are organic compounds containing exactly two carboxylic acid groups. Oxalic acid exists in all living organisms, ranging from bacteria to humans. Oxalic acid is a primary metabolite. Primary metabolites are metabolically or physiologically essential metabolites. They are directly involved in an organism’s growth, development or reproduction. Oxalic acid, with regard to humans, has been found to be associated with several diseases such as hemodialysis and uremia; oxalic acid has also been linked to several inborn metabolic disorders including primary hyperoxaluria I, fumarase deficiency, and glycolic aciduria. Oxalate is found in Actinidia arguta, Albizia julibrissin, Alocasia odora, Aloe vera, Amaranthus tricolor, Ammodendron bifolium, Beta vulgaris, Bulgaria inquinans, Parasenecio hastatus, Chlamydomonas reinhardtii, Colocasia esculenta, Colocasia escultenta, Curcuma domestica , Echinopsis chamaecereus, Glehnia littoralis, Herniaria hirsuta, Imperata cylindrica, Lotus corniculatus, Lupinus albus, Lupinus luteus, Morus nigra, Opuntia microdasys, Oxalis tuberosa, Paraburkholderia phymatum, Paris fargesii, Parthenium hysterophorus, Penicillium oxalicum, Phoenix dactylifera, Phyllostachys edulis, Plinia cauliflora, Populus lasiocarpa, Populus tremula, Portulaca oleracea, Prunus salicina, Rhodiola rosea, Rosa spinosissima, Salmonella enterica, Sambucus nigra, Sclerotinia trifoliorum, Solanum tuberosum, Sclerotium cepivorum, Telekia speciosa, Terminalia chebula , Thymus transcaucasicus, Ulmus glabra, Vaccinium macrocarpon, Viburnum opulus and Xanthosoma sagittifolium. It was first documented in 1999 (PMID: 10196036). Based on a literature review a significant number of articles have been published on Oxalic acid (PMID: 17984079) (PMID: 12563622) (PMID: 12682898) (PMID: 10886075).
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for NP0002618 (Oxalate)


     RDKit          2D

  8  7  0  0  0  0  0  0  0  0999 V2000
   -0.9517   -1.7412    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7027   -0.2620    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8593    0.6932    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7027    0.2620    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9517    1.7412    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.8593   -0.6932    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2648    0.1692    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2648   -0.1692    0.0000 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 MOL for NP0002618 (Oxalate)

NP0002618
     RDKit          3D

  8  7  0  0  0  0  0  0  0  0999 V2000
   -0.3365   -1.6885   -0.0565 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5325   -0.4574   -0.2115 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8548   -0.0650   -0.3749 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5834    0.4413   -0.2108 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4959    1.6920   -0.3582 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.8690   -0.0493   -0.0398 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4260    0.3269    0.3553 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2016   -0.2000    0.8964 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
Download

3D SDF for NP0002618 (Oxalate)


     RDKit          2D

  8  7  0  0  0  0  0  0  0  0999 V2000
   -0.9517   -1.7412    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7027   -0.2620    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8593    0.6932    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7027    0.2620    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9517    1.7412    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.8593   -0.6932    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2648    0.1692    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2648   -0.1692    0.0000 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
> <DATABASE_ID>
NP0002618

> <DATABASE_NAME>
NP-MRD

> <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 NP0002618 (Oxalate)

NP0002618
     RDKit          3D

  8  7  0  0  0  0  0  0  0  0999 V2000
   -0.3365   -1.6885   -0.0565 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5325   -0.4574   -0.2115 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8548   -0.0650   -0.3749 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5834    0.4413   -0.2108 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4959    1.6920   -0.3582 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.8690   -0.0493   -0.0398 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4260    0.3269    0.3553 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2016   -0.2000    0.8964 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 NP0002618 (Oxalate)

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 NP0002618 (Oxalate)

COMPND    NP0002618
HETATM    1  O1  UNL     1      -0.337  -1.689  -0.056  1.00  0.00           O  
HETATM    2  C1  UNL     1      -0.533  -0.457  -0.212  1.00  0.00           C  
HETATM    3  O2  UNL     1      -1.855  -0.065  -0.375  1.00  0.00           O  
HETATM    4  C2  UNL     1       0.583   0.441  -0.211  1.00  0.00           C  
HETATM    5  O3  UNL     1       0.496   1.692  -0.358  1.00  0.00           O  
HETATM    6  O4  UNL     1       1.869  -0.049  -0.040  1.00  0.00           O  
HETATM    7  H1  UNL     1      -2.426   0.327   0.355  1.00  0.00           H  
HETATM    8  H2  UNL     1       2.202  -0.200   0.896  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 NP0002618 (Oxalate)

OC(=O)C(O)=O
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INCHI for NP0002618 (Oxalate)

InChI=1S/C2H2O4/c3-1(4)2(5)6/h(H,3,4)(H,5,6)
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View in JSmol
Synonyms
ValueSource
EthandisaeureChEBI
Ethane-1,2-dioic acidChEBI
Ethanedioic acidChEBI
H2OxChEBI
HOOCCOOHChEBI
OxalsaeureChEBI
Ethane-1,2-dioateGenerator
EthanedioateGenerator
OxalateGenerator
Ammonium oxalateHMDB, MeSH
Ethanedioic acid dihydrateHMDB
EthanedionateHMDB
Ethanedionic acidHMDB
Kyselina stavelovaHMDB
OxaalzuurHMDB
Oxalic acid 2-hydrateHMDB
Oxalic acid anhydrousHMDB
Oxalic acid diammonium saltHMDB
Oxalic acid dihydrateHMDB
Acid, oxalicMeSH, HMDB
Aluminum oxalateMeSH, HMDB
Chromium (3+) oxalate (3:2)MeSH, HMDB
Dipotassium oxalateMeSH, HMDB
Iron oxalateMeSH, HMDB
Magnesium oxalateMeSH, HMDB
Magnesium oxalate (1:1)MeSH, HMDB
Oxalate, dilithiumMeSH, HMDB
Oxalate, disodiumMeSH, HMDB
Oxalate, monohydrogen monopotassiumMeSH, HMDB
Oxalate, monopotassiumMeSH, HMDB
Oxalate, potassiumMeSH, HMDB
Chromium oxalateMeSH, HMDB
Dilithium oxalateMeSH, HMDB
Manganese (2+) oxalate (1:1)MeSH, HMDB
Monosodium oxalateMeSH, HMDB
Oxalate, chromiumMeSH, HMDB
Oxalate, dipotassiumMeSH, HMDB
Oxalate, magnesiumMeSH, HMDB
Oxalate, monosodiumMeSH, HMDB
Oxalate, potassium chromiumMeSH, HMDB
Oxalate, sodiumMeSH, HMDB
Potassium oxalateMeSH, HMDB
Potassium oxalate (2:1)MeSH, HMDB
Diammonium oxalateMeSH, HMDB
Disodium oxalateMeSH, HMDB
Oxalate, aluminumMeSH, HMDB
Oxalate, diammoniumMeSH, HMDB
Oxalate, ferricMeSH, HMDB
Oxalate, monoammoniumMeSH, HMDB
Potassium chromium oxalateMeSH, HMDB
Chromium (2+) oxalateMeSH, HMDB
Ferric oxalateMeSH, HMDB
Iron (2+) oxalate (1:1)MeSH, HMDB
Iron (3+) oxalateMeSH, HMDB
Monoammonium oxalateMeSH, HMDB
Monohydrogen monopotassium oxalateMeSH, HMDB
Monopotassium oxalateMeSH, HMDB
Oxalate, ironMeSH, HMDB
Sodium oxalateMeSH, HMDB
Oxalic acidKEGG
Chemical FormulaC2H2O4
Average Mass90.0349 Da
Monoisotopic Mass89.99531 Da
IUPAC Nameoxalic acid
Traditional Nameoxalic acid
CAS Registry NumberNot Available
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
Experimental Spectra
Spectrum TypeDescriptionDepositor EmailDepositor OrganizationDepositorDeposition DateView
1D NMR13C NMR Spectrum (1D, 400 MHz, D2O, simulated)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 400 MHz, D2O, simulated)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 400 MHz, D2O, experimental)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
Predicted Spectra
Not Available
Chemical Shift Submissions
Not Available
Species
Species of Origin
Species NameSourceReference
Acacia concinnaKNApSAcK Database
Actinidia argutaLOTUS Database
Albizia julibrissinLOTUS Database
Alocasia odoraLOTUS Database
Aloe veraLOTUS Database
Amaranthus tricolorLOTUS Database
Ammodendron bifoliumLOTUS Database
Arabidopsis thalianaKNApSAcK Database
Artemisia scopariaKNApSAcK Database
Beta vulgarisLOTUS Database
Bulgaria inquinansLOTUS Database
Cacalia hastataLOTUS Database
Cannabis sativaCannabisDB
      Not Available
Capparis aegyptiaKNApSAcK Database
Capparis desertiKNApSAcK Database
Capparis leucophyllaKNApSAcK Database
Capsicum annuumKNApSAcK Database
Chlamydomonas reinhardtiiLOTUS Database
Cicer arietinumKNApSAcK Database
Colocasia esculentaLOTUS Database
Colocasia escultentaPlant
Crataegus pinnatifidaKNApSAcK Database
Curcuma domesticaKNApSAcK Database
Curcuma longaPlant
Echinopsis chamaecereusLOTUS Database
Ephedra equisetinaKNApSAcK Database
Glehnia littoralisLOTUS Database
Herniaria hirsutaLOTUS Database
Hippophae rhamnoidesKNApSAcK Database
Imperata cylindricaLOTUS Database
Lotus corniculatusLOTUS Database
Lupinus albusLOTUS Database
Lupinus luteusLOTUS Database
Mangifera indicaKNApSAcK Database
Morus nigraLOTUS Database
Opuntia microdasysLOTUS Database
Oxalis spp.KNApSAcK Database
Oxalis tuberosa MolinaLOTUS Database
Paraburkholderia phymatum-
Paris fargesiiLOTUS Database
Parthenium hysterophorusLOTUS Database
Penicillium oxalicumLOTUS Database
Phaseolus vulgarisKNApSAcK Database
Phoenix dactyliferaLOTUS Database
Phyllostachys edulisLOTUS Database
Plinia caulifloraLOTUS Database
Populus lasiocarpaLOTUS Database
Populus tremulaLOTUS Database
Portulaca oleraceaLOTUS Database
Prunus salicinaLOTUS Database
Punica granatumKNApSAcK Database
Rheum rhaponticumKNApSAcK Database
Rhodiola roseaLOTUS Database
Rosa spinosissimaLOTUS Database
Salmonella entericaLOTUS Database
Sambucus nigraLOTUS Database
Sclerotinia trifoliorumLOTUS Database
Solanum tuberosumLOTUS Database
Sophora alopecuroidesKNApSAcK Database
Spinacia oleraceaKNApSAcK Database
Stemona tuberosaKNApSAcK Database
Stromatinia cepivoraLOTUS Database
Telekia speciosaLOTUS Database
Terminalia chebulaPlant
Thymus transcaucasicusLOTUS Database
Triticum aestivumKNApSAcK Database
Ulmus campestrisLOTUS Database
Urtica dioicaKNApSAcK Database
Vaccinium macrocarponLOTUS Database
Viburnum opulusLOTUS Database
Vicia fabaKNApSAcK Database
Xanthosoma sagittifoliumLOTUS Database
Species Where Detected
Species NameSourceReference
Homo sapiens (Serum)KNApSAcK Database
Homo sapiens (Urine)KNApSAcK Database
Phoma medicaginisKNApSAcK Database
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 ParentsNot Available
SubstituentsNot Available
Molecular FrameworkAliphatic acyclic compounds
External DescriptorsNot Available
Physical Properties
StateNot Available
Experimental Properties
PropertyValueReference
Melting Point189.00 to 190.00 °C. @ 760.00 mm HgThe Good Scents Company Information System
Boiling Point365.00 to 367.00 °C. @ 760.00 mm HgThe Good Scents Company Information System
Water Solubility1000000 mg/L @ 25 °C (est)The Good Scents Company Information System
LogP-2.220The Good Scents Company Information System
Predicted Properties
PropertyValueSource
logP-0.51ALOGPS
logP-0.26ChemAxon
logS-0.14ALOGPS
pKa (Strongest Acidic)1.36ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count4ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area74.6 ŲChemAxon
Rotatable Bond Count1ChemAxon
Refractivity14.44 m³·mol⁻¹ChemAxon
Polarizability6.23 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDHMDB0002329
DrugBank IDDB03902
Phenol Explorer Compound IDNot Available
FoodDB IDFDB031074
KNApSAcK IDC00001198
Chemspider ID946
KEGG Compound IDC00209
BioCyc IDOXALATE
BiGG ID34265
Wikipedia LinkOxalic_acid
METLIN ID113
PubChem Compound971
PDB IDNot Available
ChEBI ID16995
Good Scents IDrw1271141
References
General References
  1. Ulrich EL, Akutsu H, Doreleijers JF, Harano Y, Ioannidis YE, Lin J, Livny M, Mading S, Maziuk D, Miller Z, Nakatani E, Schulte CF, Tolmie DE, Kent Wenger R, Yao H, Markley JL: BioMagResBank. Nucleic Acids Res. 2008 Jan;36(Database issue):D402-8. doi: 10.1093/nar/gkm957. Epub 2007 Nov 4. [PubMed:17984079 ]
  2. de O G Mendonca C, Martini LA, Baxmann AC, Nishiura JL, Cuppari L, Sigulem DM, Heilberg IP: Effects of an oxalate load on urinary oxalate excretion in calcium stone formers. J Ren Nutr. 2003 Jan;13(1):39-46. doi: 10.1053/jren.2003.50002. [PubMed:12563622 ]
  3. Singh S, Tai C, Ganz G, Yeung CK, Magil A, Rosenberg F, Applegarth D, Levin A: Steroid-responsive pleuropericarditis and livedo reticularis in an unusual case of adult-onset primary hyperoxaluria. Am J Kidney Dis. 1999 Apr;33(4):e5. doi: 10.1016/s0272-6386(99)70246-5. [PubMed:10196036 ]
  4. Astarcioglu I, Karademir S, Gulay H, Bora S, Astarcioglu H, Kavukcu S, Turkmen M, Soylu A: Primary hyperoxaluria: simultaneous combined liver and kidney transplantation from a living related donor. Liver Transpl. 2003 Apr;9(4):433-6. doi: 10.1053/jlts.2003.50072. [PubMed:12682898 ]
  5. Selvam R, Kalaiselvi P: A novel basic protein from human kidney which inhibits calcium oxalate crystal growth. BJU Int. 2000 Jul;86(1):7-13. doi: 10.1046/j.1464-410x.2000.00725.x. [PubMed:10886075 ]