Record Information
Version2.0
Creation Date2012-05-31 14:04:40 -0600
Update Date2015-09-13 12:56:13 -0600
Secondary Accession Numbers
  • ECMDB04088
Identification
Name:Isocitric acid
Description:Isocitric acid is a protonated form of isocitrate, which is a substrate of the citric acid cycle. Isocitrate is formed from citrate with the help of the enzyme aconitase, and is acted upon by isocitrate dehydrogenase. Salts and esters of isocitric acid are known as isocitrates. (Wikipedia)
Structure
Thumb
Synonyms:
  • (1R, 2S)-1-hydroxypropane-1,2,3-tricarboxylate
  • (1R, 2S)-1-hydroxypropane-1,2,3-tricarboxylate
  • (1R, 2S)-1-hydroxypropane-1,2,3-tricarboxylic acid
  • 1-Hydroxy-1,2,3-propanetricarboxylate
  • 1-Hydroxy-1,2,3-propanetricarboxylic acid
  • 1-Hydroxypropane-1,2,3-tricarboxylate
  • 1-Hydroxypropane-1,2,3-tricarboxylic acid
  • 1-Hydroxytricarballylate
  • 1-Hydroxytricarballylic acid
  • 3-Carboxy-2,3-dideoxy-1-hydroxypropan-1,2,3-tricarboxylate
  • 3-Carboxy-2,3-dideoxy-1-hydroxypropan-1,2,3-tricarboxylic acid
  • 3-Carboxy-2,3-dideoxy-Pentarate
  • 3-Carboxy-2,3-dideoxy-Pentaric acid
  • D-threo-isocitric acid
  • D-Isocitrate
  • D-Isocitric acid
  • D-Threo-isocitrate
  • D-Threo-isocitric acid
  • I-CIT
  • Isocitrate
  • Isocitric acid
  • Threo-D(S)-iso-citrate
  • Threo-D(S)-iso-citric acid
  • Threo-Ds-isocitrate
  • Threo-Ds-isocitrate
  • Threo-Ds-isocitric acid
Chemical Formula:C6H8O7
Weight:Average: 192.1235
Monoisotopic: 192.02700261
InChI Key:ODBLHEXUDAPZAU-UHFFFAOYSA-N
InChI: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)
CAS number:320-77-4
IUPAC Name:1-hydroxypropane-1,2,3-tricarboxylic acid
Traditional IUPAC Name:isocitric acid
SMILES:OC(C(CC(O)=O)C(O)=O)C(O)=O
Chemical Taxonomy
DescriptionThis compound 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
Physical Properties
State:Solid
Charge:-3
Melting point:162-165 °C
Experimental Properties:
PropertyValueSource
Water Solubility:466 mg/mL [HMP experimental]PhysProp
Predicted 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
Polarizability15.55 ųChemAxon
Number of Rings0ChemAxon
Bioavailability1ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations:Cytoplasm
Reactions:
SMPDB Pathways:
Glutathione metabolismPW000833 ThumbThumb?image type=greyscaleThumb?image type=simple
Secondary Metabolites: Glyoxylate cyclePW000967 ThumbThumb?image type=greyscaleThumb?image type=simple
glycolate and glyoxylate degradation IIPW002021 ThumbThumb?image type=greyscaleThumb?image type=simple
KEGG Pathways:
  • Citrate cycle (TCA cycle) ec00020
  • Glutathione metabolism ec00480
  • Glyoxylate and dicarboxylate metabolism ec00630
  • Metabolic pathways eco01100
  • Microbial metabolism in diverse environments ec01120
  • Reductive carboxylate cycle (CO2 fixation) ec00720
EcoCyc Pathways:
Concentrations
Not Available
Spectra
Spectra:
Spectrum TypeDescriptionSplash Key
GC-MSGC-MS Spectrum - GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies) (4 TMS)splash10-0002-1952000000-7c34751686a6bdb54cabView in MoNA
GC-MSGC-MS Spectrum - GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies) (4 TMS)splash10-0002-0963000000-459b45ff9246b5f55914View in MoNA
GC-MSGC-MS Spectrum - GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies) (Non-derivatized)splash10-0002-0942000000-61204d02a28e43d21607View in MoNA
GC-MSGC-MS Spectrum - GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies) (4 TMS)splash10-00di-9420000000-4e1a59fe735855d52ce2View in MoNA
GC-MSGC-MS Spectrum - GC-MS (4 TMS)splash10-00ea-3793000000-84858fa896697420275fView in MoNA
GC-MSGC-MS Spectrum - GC-EI-TOF (Non-derivatized)splash10-0002-1952000000-7c34751686a6bdb54cabView in MoNA
GC-MSGC-MS Spectrum - GC-EI-TOF (Non-derivatized)splash10-0002-0963000000-459b45ff9246b5f55914View in MoNA
GC-MSGC-MS Spectrum - GC-EI-TOF (Non-derivatized)splash10-00di-9420000000-4e1a59fe735855d52ce2View in MoNA
GC-MSGC-MS Spectrum - GC-MS (Non-derivatized)splash10-00ea-3793000000-84858fa896697420275fView in MoNA
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-00ba-7900000000-96194d87d52b155cf1b9View in MoNA
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (4 TMS) - 70eV, Positivesplash10-02vi-7029500000-2bb65fc897e48cc21750View in MoNA
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 10V, Positive (Annotated)splash10-0udi-1900000000-8e1185b0504ea1547715View in MoNA
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 25V, Positive (Annotated)splash10-05fr-7900000000-0855c1ceb168d556b7f2View in MoNA
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 40V, Positive (Annotated)splash10-0bu1-9500000000-140b46d0f1dc8fcd9e49View in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Positivesplash10-00fu-0940000000-033739944b190c47c6a7View in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Positivesplash10-053r-1900000000-89ff897aa220452bfa16View in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Positivesplash10-00di-0900000000-36aeb28d857c9039938bView in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Positivesplash10-03di-1900000000-53373dc0755caa954310View in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Negativesplash10-0006-0901310000-883764bf7b686ca7fd17View in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Negativesplash10-03di-0900000000-66d03405eeb126c6ad9dView in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Negativesplash10-00di-0900000000-cdad17a11f419421c787View in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Negativesplash10-0udi-0009000000-d3440c84a488b3e22212View in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 10V, Negativesplash10-0006-0900000000-3aa263561a7a49df7d3dView in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 20V, Negativesplash10-0006-1900000000-3636f87026e4206a1638View in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 30V, Negativesplash10-01w3-9600000000-ab1a2b9a29528a623d0bView in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 40V, Negativesplash10-0079-9000000000-3c33cefeb87f85efd5deView in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 50V, Negativesplash10-059m-9000000000-34775db8bbc008018633View in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , negativesplash10-0006-0900000000-3aa263561a7a49df7d3dView in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , negativesplash10-0006-1900000000-3636f87026e4206a1638View in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , negativesplash10-01w3-9600000000-ab1a2b9a29528a623d0bView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-004j-0900000000-a75a4b486df1552d6d93View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-0gla-4900000000-d04fec4218cafd6195dfView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-0fk9-8900000000-4e5fbbb415df9fbc8f31View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-00ke-1900000000-c364bae4640e201c366dView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-0v4j-4900000000-d00f263a75673b7981c7View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-0pk9-9200000000-156693398229f972d717View in MoNA
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
2D NMR[1H,13C] 2D NMR SpectrumNot AvailableView in JSpectraViewer
References
References:
  • Ebeling K, Ruckhaberle KE, Bilek K: [Studies on the recording of cytostatic effects on organ cultures of squamous cell carcinoma of the uterine cervix] Zentralbl Gynakol. 1977;99(20):1249-59. Pubmed: 595962
  • Guneral F, Bachmann C: Age-related reference values for urinary organic acids in a healthy Turkish pediatric population. Clin Chem. 1994 Jun;40(6):862-6. Pubmed: 8087979
  • Hennequin C, Lalanne V, Daudon M, Lacour B, Drueke T: A new approach to studying inhibitors of calcium oxalate crystal growth. Urol Res. 1993 Mar;21(2):101-8. Pubmed: 8389069
  • Hoffmann GF, Meier-Augenstein W, Stockler S, Surtees R, Rating D, Nyhan WL: Physiology and pathophysiology of organic acids in cerebrospinal fluid. J Inherit Metab Dis. 1993;16(4):648-69. Pubmed: 8412012
  • Kanehisa, M., Goto, S., Sato, Y., Furumichi, M., Tanabe, M. (2012). "KEGG for integration and interpretation of large-scale molecular data sets." Nucleic Acids Res 40:D109-D114. Pubmed: 22080510
  • Kavanagh JP: Isocitric and citric acid in human prostatic and seminal fluid: implications for prostatic metabolism and secretion. Prostate. 1994;24(3):139-42. Pubmed: 8115279
  • Keseler, I. M., Collado-Vides, J., Santos-Zavaleta, A., Peralta-Gil, M., Gama-Castro, S., Muniz-Rascado, L., Bonavides-Martinez, C., Paley, S., Krummenacker, M., Altman, T., Kaipa, P., Spaulding, A., Pacheco, J., Latendresse, M., Fulcher, C., Sarker, M., Shearer, A. G., Mackie, A., Paulsen, I., Gunsalus, R. P., Karp, P. D. (2011). "EcoCyc: a comprehensive database of Escherichia coli biology." Nucleic Acids Res 39:D583-D590. Pubmed: 21097882
  • Mikosha AS, Monissarenko VP, Bychkovskaia LA: [Properties of adrenocortical isocitrate dehydrogenase] Vopr Med Khim. 1981 Nov-Dec;27(6):736-9. Pubmed: 7336646
  • Stromme JH, Borud O, Moe PJ: Fatal lactic acidosis in a newborn attributable to a congenital defect of pyruvate dehydrogenase. Pediatr Res. 1976 Jan;10(1):62-6. Pubmed: 813176
  • Sutor DJ, Percival JM, Doonan S: Isolation and identification of some urinary inhibitors of calcium phosphate formation. Clin Chim Acta. 1978 Oct 16;89(2):273-8. Pubmed: 213213
  • Sutor DJ, Percival JM, Doonan S: Urinary inhibitor of the formation of calcium oxalate. Br J Urol. 1979 Aug;51(4):253-5. Pubmed: 223711
  • Sutor DJ, Percival JM: The estimation of D-isocitric acid in urine using isocitrate dehydrogenase. Clin Chim Acta. 1978 Jun;86(2):223-5. Pubmed: 657545
  • van der Werf, M. J., Overkamp, K. M., Muilwijk, B., Coulier, L., Hankemeier, T. (2007). "Microbial metabolomics: toward a platform with full metabolome coverage." Anal Biochem 370:17-25. Pubmed: 17765195
  • Vijayendran, C., Barsch, A., Friehs, K., Niehaus, K., Becker, A., Flaschel, E. (2008). "Perceiving molecular evolution processes in Escherichia coli by comprehensive metabolite and gene expression profiling." Genome Biol 9:R72. Pubmed: 18402659
  • Winder, C. L., Dunn, W. B., Schuler, S., Broadhurst, D., Jarvis, R., Stephens, G. M., Goodacre, R. (2008). "Global metabolic profiling of Escherichia coli cultures: an evaluation of methods for quenching and extraction of intracellular metabolites." Anal Chem 80:2939-2948. Pubmed: 18331064
  • Zupke C, Sinskey AJ, Stephanopoulos G: Intracellular flux analysis applied to the effect of dissolved oxygen on hybridomas. Appl Microbiol Biotechnol. 1995 Dec;44(1-2):27-36. Pubmed: 8579834
Synthesis Reference:Finogenova, T. V.; Kamzolova, S. V.; Dedyukhina, E. G.; Shishkanova, N. V.; Il'chenko, A. P.; Morgunov, I. G.; Chernyavskaya, O. G.; Sokolov, A. P. Biosynthesis of citric and isocitric acids from ethanol by mutant Yarrowia lipolytica N 1 under continuous
Material Safety Data Sheet (MSDS)Download (PDF)
External Links:
ResourceLink
CHEBI ID16087
HMDB IDHMDB00193
Pubchem Compound ID1198
Kegg IDC00311
ChemSpider ID1161
WikipediaIsocitric acid
BioCyc IDTHREO-DS-ISO-CITRATE
EcoCyc IDTHREO-DS-ISO-CITRATE

Enzymes

General function:
Involved in magnesium ion binding
Specific function:
Isocitrate + NADP(+) = 2-oxoglutarate + CO(2) + NADPH
Gene Name:
icd
Uniprot ID:
P08200
Molecular weight:
45756
Reactions
Isocitrate + NADP(+) = 2-oxoglutarate + CO(2) + NADPH.
General function:
Involved in isocitrate lyase activity
Specific function:
Catalyzes the formation of succinate and glyoxylate from isocitrate, a key step of the glyoxylate cycle. May be involved in the assimilation of one-carbon compounds via the isocitrate lyase- positive serine pathway
Gene Name:
aceA
Uniprot ID:
P0A9G6
Molecular weight:
47521
Reactions
Isocitrate = succinate + glyoxylate.
General function:
Involved in metabolic process
Specific function:
May have an iron-responsive regulatory function
Gene Name:
acnA
Uniprot ID:
P25516
Molecular weight:
97676
Reactions
Citrate = isocitrate.
General function:
Involved in metabolic process
Specific function:
Citrate = isocitrate
Gene Name:
acnB
Uniprot ID:
P36683
Molecular weight:
93497
Reactions
Citrate = isocitrate.
(2S,3R)-3-hydroxybutane-1,2,3-tricarboxylate = (Z)-but-2-ene-1,2,3-tricarboxylate + H(2)O.
General function:
Involved in metabolic process
Specific function:
Unknown Function
Gene Name:
ybhJ
Uniprot ID:
P75764
Molecular weight:
81504