Showing metabocard for Isocitric acid (BMDB0000193)

IdentificationTaxonomyPhysical propertiesPathwaysSpectraConcentrationsLinksReferencesenzymes (8) Show 8 proteinsXML
Record Information
Version1.0
Creation Date2016-09-30 22:26:33 UTC
Update Date2020-06-04 20:52:13 UTC
BMDB IDBMDB0000193
Secondary Accession Numbers
  • BMDB00193
Metabolite Identification
Common NameIsocitric acid
DescriptionIsocitric acid, also known as isocitrate or i-cit, belongs to the class of organic compounds known as tricarboxylic acids and derivatives. These are carboxylic acids containing exactly three carboxyl groups. Isocitric acid exists as a solid, possibly soluble (in water), and an extremely weak basic (essentially neutral) compound (based on its pKa) molecule. Isocitric acid exists in all living species, ranging from bacteria to humans.
Structure
Thumb
MOLSDFPDBSMILESInChI
Synonyms
ValueSource
1-Hydroxypropane-1,2,3-tricarboxylic acidChEBI
1-Hydroxytricarballylic acidChEBI
1-Hydroxypropane-1,2,3-tricarboxylateGenerator
1-HydroxytricarballylateGenerator
IsocitrateGenerator
1-Hydroxy-1,2,3-propanetricarboxylateHMDB
1-Hydroxy-1,2,3-propanetricarboxylic acidHMDB
3-Carboxy-2,3-dideoxy-1-hydroxypropan-1,2,3-tricarboxylateHMDB
3-Carboxy-2,3-dideoxy-1-hydroxypropan-1,2,3-tricarboxylic acidHMDB
3-Carboxy-2,3-dideoxy-pentarateHMDB
3-Carboxy-2,3-dideoxy-pentaric acidHMDB
D-IsocitrateHMDB
I-citHMDB
Threo-D(S)-iso-citrateHMDB
Threo-DS-isocitrateHMDB
Isocitric acid, sodium saltHMDB
Isocitric acid, trisodium saltHMDB
Isocitric acid, disodium saltHMDB
Isocitric acid, (11)C-labeledHMDB
Isocitric acid, calcium saltHMDB
Isocitric acid, potassium saltHMDB
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
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
StatusDetected and Quantified
Origin
  • Endogenous
BiofunctionNot Available
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
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
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
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
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, PositiveNot AvailableView in JSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_1_1) - 70eV, PositiveNot AvailableView in JSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_1_2) - 70eV, PositiveNot AvailableView in JSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_1_3) - 70eV, PositiveNot AvailableView in JSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_1_4) - 70eV, PositiveNot AvailableView in JSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_2_1) - 70eV, PositiveNot AvailableView in JSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_2_2) - 70eV, PositiveNot AvailableView in JSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_2_3) - 70eV, PositiveNot AvailableView in JSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_2_4) - 70eV, PositiveNot AvailableView in JSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_2_5) - 70eV, PositiveNot AvailableView in JSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_2_6) - 70eV, PositiveNot AvailableView in JSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_3_1) - 70eV, PositiveNot AvailableView in JSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_3_2) - 70eV, PositiveNot AvailableView in JSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_3_3) - 70eV, PositiveNot AvailableView in JSpectraViewer
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
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , negativesplash10-0079-9000000000-3c33cefeb87f85efd5deView in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , negativesplash10-059m-9000000000-34775db8bbc008018633View in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-ITFT , negativesplash10-03di-0900000000-66d03405eeb126c6ad9dView in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-ITFT , negativesplash10-00di-0900000000-cdad17a11f419421c787View in MoNA
LC-MS/MSLC-MS/MS Spectrum - , negativesplash10-03k9-2900000000-e5336d859bf90bcd904cView in MoNA
LC-MS/MSLC-MS/MS Spectrum - 10V, Negativesplash10-03k9-2900000000-8ef1bf8afd67194ddf65View in MoNA
LC-MS/MSLC-MS/MS Spectrum - 40V, Negativesplash10-059f-9000000000-37227e36af9ba4db4a7eView in MoNA
LC-MS/MSLC-MS/MS Spectrum - 20V, Negativesplash10-022i-9500000000-cb0234d7a355d54f1755View in MoNA
LC-MS/MSLC-MS/MS Spectrum - 10V, Negativesplash10-03k9-3900000000-1b8cb16b24c65e87915bView in MoNA
LC-MS/MSLC-MS/MS Spectrum - 20V, Negativesplash10-03ki-9500000000-d264dd60719df8b72ef3View in MoNA
LC-MS/MSLC-MS/MS Spectrum - 40V, Negativesplash10-00di-9000000000-bf62fc70edcee073c517View in MoNA
LC-MS/MSLC-MS/MS Spectrum - 30V, Negativesplash10-02mi-9200000000-42ca838ca7f08cc3882eView in MoNA
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 10V, Positive (Annotated)splash10-0udi-1900000000-8e1185b0504ea1547715View in MoNA
1D NMR1H NMR Spectrum (1D, 500 MHz, H2O, experimental)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 100 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 1000 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 1000 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 200 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 200 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 300 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 300 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 400 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 500 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 600 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 600 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 700 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 700 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 800 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 800 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 900 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
2D NMR[1H, 13C]-HSQC NMR Spectrum (2D, 600 MHz, H2O, experimental)Not AvailableView in JSpectraViewer
Biological Properties
Cellular Locations
  • Cytoplasm
  • Mitochondria
  • Peroxisome
Biospecimen Locations
  • Adrenal Gland
  • Mammary Gland
  • Milk
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
Adrenal GlandExpected but not QuantifiedNot QuantifiedNot SpecifiedNot SpecifiedNormal
  • Not Applicable
 details
Mammary GlandDetected but not QuantifiedNot QuantifiedNot SpecifiedNot Specified
Normal		 details
Mammary GlandDetected but not QuantifiedNot QuantifiedNot SpecifiedNot Specified
Normal		 details
MilkDetected but not QuantifiedNot QuantifiedNot SpecifiedNot Specified
Normal		 details
MilkDetected and Quantified108.4 uMNot SpecifiedNot Specified
Normal		 details
MilkDetected and Quantified243 uMNot SpecifiedNot Specified
Normal		 details
MilkDetected and Quantified191 uMNot SpecifiedNot Specified
Normal		 details
MilkDetected and Quantified219 uMNot SpecifiedNot Specified
Normal		 details
Abnormal Concentrations
Not Available
HMDB IDHMDB0000193
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB003281
KNApSAcK IDC00001188
Chemspider ID1161
KEGG Compound IDC00311
BioCyc IDIsocitrate
BiGG ID34579
Wikipedia LinkIsocitric_acid
METLIN ID3328
PubChem Compound1198
PDB IDNot Available
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)Not Available
General References
  1. Faulkner A, Pollock HT: Changes in the concentration of metabolites in milk from cows fed on diets supplemented with soyabean oil or fatty acids. J Dairy Res. 1989 May;56(2):179-83. [PubMed:2760296 ]
  2. Hurtaud C, Rulquin H, Verite R: Effects of graded duodenal infusions of glucose on yield and composition of milk from dairy cows. 1. Diets based on corn silage. J Dairy Sci. 1998 Dec;81(12):3239-47. doi: 10.3168/jds.S0022-0302(98)75888-6. [PubMed:9891269 ]
  3. Hurtaud C, Lemosquet S, Rulquin H: Effect of graded duodenal infusions of glucose on yield and composition of milk from dairy cows. 2. Diets based on grass silage. J Dairy Sci. 2000 Dec;83(12):2952-62. doi: 10.3168/jds.S0022-0302(00)75195-2. [PubMed:11132867 ]
  4. Melzer N, Wittenburg D, Hartwig S, Jakubowski S, Kesting U, Willmitzer L, Lisec J, Reinsch N, Repsilber D: Investigating associations between milk metabolite profiles and milk traits of Holstein cows. J Dairy Sci. 2013 Mar;96(3):1521-34. doi: 10.3168/jds.2012-5743. [PubMed:23438684 ]

Enzymes

Enzyme Details
1. Isocitrate dehydrogenase [NADP], mitochondrial
General function:
Energy production and conversion
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:
Q04467
Molecular weight:
50739.0
Enzyme Details
2. Isocitrate dehydrogenase [NAD] subunit gamma, mitochondrial
General function:
Energy production and conversion
Specific function:
Regulatory subunit which plays a role in the allosteric regulation of the enzyme catalyzing the decarboxylation of isocitrate (ICT) into alpha-ketoglutarate. The heterodimer composed of the alpha (IDH3A) and beta (IDH3B) subunits and the heterodimer composed of the alpha (IDH3A) and gamma (IDH3G) subunits, have considerable basal activity but the full activity of the heterotetramer (containing two subunits of IDH3A, one of IDH3B and one of IDH3G) requires the assembly and cooperative function of both heterodimers.
Gene Name:
IDH3G
Uniprot ID:
Q58CP0
Molecular weight:
42863.0
Enzyme Details
3. Isocitrate dehydrogenase [NAD] subunit beta, mitochondrial
General function:
Energy production and conversion
Specific function:
Plays a structural role to facilitate the assembly and ensure the full activity of the enzyme catalyzing the decarboxylation of isocitrate (ICT) into alpha-ketoglutarate. The heterodimer composed of the alpha (IDH3A) and beta (IDH3B) subunits and the heterodimer composed of the alpha (IDH3A) and gamma (IDH3G) subunits, have considerable basal activity but the full activity of the heterotetramer (containing two subunits of IDH3A, one of IDH3B and one of IDH3G) requires the assembly and cooperative function of both heterodimers.
Gene Name:
IDH3B
Uniprot ID:
O77784
Molecular weight:
42497.0
Enzyme Details
4. Isocitrate dehydrogenase [NADP] cytoplasmic
General function:
Energy production and conversion
Specific function:
May act as a corneal epithelial crystallin and may be involved in maintaining corneal epithelial transparency.
Gene Name:
IDH1
Uniprot ID:
Q9XSG3
Molecular weight:
46785.0
Reactions
Isocitric acid + NADP → Oxoglutaric acid + NADPH + Carbon dioxidedetails
Enzyme Details
5. Isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial
General function:
Energy production and conversion
Specific function:
Catalytic subunit of the enzyme which catalyzes the decarboxylation of isocitrate (ICT) into alpha-ketoglutarate. The heterodimer composed of the alpha (IDH3A) and beta (IDH3B) subunits and the heterodimer composed of the alpha (IDH3A) and gamma (IDH3G) subunits, have considerable basal activity but the full activity of the heterotetramer (containing two subunits of IDH3A, one of IDH3B and one of IDH3G) requires the assembly and cooperative function of both heterodimers.
Gene Name:
IDH3A
Uniprot ID:
P41563
Molecular weight:
39668.0
Enzyme Details
6. Cytoplasmic aconitate hydratase
General function:
Energy production and conversion
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.
Gene Name:
ACO1
Uniprot ID:
Q0VCU1
Molecular weight:
98204.0
Reactions
Citric acid → Isocitric aciddetails
Enzyme Details
7. Aconitate hydratase, mitochondrial
General function:
Energy production and conversion
Specific function:
Catalyzes the isomerization of citrate to isocitrate via cis-aconitate.
Gene Name:
ACO2
Uniprot ID:
P20004
Molecular weight:
85359.0
Reactions
cis-Aconitic acid + Water → Isocitric aciddetails
Citric acid → Isocitric aciddetails
Enzyme Details
8. Mitochondrial 2-oxoglutarate/malate carrier protein
General function:
Involved in binding
Specific function:
Catalyzes the transport of 2-oxoglutarate across the inner mitochondrial membrane in an electroneutral exchange for malate or other dicarboxylic acids, and plays an important role in several metabolic processes, including the malate-aspartate shuttle, the oxoglutarate/isocitrate shuttle, in gluconeogenesis from lactate, and in nitrogen metabolism. Maintains mitochondrial fusion and fission events, and the organization and morphology of cristae. Involved in the regulation of apoptosis.
Gene Name:
SLC25A11
Uniprot ID:
P22292
Molecular weight:
34172.0