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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2012-09-11 18:28:30 UTC
Update Date2023-02-21 17:23:32 UTC
HMDB IDHMDB0033717
Secondary Accession Numbers
  • HMDB33717
Metabolite Identification
Common Name(1R,2R)-Isocitric acid
Description(1R,2R)-Isocitric acid, also known as (1R,2R)-isocitrate, belongs to the class of organic compounds known as tricarboxylic acids and derivatives. These are carboxylic acids containing exactly three carboxyl groups (1R,2R)-Isocitric acid has been detected, but not quantified in, citrus. This could make (1R,2R)-isocitric acid a potential biomarker for the consumption of these foods. Based on a literature review very few articles have been published on (1R,2R)-Isocitric acid.
Structure
Data?1677000212
Synonyms
ValueSource
(1R,2R)-IsocitrateGenerator
(-)-Alloisocitric acidHMDB
(-)-erythro-FormHMDB
3-Carboxy-2,3-dideoxy-D-erythro-pentaric acidHMDB
D-erythro-Isocitric acidHMDB
Isocitric acidHMDB
L-Erythro-isocitrateGenerator
Chemical FormulaC6H8O7
Average Molecular Weight192.1235
Monoisotopic Molecular Weight192.02700261
IUPAC Name(1R,2R)-1-hydroxypropane-1,2,3-tricarboxylic acid
Traditional NameL-erythro-isocitric acid
CAS Registry Number30810-51-6
SMILES
O[C@H]([C@@H](CC(O)=O)C(O)=O)C(O)=O
InChI Identifier
InChI=1S/C6H8O7/c7-3(8)1-2(5(10)11)4(9)6(12)13/h2,4,9H,1H2,(H,7,8)(H,10,11)(H,12,13)/t2-,4-/m1/s1
InChI KeyODBLHEXUDAPZAU-VVJJHMBFSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as tricarboxylic acids and derivatives. These are carboxylic acids containing exactly three carboxyl groups.
KingdomOrganic compounds
Super ClassOrganic acids and derivatives
ClassCarboxylic acids and derivatives
Sub ClassTricarboxylic acids and derivatives
Direct ParentTricarboxylic acids and derivatives
Alternative Parents
Substituents
  • Tricarboxylic acid or derivatives
  • Beta-hydroxy acid
  • Monosaccharide
  • Hydroxy acid
  • Alpha-hydroxy acid
  • Secondary alcohol
  • Carboxylic acid
  • Organic oxygen compound
  • Organic oxide
  • Hydrocarbon derivative
  • Organooxygen compound
  • Carbonyl group
  • Alcohol
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Ontology
Physiological effectNot Available
Disposition
ProcessNot Available
Role
Physical Properties
StateNot Available
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
Water Solubility52.5 g/LALOGPS
logP-0.35ALOGPS
logP-1.4ChemAxon
logS-0.56ALOGPS
pKa (Strongest Acidic)3.07ChemAxon
pKa (Strongest Basic)-4ChemAxon
Physiological Charge-3ChemAxon
Hydrogen Acceptor Count7ChemAxon
Hydrogen Donor Count4ChemAxon
Polar Surface Area132.13 ŲChemAxon
Rotatable Bond Count5ChemAxon
Refractivity35.72 m³·mol⁻¹ChemAxon
Polarizability15.4 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
DarkChem[M+H]+144.5731661259
DarkChem[M-H]-138.73631661259
DeepCCS[M+H]+138.22130932474
DeepCCS[M-H]-135.82630932474
DeepCCS[M-2H]-169.3230932474
DeepCCS[M+Na]+144.18830932474
AllCCS[M+H]+141.832859911
AllCCS[M+H-H2O]+138.132859911
AllCCS[M+NH4]+145.332859911
AllCCS[M+Na]+146.332859911
AllCCS[M-H]-132.732859911
AllCCS[M+Na-2H]-133.932859911
AllCCS[M+HCOO]-135.232859911

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
(1R,2R)-Isocitric acidO[C@H]([C@@H](CC(O)=O)C(O)=O)C(O)=O2841.6Standard polar33892256
(1R,2R)-Isocitric acidO[C@H]([C@@H](CC(O)=O)C(O)=O)C(O)=O1380.6Standard non polar33892256
(1R,2R)-Isocitric acidO[C@H]([C@@H](CC(O)=O)C(O)=O)C(O)=O1815.7Semi standard non polar33892256

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
(1R,2R)-Isocitric acid,1TMS,isomer #1C[Si](C)(C)O[C@@H](C(=O)O)[C@@H](CC(=O)O)C(=O)O1641.8Semi standard non polar33892256
(1R,2R)-Isocitric acid,1TMS,isomer #2C[Si](C)(C)OC(=O)C[C@@H](C(=O)O)[C@@H](O)C(=O)O1646.8Semi standard non polar33892256
(1R,2R)-Isocitric acid,1TMS,isomer #3C[Si](C)(C)OC(=O)[C@H](CC(=O)O)[C@@H](O)C(=O)O1629.7Semi standard non polar33892256
(1R,2R)-Isocitric acid,1TMS,isomer #4C[Si](C)(C)OC(=O)[C@H](O)[C@@H](CC(=O)O)C(=O)O1640.3Semi standard non polar33892256
(1R,2R)-Isocitric acid,2TMS,isomer #1C[Si](C)(C)OC(=O)[C@H](O[Si](C)(C)C)[C@@H](CC(=O)O)C(=O)O1694.8Semi standard non polar33892256
(1R,2R)-Isocitric acid,2TMS,isomer #2C[Si](C)(C)OC(=O)C[C@@H](C(=O)O)[C@@H](O[Si](C)(C)C)C(=O)O1709.3Semi standard non polar33892256
(1R,2R)-Isocitric acid,2TMS,isomer #3C[Si](C)(C)OC(=O)[C@H](CC(=O)O)[C@@H](O[Si](C)(C)C)C(=O)O1698.4Semi standard non polar33892256
(1R,2R)-Isocitric acid,2TMS,isomer #4C[Si](C)(C)OC(=O)C[C@@H](C(=O)O[Si](C)(C)C)[C@@H](O)C(=O)O1706.7Semi standard non polar33892256
(1R,2R)-Isocitric acid,2TMS,isomer #5C[Si](C)(C)OC(=O)C[C@@H](C(=O)O)[C@@H](O)C(=O)O[Si](C)(C)C1695.0Semi standard non polar33892256
(1R,2R)-Isocitric acid,2TMS,isomer #6C[Si](C)(C)OC(=O)[C@H](O)[C@@H](CC(=O)O)C(=O)O[Si](C)(C)C1693.4Semi standard non polar33892256
(1R,2R)-Isocitric acid,3TMS,isomer #1C[Si](C)(C)OC(=O)C[C@@H](C(=O)O)[C@@H](O[Si](C)(C)C)C(=O)O[Si](C)(C)C1765.6Semi standard non polar33892256
(1R,2R)-Isocitric acid,3TMS,isomer #2C[Si](C)(C)OC(=O)[C@H](CC(=O)O)[C@@H](O[Si](C)(C)C)C(=O)O[Si](C)(C)C1773.4Semi standard non polar33892256
(1R,2R)-Isocitric acid,3TMS,isomer #3C[Si](C)(C)OC(=O)C[C@@H](C(=O)O[Si](C)(C)C)[C@@H](O[Si](C)(C)C)C(=O)O1770.7Semi standard non polar33892256
(1R,2R)-Isocitric acid,3TMS,isomer #4C[Si](C)(C)OC(=O)C[C@@H](C(=O)O[Si](C)(C)C)[C@@H](O)C(=O)O[Si](C)(C)C1783.6Semi standard non polar33892256
(1R,2R)-Isocitric acid,4TMS,isomer #1C[Si](C)(C)OC(=O)C[C@@H](C(=O)O[Si](C)(C)C)[C@@H](O[Si](C)(C)C)C(=O)O[Si](C)(C)C1880.1Semi standard non polar33892256
(1R,2R)-Isocitric acid,1TBDMS,isomer #1CC(C)(C)[Si](C)(C)O[C@@H](C(=O)O)[C@@H](CC(=O)O)C(=O)O1907.7Semi standard non polar33892256
(1R,2R)-Isocitric acid,1TBDMS,isomer #2CC(C)(C)[Si](C)(C)OC(=O)C[C@@H](C(=O)O)[C@@H](O)C(=O)O1926.2Semi standard non polar33892256
(1R,2R)-Isocitric acid,1TBDMS,isomer #3CC(C)(C)[Si](C)(C)OC(=O)[C@H](CC(=O)O)[C@@H](O)C(=O)O1904.2Semi standard non polar33892256
(1R,2R)-Isocitric acid,1TBDMS,isomer #4CC(C)(C)[Si](C)(C)OC(=O)[C@H](O)[C@@H](CC(=O)O)C(=O)O1913.2Semi standard non polar33892256
(1R,2R)-Isocitric acid,2TBDMS,isomer #1CC(C)(C)[Si](C)(C)OC(=O)[C@H](O[Si](C)(C)C(C)(C)C)[C@@H](CC(=O)O)C(=O)O2144.7Semi standard non polar33892256
(1R,2R)-Isocitric acid,2TBDMS,isomer #2CC(C)(C)[Si](C)(C)OC(=O)C[C@@H](C(=O)O)[C@@H](O[Si](C)(C)C(C)(C)C)C(=O)O2162.7Semi standard non polar33892256
(1R,2R)-Isocitric acid,2TBDMS,isomer #3CC(C)(C)[Si](C)(C)OC(=O)[C@H](CC(=O)O)[C@@H](O[Si](C)(C)C(C)(C)C)C(=O)O2153.8Semi standard non polar33892256
(1R,2R)-Isocitric acid,2TBDMS,isomer #4CC(C)(C)[Si](C)(C)OC(=O)C[C@@H](C(=O)O[Si](C)(C)C(C)(C)C)[C@@H](O)C(=O)O2156.3Semi standard non polar33892256
(1R,2R)-Isocitric acid,2TBDMS,isomer #5CC(C)(C)[Si](C)(C)OC(=O)C[C@@H](C(=O)O)[C@@H](O)C(=O)O[Si](C)(C)C(C)(C)C2161.1Semi standard non polar33892256
(1R,2R)-Isocitric acid,2TBDMS,isomer #6CC(C)(C)[Si](C)(C)OC(=O)[C@H](O)[C@@H](CC(=O)O)C(=O)O[Si](C)(C)C(C)(C)C2152.4Semi standard non polar33892256
(1R,2R)-Isocitric acid,3TBDMS,isomer #1CC(C)(C)[Si](C)(C)OC(=O)C[C@@H](C(=O)O)[C@@H](O[Si](C)(C)C(C)(C)C)C(=O)O[Si](C)(C)C(C)(C)C2426.0Semi standard non polar33892256
(1R,2R)-Isocitric acid,3TBDMS,isomer #2CC(C)(C)[Si](C)(C)OC(=O)[C@H](CC(=O)O)[C@@H](O[Si](C)(C)C(C)(C)C)C(=O)O[Si](C)(C)C(C)(C)C2421.2Semi standard non polar33892256
(1R,2R)-Isocitric acid,3TBDMS,isomer #3CC(C)(C)[Si](C)(C)OC(=O)C[C@@H](C(=O)O[Si](C)(C)C(C)(C)C)[C@@H](O[Si](C)(C)C(C)(C)C)C(=O)O2448.8Semi standard non polar33892256
(1R,2R)-Isocitric acid,3TBDMS,isomer #4CC(C)(C)[Si](C)(C)OC(=O)C[C@@H](C(=O)O[Si](C)(C)C(C)(C)C)[C@@H](O)C(=O)O[Si](C)(C)C(C)(C)C2422.5Semi standard non polar33892256
(1R,2R)-Isocitric acid,4TBDMS,isomer #1CC(C)(C)[Si](C)(C)OC(=O)C[C@@H](C(=O)O[Si](C)(C)C(C)(C)C)[C@@H](O[Si](C)(C)C(C)(C)C)C(=O)O[Si](C)(C)C(C)(C)C2646.9Semi standard non polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - (1R,2R)-Isocitric acid GC-MS (Non-derivatized) - 70eV, Positivesplash10-0f95-6900000000-218acce4c9847643adc32017-09-01Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - (1R,2R)-Isocitric acid GC-MS (4 TMS) - 70eV, Positivesplash10-02vi-7029500000-2bb65fc897e48cc217502017-10-06Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - (1R,2R)-Isocitric acid GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart LabView Spectrum

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - (1R,2R)-Isocitric acid 10V, Positive-QTOFsplash10-004j-0900000000-a75a4b486df1552d6d932016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - (1R,2R)-Isocitric acid 20V, Positive-QTOFsplash10-0gla-4900000000-d04fec4218cafd6195df2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - (1R,2R)-Isocitric acid 40V, Positive-QTOFsplash10-0fk9-8900000000-4e5fbbb415df9fbc8f312016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - (1R,2R)-Isocitric acid 10V, Negative-QTOFsplash10-00ke-1900000000-c364bae4640e201c366d2016-08-04Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - (1R,2R)-Isocitric acid 20V, Negative-QTOFsplash10-0v4j-4900000000-d00f263a75673b7981c72016-08-04Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - (1R,2R)-Isocitric acid 40V, Negative-QTOFsplash10-0pk9-9200000000-156693398229f972d7172016-08-04Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - (1R,2R)-Isocitric acid 10V, Positive-QTOFsplash10-056r-0900000000-4e17b6a1e2aad4076c032021-09-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - (1R,2R)-Isocitric acid 20V, Positive-QTOFsplash10-0ufr-1900000000-15b65374b78661650dfa2021-09-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - (1R,2R)-Isocitric acid 40V, Positive-QTOFsplash10-00di-9100000000-f126784f2170bc8d341a2021-09-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - (1R,2R)-Isocitric acid 10V, Negative-QTOFsplash10-002f-1900000000-33d42ec37993dc6475132021-09-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - (1R,2R)-Isocitric acid 20V, Negative-QTOFsplash10-0ufr-4900000000-7b0e1ae548050695b9d62021-09-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - (1R,2R)-Isocitric acid 40V, Negative-QTOFsplash10-0ufu-9600000000-3667240157dc2ec377ae2021-09-25Wishart LabView Spectrum

NMR Spectra

Spectrum TypeDescriptionDeposition DateSourceView
Predicted 1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum

IR Spectra

Spectrum TypeDescriptionDeposition DateSourceView
Predicted IR SpectrumIR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M-H]-)2023-02-04FELIX labView Spectrum
Predicted IR SpectrumIR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M+H]+)2023-02-04FELIX labView Spectrum
Predicted IR SpectrumIR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M+Na]+)2023-02-04FELIX labView Spectrum
Biological Properties
Cellular Locations
  • Cytoplasm
  • Extracellular
Biospecimen LocationsNot Available
Tissue LocationsNot Available
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB011836
KNApSAcK IDNot Available
Chemspider ID388375
KEGG Compound IDC04617
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound439238
PDB IDNot Available
ChEBI ID43291
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General References
  1. (). Yannai, Shmuel. (2004) Dictionary of food compounds with CD-ROM: Additives, flavors, and ingredients. Boca Raton: Chapman & Hall/CRC.. .