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Human Metabolome Database Version 3.5

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Showing metabocard for Isocitric acid (HMDB00193)

Record Information
Version 3.5
Creation Date 2005-11-16 08:48:42 -0700
Update Date 2013-02-08 17:08:03 -0700
HMDB ID HMDB00193
Secondary Accession Numbers None
Metabolite Identification
Common Name Isocitric acid
Description The 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
Download: MOL | SDF | SMILES | InChI
Display: 2D Structure | 3D Structure
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 Formula C6H8O7
Average Molecular Weight 192.1235
Monoisotopic Molecular Weight 192.02700261
IUPAC Name 1-hydroxypropane-1,2,3-tricarboxylic acid
Traditional IUPAC Name isocitric acid
CAS Registry Number 320-77-4
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 Key ODBLHEXUDAPZAU-UHFFFAOYSA-N
Chemical Taxonomy
Kingdom Organic Compounds
Super Class Organic Acids and Derivatives
Class Carboxylic Acids and Derivatives
Sub Class Tricarboxylic 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 Parent Tricarboxylic Acids and Derivatives
Ontology
Status Detected and Quantified
Origin
  • Endogenous
Biofunction
  • Component of Glutathione metabolism
Application Not Available
Cellular locations
  • Cytoplasm
  • Mitochondria
  • Peroxisome
Physical Properties
State Solid
Experimental Properties
Property Value Reference
Melting Point 162 - 165 °C Not Available
Boiling Point Not Available Not Available
Water Solubility 466 mg/mL Not Available
LogP Not Available Not Available
Predicted Properties
Property Value Source
Water Solubility 52.5 g/L ALOGPS
LogP -0.35 ALOGPS
LogP -1.4 ChemAxon
LogS -0.56 ALOGPS
pKa (strongest acidic) 3.07 ChemAxon
pKa (strongest basic) -4 ChemAxon
Hydrogen Acceptor Count 7 ChemAxon
Hydrogen Donor Count 4 ChemAxon
Polar Surface Area 132.13 A2 ChemAxon
Rotatable Bond Count 5 ChemAxon
Refractivity 35.72 ChemAxon
Polarizability 15.55 ChemAxon
Formal Charge 0 ChemAxon
Physiological Charge -3 ChemAxon
Spectra
Gas-MS Spectrum
1H NMR Spectrum
MS/MS Spectrum Quattro_QQQ 10
MS/MS Spectrum Quattro_QQQ 25
MS/MS Spectrum Quattro_QQQ 40
MS/MS Spectrum LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic)
MS/MS Spectrum LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic)
MS/MS Spectrum LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic)
MS/MS Spectrum LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic)
MS/MS Spectrum LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic)
MS/MS Spectrum LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic)
MS/MS Spectrum LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic)
MS/MS Spectrum LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic)
MS/MS Spectrum LC-ESI-QQ (API3000, Applied Biosystems) 10
MS/MS Spectrum LC-ESI-QQ (API3000, Applied Biosystems) 20
MS/MS Spectrum LC-ESI-QQ (API3000, Applied Biosystems) 30
MS/MS Spectrum LC-ESI-QQ (API3000, Applied Biosystems) 40
[1H,13C] 2D NMR Spectrum
Biological Properties
Cellular Locations
  • Cytoplasm
  • Mitochondria
  • Peroxisome
Biofluid Locations
  • Blood
  • Cellular Cytoplasm
  • Cerebrospinal Fluid (CSF)
  • Semen
  • Urine
Tissue Location
  • Adrenal Gland
Pathways
Name SMPDB Link KEGG Link
Citric Acid Cycle SMP00057 map00020 Link_out
Normal Concentrations
Biofluid Status Value Age Sex Condition Comments
Blood Detected and Quantified
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6.0 (0.0-10.0) uM Adult (>18 years old) Both Normal Not Available
Cellular Cytoplasm Detected and Quantified
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38 (23-53) uM Adult (>18 years old) Both Normal Not Available
Cerebrospinal Fluid (CSF) Detected and Quantified
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10.0 +/- 9.0 uM Adult (>18 years old) Not Specified Normal Not Available
Semen Detected and Quantified
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400 - 1500 uM Adult (>18 years old) Both Normal Not Available
Urine Detected and Quantified
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56.8(19.4-119.1) umol/mmol creatinine Adult (>18 years old) Both Normal by GC-MS
Urine Detected and not Quantified
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Not Applicable Adult (>18 years old) Both Normal Urine compound detected by GC-MS
Urine Detected and not Quantified
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Not Applicable Adult (>18 years old) Both Normal Not Available
Urine Detected and Quantified
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94.3 (29.8-154.4) umol/mmol creatinine Newborn (0-30 days old) Both Normal Not Available
Urine Detected and Quantified
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120.1 (101.1-265.3) umol/mmol creatinine Infant (0-1 year old) Both Normal Not Available
Urine Detected and Quantified
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53.7 (31.9-83.1) umol/mmol creatinine Children (1-13 year old) Both Normal 2-6 years
Urine Detected and Quantified
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45.0 (18.0-69.9) umol/mmol creatinine Children (1-13 year old) Both Normal 6-10 years
Urine Detected and Quantified
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38.9 (16.0-118.0) umol/mmol creatinine Adult (>18 years old) Both Normal Not Available
Urine Detected and Quantified
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19.0 (5.0-34.0) umol/mmol creatinine Newborn (0-30 days old) Both Normal Not Available
Urine Detected and Quantified
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7.7 (5.0-12.0) umol/mmol creatinine Adult (>18 years old) Both Normal Not Available
Urine Detected and Quantified
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24.52 umol/mmol creatinine Adult (>18 years old) Male Normal Based on one measurement
Urine Detected and Quantified
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58 (36-84) umol/mmol creatinine Adult (>18 years old) Both Normal Not Available
Urine Detected and Quantified
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46.9 (20.4-89.2) umol/mmol creatinine Adult (>18 years old) Both Normal urine by NMR
Urine Detected and Quantified
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19.08 (5.26 - 42.76) umol/mmol creatinine Adult (>18 years old) Both Normal Not Available
Urine Detected and Quantified
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22.0 +/- 13.8 umol/mmol creatinine Adult (>18 years old) Both Normal Not Available
Urine Detected and Quantified
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14.7 umol/mmol creatinine Adult (>18 years old) Both Normal Not Available
Abnormal Concentrations
Biofluid Status Value Age Sex Condition Comments
Cellular Cytoplasm Detected and Quantified
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15 (14.8-15.2) uM Adult (>18 years old) Both Anoxia Not Available
Urine Detected and not Quantified
Article_icon
Not Applicable Adult (>18 years old) Both Autosomal dominant polycystic kidney disease Not Available
Associated Disorders and Diseases
Disease References
Anoxia
  • 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 Link_out
    Associated OMIM IDs None
    DrugBank ID Not Available
    Phenol Explorer Compound ID Not Available
    Phenol Explorer Metabolite ID Not Available
    FoodDB ID FDB003281
    KNApSAcK ID Not Available
    Chemspider ID 1161 Link_out
    KEGG Compound ID C00311 Link_out
    BioCyc ID threo-d(s)-iso-citrate Link_out
    BiGG ID 34579 Link_out
    Wikipedia Link Isocitric acid Link_out
    NuGOwiki Link HMDB00193 Link_out
    Metagene Link HMDB00193 Link_out
    METLIN ID 3328 Link_out
    PubChem Compound 1198 Link_out
    PDB ID 1B0J Link_out
    ChEBI ID 30887 Link_out
    References
    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 cultivation. Applied Microbiology and Biotechnology (2002), 59(4-5), 493-500.
    Material Safety Data Sheet (MSDS) Download (PDF)
    General References
    1. 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 Link_out
    2. 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 Link_out
    3. 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 Link_out
    4. 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 Link_out
    5. 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 Link_out
    6. 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 Link_out
    7. 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 Link_out
    8. 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 Link_out
    9. Mikosha AS, Monissarenko VP, Bychkovskaia LA: [Properties of adrenocortical isocitrate dehydrogenase] Vopr Med Khim. 1981 Nov-Dec;27(6):736-9. Pubmed: 7336646 Link_out
    10. 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 Link_out
    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 Link_out
    Enzymes
    Name: Aconitate hydratase, mitochondrial
    Reactions:
    • (1) citrate = isocitrate [RN:R01324]
    • (2) (1a) citrate = cis-aconitate + H2O [RN:R01325]
    • (3) (1b) cis-aconitate + H2O = isocitrate [RN:R01900]
    Gene Name: ACO2
    Uniprot ID: Q99798 Link_out
    Protein Sequence: FASTA
    Gene Sequence: FASTA
    Name: Cytoplasmic aconitate hydratase
    Reactions:
    • (1) citrate = isocitrate [RN:R01324]
    • (2) (1a) citrate = cis-aconitate + H2O [RN:R01325]
    • (3) (1b) cis-aconitate + H2O = isocitrate [RN:R01900]
    Gene Name: ACO1
    Uniprot ID: P21399 Link_out
    Protein Sequence: FASTA
    Gene Sequence: FASTA
    Name: Isocitrate dehydrogenase [NADP], mitochondrial
    Reactions:
    • (1) isocitrate + NADP+ = 2-oxoglutarate + CO2 + NADPH + H+ (overall reaction) [RN:R00267]
    • (2) (1a) isocitrate + NADP+ = oxalosuccinate + NADPH + H+ [RN:R01899]
    • (3) (1b) oxalosuccinate = 2-oxoglutarate + CO2 [RN:R00268]
    Gene Name: IDH2
    Uniprot ID: P48735 Link_out
    Protein Sequence: FASTA
    Gene Sequence: FASTA
    Name: Isocitrate dehydrogenase [NAD] subunit beta, mitochondrial
    Reactions:
    • isocitrate + NAD+ = 2-oxoglutarate + CO2 + NADH [RN:R00709]
    Gene Name: IDH3B
    Uniprot ID: O43837 Link_out
    Protein Sequence: FASTA
    Gene Sequence: FASTA
    Name: Isocitrate dehydrogenase [NADP] cytoplasmic
    Reactions:
    • (1) isocitrate + NADP+ = 2-oxoglutarate + CO2 + NADPH + H+ (overall reaction) [RN:R00267]
    • (2) (1a) isocitrate + NADP+ = oxalosuccinate + NADPH + H+ [RN:R01899]
    • (3) (1b) oxalosuccinate = 2-oxoglutarate + CO2 [RN:R00268]
    Gene Name: IDH1
    Uniprot ID: O75874 Link_out
    Protein Sequence: FASTA
    Gene Sequence: FASTA
    Name: Isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial
    Reactions:
    • isocitrate + NAD+ = 2-oxoglutarate + CO2 + NADH [RN:R00709]
    Gene Name: IDH3A
    Uniprot ID: P50213 Link_out
    Protein Sequence: FASTA
    Gene Sequence: FASTA
    Name: Isocitrate dehydrogenase [NAD] subunit gamma, mitochondrial
    Reactions:
    • isocitrate + NAD+ = 2-oxoglutarate + CO2 + NADH [RN:R00709]
    Gene Name: IDH3G
    Uniprot ID: P51553 Link_out
    Protein Sequence: FASTA
    Gene Sequence: FASTA