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Record Information
Version3.6
Creation Date2005-11-16 15:48:42 UTC
Update Date2014-10-29 21:47:43 UTC
HMDB IDHMDB00193
Secondary Accession NumbersNone
Metabolite Identification
Common NameIsocitric acid
DescriptionThe citrate oxidation to isocitrate is catalyzed by the enzyme aconitase. Human prostatic secretion is remarkably rich in citric acid and low aconitase activity will therefore play a significant role in enabling accumulation of high citrate levels (PubMed ID 8115279).
Structure
Thumb
Synonyms
  1. 1-Hydroxy-1,2,3-propanetricarboxylate
  2. 1-Hydroxy-1,2,3-propanetricarboxylic acid
  3. 1-Hydroxypropane-1,2,3-tricarboxylate
  4. 1-Hydroxypropane-1,2,3-tricarboxylic acid
  5. 1-Hydroxytricarballylate
  6. 1-Hydroxytricarballylic acid
  7. 3-Carboxy-2,3-dideoxy-1-hydroxypropan-1,2,3-tricarboxylate
  8. 3-Carboxy-2,3-dideoxy-1-hydroxypropan-1,2,3-tricarboxylic acid
  9. 3-Carboxy-2,3-dideoxy-Pentarate
  10. 3-Carboxy-2,3-dideoxy-Pentaric acid
  11. D-Isocitrate
  12. I-CIT
  13. Isocitrate
  14. Threo-D(S)-iso-citrate
  15. Threo-Ds-isocitrate
Chemical FormulaC6H8O7
Average Molecular Weight192.1235
Monoisotopic Molecular Weight192.02700261
IUPAC Name1-hydroxypropane-1,2,3-tricarboxylic acid
Traditional Nameisocitric acid
CAS Registry Number320-77-4
SMILES
OC(C(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)
InChI KeyODBLHEXUDAPZAU-UHFFFAOYSA-N
Chemical Taxonomy
KingdomOrganic Compounds
Super ClassOrganic Acids and Derivatives
ClassCarboxylic Acids and Derivatives
Sub ClassTricarboxylic Acids and Derivatives
Other Descriptors
  • Aliphatic Acyclic Compounds
  • Branched Fatty Acids
  • Organic Compounds
  • isocitric acid(ChEBI)
Substituents
  • Alpha Hydroxy Acid
  • Beta Hydroxy Acid
  • Carboxylic Acid
  • Secondary Alcohol
  • Short Chain Hydroxy Acid
  • Succinic Acid
Direct ParentTricarboxylic Acids and Derivatives
Ontology
StatusDetected and Quantified
Origin
  • Endogenous
Biofunction
  • Component of Glutathione metabolism
ApplicationNot Available
Cellular locations
  • Cytoplasm
  • Mitochondria
  • Peroxisome
Physical Properties
StateSolid
Experimental Properties
PropertyValueReference
Melting Point162 - 165 °CNot Available
Boiling PointNot AvailableNot Available
Water Solubility466 mg/mLNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
Water Solubility52.5ALOGPS
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 Å2ChemAxon
Rotatable Bond Count5ChemAxon
Refractivity35.72 m3·mol-1ChemAxon
Polarizability15.55 Å3ChemAxon
Spectra
SpectraGC-MSMS/MSLC-MS1D NMR2D NMR
Biological Properties
Cellular Locations
  • Cytoplasm
  • Mitochondria
  • Peroxisome
Biofluid Locations
  • Blood
  • Cellular Cytoplasm
  • Cerebrospinal Fluid (CSF)
  • Saliva
  • Semen
  • Urine
Tissue Location
  • Adrenal Gland
Pathways
NameSMPDB LinkKEGG Link
Citric Acid CycleSMP00057map00020
Normal Concentrations
BiofluidStatusValueAgeSexConditionReferenceDetails
BloodDetected and Quantified6.0 (0.0-10.0) uMAdult (>18 years old)BothNormal details
Cellular CytoplasmDetected and Quantified38 (23-53) uMAdult (>18 years old)BothNormal details
Cerebrospinal Fluid (CSF)Detected and Quantified10.0 +/- 9.0 uMAdult (>18 years old)Not SpecifiedNormal details
SalivaDetected and Quantified4.17 +/- 1.75 uMAdult (>18 years old)FemaleNormal details
SalivaDetected and Quantified0.988 +/- 0.531 uMAdult (>18 years old)Not Specified
Normal
    • Sugimoto et al. (...
details
SalivaDetected and Quantified0.294 +/- 0.267 uMAdult (>18 years old)Female
Normal
    • Sugimoto et al. (...
details
SalivaDetected but not QuantifiedNot ApplicableAdult (>18 years old)Both
Normal
    • Dame, ZT. et al. ...
details
SalivaDetected and Quantified0.616 +/- 0.351 uMAdult (>18 years old)Female
Normal
    • Sugimoto et al. (...
details
SalivaDetected and Quantified0.616 +/- 0.351 uMAdult (>18 years old)Not Specified
Normal
    • Sugimoto et al. (...
details
SemenDetected and Quantified400 - 1500 uMAdult (>18 years old)BothNormal details
UrineDetected and Quantified56.8(19.4-119.1) umol/mmol creatinineAdult (>18 years old)Both
Normal
details
UrineDetected but not QuantifiedNot ApplicableAdult (>18 years old)Both
Normal
details
UrineDetected but not QuantifiedNot ApplicableAdult (>18 years old)BothNormal details
UrineDetected and Quantified94.3 (29.8-154.4) umol/mmol creatinineNewborn (0-30 days old)BothNormal details
UrineDetected and Quantified120.1 (101.1-265.3) umol/mmol creatinineInfant (0-1 year old)BothNormal details
UrineDetected and Quantified53.7 (31.9-83.1) umol/mmol creatinineChildren (1-13 years old)Both
Normal
details
UrineDetected and Quantified45.0 (18.0-69.9) umol/mmol creatinineChildren (1-13 years old)Both
Normal
details
UrineDetected and Quantified38.9 (16.0-118.0) umol/mmol creatinineAdult (>18 years old)BothNormal details
UrineDetected and Quantified19.0 (5.0-34.0) umol/mmol creatinineNewborn (0-30 days old)BothNormal
    • Geigy Scientific ...
details
UrineDetected and Quantified7.7 (5.0-12.0) umol/mmol creatinineAdult (>18 years old)BothNormal
    • Geigy Scientific ...
details
UrineDetected and Quantified24.52 umol/mmol creatinineAdult (>18 years old)Male
Normal
    • Shaykhutdinov RA,...
details
UrineDetected and Quantified58 (36-84) umol/mmol creatinineAdult (>18 years old)BothNormal details
UrineDetected and Quantified46.9 (20.4-89.2) umol/mmol creatinineAdult (>18 years old)Both
Normal
details
UrineDetected and Quantified19.08 (5.26 - 42.76) umol/mmol creatinineAdult (>18 years old)BothNormal details
UrineDetected and Quantified22.0 +/- 13.8 umol/mmol creatinineAdult (>18 years old)BothNormal details
UrineDetected and Quantified14.7 umol/mmol creatinineAdult (>18 years old)BothNormal details
Abnormal Concentrations
BiofluidStatusValueAgeSexConditionReferenceDetails
Cellular CytoplasmDetected and Quantified15 (14.8-15.2) uMAdult (>18 years old)BothAnoxia details
SalivaDetected and Quantified3.75 +/- 2.89 uMAdult (>18 years old)MaleAlzheimer's disease details
SalivaDetected and Quantified3.28 +/- 1.43 uMAdult (>18 years old)MaleFrontotemporal lobe dementia details
SalivaDetected and Quantified3.98 +/- 0.15 uMAdult (>18 years old)BothLewy body disease details
UrineDetected but not QuantifiedNot ApplicableAdult (>18 years old)BothAutosomal dominant polycystic kidney disease (ADPKD) details
Associated Disorders and Diseases
Disease References
Anoxia
  1. 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
Associated OMIM IDsNone
DrugBank IDNot Available
DrugBank Metabolite IDNot Available
Phenol Explorer Compound IDNot Available
Phenol Explorer Metabolite IDNot Available
FoodDB IDFDB003281
KNApSAcK IDNot Available
Chemspider ID1161
KEGG Compound IDC00311
BioCyc IDthreo-d(s)-iso-citrate
BiGG ID34579
Wikipedia LinkIsocitric acid
NuGOwiki LinkHMDB00193
Metagene LinkHMDB00193
METLIN ID3328
PubChem Compound1198
PDB ID1B0J
ChEBI ID30887
References
Synthesis ReferenceFinogenova, 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 cultivation. Applied Microbiology and Biotechnology (2002), 59(4-5), 493-500.
Material Safety Data Sheet (MSDS)Download (PDF)
General References
  1. 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
  2. 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
  3. 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
  4. 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
  5. 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
  6. 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
  7. 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
  8. 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
  9. 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
  10. Mikosha AS, Monissarenko VP, Bychkovskaia LA: [Properties of adrenocortical isocitrate dehydrogenase] Vopr Med Khim. 1981 Nov-Dec;27(6):736-9. Pubmed: 7336646
  11. 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

Enzymes

General function:
Involved in metabolic process
Specific function:
Catalyzes the isomerization of citrate to isocitrate via cis-aconitate (By similarity).
Gene Name:
ACO2
Uniprot ID:
Q99798
Molecular weight:
85424.745
Reactions
Citric acid → Isocitric aciddetails
Isocitric acid → cis-Aconitic acid + Waterdetails
General function:
Involved in metabolic process
Specific function:
Iron sensor. Binds a 4Fe-4S cluster and functions as aconitase when cellular iron levels are high. Functions as mRNA binding protein that regulates uptake, sequestration and utilization of iron when cellular iron levels are low. Binds to iron-responsive elements (IRES) in target mRNA species when iron levels are low. Binding of a 4Fe-4S cluster precludes RNA binding. Catalyzes the isomerization of citrate to isocitrate via cis-aconitate (By similarity).
Gene Name:
ACO1
Uniprot ID:
P21399
Molecular weight:
98398.14
Reactions
Citric acid → Isocitric aciddetails
Isocitric acid → cis-Aconitic acid + Waterdetails
General function:
Involved in magnesium ion binding
Specific function:
Plays a role in intermediary metabolism and energy production. It may tightly associate or interact with the pyruvate dehydrogenase complex.
Gene Name:
IDH2
Uniprot ID:
P48735
Molecular weight:
50908.915
Reactions
Isocitric acid + NADP → Oxoglutaric acid + CO(2) + NADPHdetails
Isocitric acid + NADP → Oxoglutaric acid + Carbon dioxide + NADPH + Hydrogen Iondetails
Isocitric acid + NADP → Oxalosuccinic acid + NADPH + Hydrogen Iondetails
General function:
Involved in magnesium ion binding
Specific function:
Not Available
Gene Name:
IDH3B
Uniprot ID:
O43837
Molecular weight:
42183.39
Reactions
Isocitric acid + NAD → Oxoglutaric acid + CO(2) + NADHdetails
Isocitric acid + NAD → Oxoglutaric acid + Carbon dioxide + NADH + Hydrogen Iondetails
General function:
Involved in magnesium ion binding
Specific function:
Not Available
Gene Name:
IDH1
Uniprot ID:
O75874
Molecular weight:
46659.005
Reactions
Isocitric acid + NADP → Oxoglutaric acid + CO(2) + NADPHdetails
Isocitric acid + NADP → Oxoglutaric acid + Carbon dioxide + NADPH + Hydrogen Iondetails
Isocitric acid + NADP → Oxalosuccinic acid + NADPH + Hydrogen Iondetails
General function:
Involved in magnesium ion binding
Specific function:
Not Available
Gene Name:
IDH3A
Uniprot ID:
P50213
Molecular weight:
39591.365
Reactions
Isocitric acid + NAD → Oxoglutaric acid + CO(2) + NADHdetails
Isocitric acid + NAD → Oxoglutaric acid + Carbon dioxide + NADH + Hydrogen Iondetails
General function:
Involved in magnesium ion binding
Specific function:
Not Available
Gene Name:
IDH3G
Uniprot ID:
P51553
Molecular weight:
42793.97
Reactions
Isocitric acid + NAD → Oxoglutaric acid + CO(2) + NADHdetails
Isocitric acid + NAD → Oxoglutaric acid + Carbon dioxide + NADH + Hydrogen Iondetails