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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2006-02-23 12:38:32 UTC
Update Date2021-09-14 15:18:11 UTC
HMDB IDHMDB0001874
Secondary Accession Numbers
  • HMDB01874
Metabolite Identification
Common NameD-threo-Isocitric acid
DescriptionD-threo-Isocitric acid, also known as isocitrate or isocitrIC ACID, belongs to the class of organic compounds known as tricarboxylic acids and derivatives. These are carboxylic acids containing exactly three carboxyl groups. D-threo-Isocitric acid exists in all living species, ranging from bacteria to plants to humans. D-threo-Isocitric acid has been detected, but not quantified in, several different foods, such as salmonberries (Rubus spectabilis), black elderberries (Sambucus nigra), common peas (Pisum sativum), nectarines (Prunus persica var. nucipersica), and olives (Olea europaea). This could make D-threo-isocitric acid a potential biomarker for the consumption of these foods. D-threo-Isocitric 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. Based on a literature review a significant number of articles have been published on D-threo-Isocitric acid.
Structure
Data?1582752213
Synonyms
ValueSource
(+)-Threo-isocitric acidChEBI
ISOCITRIC ACIDChEBI
(+)-Threo-isocitrateGenerator
ISOCITRateGenerator
D-Threo-isocitrateGenerator
(1R,2S)-1-Hydroxypropane-1,2,3-tricarboxylateHMDB
(1R,2S)-1-Hydroxypropane-1,2,3-tricarboxylic acidHMDB
(2R,3S)-IsocitrateHMDB
3-Carboxy-2,3-dideoxy-L-threo-pentaric acidHMDB
D-(+)-threo-Isocitric acid(2R,3S)-isocitric acidHMDB
DS-threo-IsocitrateHMDB
DS-threo-Isocitric acidHMDB
ICIHMDB
ICTHMDB
threo-D-(+)-IsocitrateHMDB
threo-D-(+)-Isocitric acidHMDB
threo-DS(+)-IsocitrateHMDB
threo-DS(+)-Isocitric acidHMDB
threo-IsocitrateHMDB
Isocitric acid, trisodium saltMeSH, HMDB
Isocitric acid, (11)C-labeledMeSH, HMDB
Isocitric acid, disodium saltMeSH, HMDB
Isocitric acid, calcium saltMeSH, HMDB
Isocitric acid, potassium saltMeSH, HMDB
Isocitric acid, sodium saltMeSH, HMDB
Chemical FormulaC6H8O7
Average Molecular Weight192.1235
Monoisotopic Molecular Weight192.02700261
IUPAC Name(1R,2S)-1-hydroxypropane-1,2,3-tricarboxylic acid
Traditional Namethreo-DS(+)-isocitrate
CAS Registry Number6061-97-8
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+/m0/s1
InChI KeyODBLHEXUDAPZAU-ZAFYKAAXSA-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
Disposition

Biological location

Physical Properties
StateSolid
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
Polarizability15.54 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]+143.66731661259
DarkChem[M-H]-136.89431661259
AllCCS[M+H]+141.80432859911
AllCCS[M-H]-132.73832859911
DeepCCS[M+H]+138.03930932474
DeepCCS[M-H]-135.64430932474
DeepCCS[M-2H]-169.16630932474
DeepCCS[M+Na]+144.01930932474

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
D-threo-Isocitric acidO[C@H]([C@H](CC(O)=O)C(O)=O)C(O)=O2841.6Standard polar33892256
D-threo-Isocitric acidO[C@H]([C@H](CC(O)=O)C(O)=O)C(O)=O1380.6Standard non polar33892256
D-threo-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
D-threo-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
D-threo-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
D-threo-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
D-threo-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
D-threo-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
D-threo-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
D-threo-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
D-threo-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
D-threo-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
D-threo-Isocitric acid,2TMS,isomer #6C[Si](C)(C)OC(=O)[C@@H](CC(=O)O)[C@@H](O)C(=O)O[Si](C)(C)C1693.4Semi standard non polar33892256
D-threo-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
D-threo-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
D-threo-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
D-threo-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
D-threo-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
D-threo-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
D-threo-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
D-threo-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
D-threo-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
D-threo-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
D-threo-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
D-threo-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
D-threo-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
D-threo-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
D-threo-Isocitric acid,2TBDMS,isomer #6CC(C)(C)[Si](C)(C)OC(=O)[C@@H](CC(=O)O)[C@@H](O)C(=O)O[Si](C)(C)C(C)(C)C2152.4Semi standard non polar33892256
D-threo-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
D-threo-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
D-threo-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
D-threo-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
D-threo-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
Experimental GC-MSGC-MS Spectrum - D-threo-Isocitric acid GC-EI-TOF (Non-derivatized)splash10-0002-0952000000-aeb4dfa5b7b1d6eba92f2017-09-12HMDB team, MONA, MassBankView Spectrum
Experimental GC-MSGC-MS Spectrum - D-threo-Isocitric acid GC-EI-TOF (Non-derivatized)splash10-0002-1920000000-b56fdff61401e2340d502017-09-12HMDB team, MONA, MassBankView Spectrum
Experimental GC-MSGC-MS Spectrum - D-threo-Isocitric acid GC-EI-TOF (Non-derivatized)splash10-0002-0952000000-aeb4dfa5b7b1d6eba92f2018-05-18HMDB team, MONA, MassBankView Spectrum
Experimental GC-MSGC-MS Spectrum - D-threo-Isocitric acid GC-EI-TOF (Non-derivatized)splash10-0002-1920000000-b56fdff61401e2340d502018-05-18HMDB team, MONA, MassBankView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - D-threo-Isocitric acid GC-MS (Non-derivatized) - 70eV, Positivesplash10-00ba-7900000000-96194d87d52b155cf1b92016-09-22Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - D-threo-Isocitric acid GC-MS (4 TMS) - 70eV, Positivesplash10-02vi-7029500000-2bb65fc897e48cc217502017-10-06Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - D-threo-Isocitric acid GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - D-threo-Isocitric acid GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart LabView Spectrum

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Experimental LC-MS/MSLC-MS/MS Spectrum - D-threo-Isocitric acid Quattro_QQQ 10V, Negative-QTOF (Annotated)splash10-0udi-0900000000-24949c0952ed64de70832012-07-24HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - D-threo-Isocitric acid Quattro_QQQ 25V, Negative-QTOF (Annotated)splash10-0w29-1900000000-c9bdca817d12cb4b091b2012-07-24HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - D-threo-Isocitric acid Quattro_QQQ 40V, Negative-QTOF (Annotated)splash10-014l-9300000000-66e9d659711c1d339f762012-07-24HMDB team, MONAView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - D-threo-Isocitric acid 10V, Negative-QTOFsplash10-00ke-1900000000-c364bae4640e201c366d2016-09-14Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - D-threo-Isocitric acid 20V, Negative-QTOFsplash10-0v4j-4900000000-d00f263a75673b7981c72016-09-14Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - D-threo-Isocitric acid 40V, Negative-QTOFsplash10-0pk9-9200000000-156693398229f972d7172016-09-14Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - D-threo-Isocitric acid 10V, Negative-QTOFsplash10-002f-1900000000-33d42ec37993dc6475132021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - D-threo-Isocitric acid 20V, Negative-QTOFsplash10-0ufr-4900000000-7b0e1ae548050695b9d62021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - D-threo-Isocitric acid 40V, Negative-QTOFsplash10-0ufu-9600000000-3667240157dc2ec377ae2021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - D-threo-Isocitric acid 10V, Positive-QTOFsplash10-004j-0900000000-a75a4b486df1552d6d932016-09-14Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - D-threo-Isocitric acid 20V, Positive-QTOFsplash10-0gla-4900000000-d04fec4218cafd6195df2016-09-14Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - D-threo-Isocitric acid 40V, Positive-QTOFsplash10-0fk9-8900000000-4e5fbbb415df9fbc8f312016-09-14Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - D-threo-Isocitric acid 10V, Positive-QTOFsplash10-056r-0900000000-4e17b6a1e2aad4076c032021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - D-threo-Isocitric acid 20V, Positive-QTOFsplash10-0ufr-1900000000-15b65374b78661650dfa2021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - D-threo-Isocitric acid 40V, Positive-QTOFsplash10-00di-9100000000-f126784f2170bc8d341a2021-09-24Wishart LabView Spectrum

NMR Spectra

Spectrum TypeDescriptionDeposition DateSourceView
Experimental 1D NMR1H NMR Spectrum (1D, 500 MHz, H2O, experimental)2012-12-04Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-09-16Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-09-16Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-09-16Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-09-16Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-09-16Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-09-16Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-09-16Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-09-16Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-09-16Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-09-16Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-09-16Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-09-16Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-09-16Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-09-16Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-09-16Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-09-16Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-09-16Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-09-16Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-09-16Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-09-16Wishart LabView Spectrum
Experimental 2D NMR[1H, 13C]-HSQC NMR Spectrum (2D, 600 MHz, H2O, experimental)2012-12-05Wishart LabView Spectrum
Biological Properties
Cellular Locations
  • Mitochondria
  • Peroxisome
Biospecimen Locations
  • Blood
Tissue LocationsNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodExpected but not QuantifiedNot QuantifiedNot AvailableNot Available
Normal
      Not Available
details
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB012771
KNApSAcK IDC00001188
Chemspider ID4477081
KEGG Compound IDC00451
BioCyc IDTHREO-DS-ISO-CITRATE
BiGG ID34579
Wikipedia LinkNot Available
METLIN ID3328
PubChem Compound5318532
PDB IDNot Available
ChEBI ID151
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceWong, Chi Huey; Whitesides, George M. Enzyme-catalyzed transhydrogenation between nicotinamide cofactors and its application in organic synthesis. Journal of the American Chemical Society (1982), 104(12), 3542-4.
Material Safety Data Sheet (MSDS)Download (PDF)
General ReferencesNot Available