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Identification Taxonomy Ontology Physical properties Spectra Biological properties Concentrations Links References enzymes (7) Show 7 proteins XML

enzymes (7) Show 7 proteins

Record Information

Version

5.0

Status

Detected and Quantified

Creation Date

2005-11-16 15:48:42 UTC

Update Date

2021-09-14 15:37:54 UTC

HMDB ID

HMDB0000193

Secondary Accession Numbers

HMDB00193

Metabolite Identification

Common Name

Isocitric acid

Description

Isocitric acid, also known as isocitrate belongs to the class of organic compounds known as tricarboxylic acids and derivatives. These are carboxylic acids containing exactly three carboxyl groups. Isocitric acid is a TCA (tricarboxylic acid) cycle intermediate. It is a structural isomer of citric acid and is formed from citrate with the help of the enzyme aconitase. More specifically, Isocitric acid is synthesized from citric acid via the intermediate cis-aconitic acid by the enzyme aconitase (aconitate hydratase). Isocitrate is acted upon by isocitrate dehydrogenase (IDH) to form alpha-ketoglutarate. This is a two-step process, which involves oxidation of isocitrate to oxalosuccinate (a ketone), followed by the decarboxylation of the carboxyl group beta to the ketone, forming alpha-ketoglutarate. In humans, IDH exists in three isoforms: IDH3 catalyzes the third step of the citric acid cycle while converting NAD+ to NADH in the mitochondria. The isoforms IDH1 and IDH2 catalyze the same reaction outside the context of the citric acid cycle and use NADP+ as a cofactor instead of NAD+. They localize to the cytosol as well as the mitochondrion and peroxisome. Isocitric acid exists in all living species, ranging from bacteria to plants to humans. Isocitric acid is a minor organic acid found in most fruit juices, especially in blackberries, youngberries, and boyberries, and in vegetables, especially in carrots. The determination of D-isocitric acid has become of importance in the analysis of fruit juices for the detection of illegal additives (adulteration). Since the quantities of citric and isocitric acids are correlated in fruit juices, a high ratio of citric to isocitric acid can indicate the addition of citric acid as an alduterant. In authentic orange juice, for example, the ratio of citric acid to D-isocitric acid is usually less than 130. Isocitric acid is mostly used in the food industry (food additive) as a food acidulant.

Structure

MOL 3D MOL SDF 3D SDF PDB 3D PDB SMILES InChI

HEADER    PROTEIN                                 27-MAY-19   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   27-MAY-19         0                                  
HETATM    1  C   UNK     0       8.621   3.437   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       7.287   2.667   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       5.954   3.437   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       4.620   2.667   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0       3.286   3.437   0.000  0.00  0.00           O+0
HETATM    6  O   UNK     0       4.620   1.127   0.000  0.00  0.00           O+0
HETATM    7  O   UNK     0       5.954   4.977   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0       7.287   1.127   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0       5.954   0.357   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0       8.621   0.357   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0       9.955   2.667   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0      11.288   3.437   0.000  0.00  0.00           O+0
HETATM   13  O   UNK     0       9.955   1.127   0.000  0.00  0.00           O+0
CONECT    1    2   11                                                       
CONECT    2    1    3    8                                                  
CONECT    3    2    4    7                                                  
CONECT    4    3    5    6                                                  
CONECT    5    4                                                            
CONECT    6    4                                                            
CONECT    7    3                                                            
CONECT    8    2    9   10                                                  
CONECT    9    8                                                            
CONECT   10    8                                                            
CONECT   11    1   12   13                                                  
CONECT   12   11                                                            
CONECT   13   11                                                            
MASTER        0    0    0    0    0    0    0    0   13    0   24    0
END

View in JSmol View Stereo Labels

Synonyms

Value	Source
1-Hydroxypropane-1,2,3-tricarboxylic acid	ChEBI
1-Hydroxytricarballylic acid	ChEBI
1-Hydroxypropane-1,2,3-tricarboxylate	Generator
1-Hydroxytricarballylate	Generator
Isocitrate	Generator
1-Hydroxy-1,2,3-propanetricarboxylate	HMDB
1-Hydroxy-1,2,3-propanetricarboxylic acid	HMDB
3-Carboxy-2,3-dideoxy-1-hydroxypropan-1,2,3-tricarboxylate	HMDB
3-Carboxy-2,3-dideoxy-1-hydroxypropan-1,2,3-tricarboxylic acid	HMDB
3-Carboxy-2,3-dideoxy-pentarate	HMDB
3-Carboxy-2,3-dideoxy-pentaric acid	HMDB
D-Isocitrate	HMDB
I-cit	HMDB
Threo-D(S)-iso-citrate	HMDB
Threo-DS-isocitrate	HMDB
Isocitric acid, sodium salt	HMDB
Isocitric acid, trisodium salt	HMDB
Isocitric acid, disodium salt	HMDB
Isocitric acid, (11)C-labeled	HMDB
Isocitric acid, calcium salt	HMDB
Isocitric acid, potassium salt	HMDB

Chemical Formula

C₆H₈O₇

Average Molecular Weight

192.1235

Monoisotopic Molecular Weight

192.02700261

IUPAC Name

1-hydroxypropane-1,2,3-tricarboxylic acid

Traditional 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

Description

Belongs to the class of organic compounds known as tricarboxylic acids and derivatives. These are carboxylic acids containing exactly three carboxyl groups.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Carboxylic acids and derivatives

Sub Class

Tricarboxylic acids and derivatives

Direct Parent

Tricarboxylic 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 Framework

Aliphatic acyclic compounds

External Descriptors

tricarboxylic acid (CHEBI:30887 )

Ontology

Physiological effect

Adverse health effect

Digestive system disorder

Gastrointestinal disorder

Upper GI Disorder

Eosinophilic esophagitis

Genetic disorder

Inborn errors of metabolism

Organic acidemia

Fumarase deficiency

2-ketoglutarate dehydrogenase complex deficiency

Adrenal gland

Excreta

Cellular substructure

Macromolecular complex

Organelle

Peroxisome

Cytoplasm

Ingestion

Process

Naturally occurring process

Biological process

Biochemical pathway

Metabolic pathway

Citric acid cycle

Cellular process

Warburg effect

Physical Properties

State

Solid

Experimental Molecular 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

Experimental Spectral Properties

Experimental Collision Cross Sections

Predictor	Adduct Type	Data Source	CCS Value (Å²)	Reference
AllCCS	[M-H]-	Not Available	127.6	http://allccs.zhulab.cn/database/detail?ID=AllCCS00000008

Predicted Molecular Properties

Property	Value	Source
Water Solubility	52.5 g/L	ALOGPS
logP	10^(-0.35) g/L	ALOGPS
logP	10^(-1.4) g/L	ChemAxon
logS	10^(-0.56) g/L	ALOGPS
pKa (Strongest Acidic)	3.07	ChemAxon
pKa (Strongest Basic)	-4	ChemAxon
Physiological Charge	-3	ChemAxon
Hydrogen Acceptor Count	7	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	132.13 Å²	ChemAxon
Rotatable Bond Count	5	ChemAxon
Refractivity	35.72 m³·mol⁻¹	ChemAxon
Polarizability	15.55 Å³	ChemAxon
Number of Rings	0	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Predicted Spectral Properties

Predicted Collision Cross Sections

Predictor	Adduct Type	CCS Value (Å²)	Reference
DarkChem	[M+H]+	142.236	31661259
DarkChem	[M-H]-	136.977	31661259
AllCCS	[M+H]+	141.804	32859911
AllCCS	[M-H]-	132.738	32859911

Predicted Kovats Retention Indices

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
Isocitric acid,1TMS,#1	C[Si](C)(C)OC(C(=O)O)C(CC(=O)O)C(=O)O	1727.0	Semi standard non polar	https://arxiv.org/abs/1905.12712
Isocitric acid,1TMS,#2	C[Si](C)(C)OC(=O)CC(C(=O)O)C(O)C(=O)O	1715.6	Semi standard non polar	https://arxiv.org/abs/1905.12712
Isocitric acid,1TMS,#3	C[Si](C)(C)OC(=O)C(CC(=O)O)C(O)C(=O)O	1720.3	Semi standard non polar	https://arxiv.org/abs/1905.12712
Isocitric acid,1TMS,#4	C[Si](C)(C)OC(=O)C(O)C(CC(=O)O)C(=O)O	1702.5	Semi standard non polar	https://arxiv.org/abs/1905.12712
Isocitric acid,2TMS,#1	C[Si](C)(C)OC(=O)C(O[Si](C)(C)C)C(CC(=O)O)C(=O)O	1763.5	Semi standard non polar	https://arxiv.org/abs/1905.12712
Isocitric acid,2TMS,#2	C[Si](C)(C)OC(=O)CC(C(=O)O)C(O[Si](C)(C)C)C(=O)O	1759.1	Semi standard non polar	https://arxiv.org/abs/1905.12712
Isocitric acid,2TMS,#3	C[Si](C)(C)OC(=O)C(CC(=O)O)C(O[Si](C)(C)C)C(=O)O	1779.8	Semi standard non polar	https://arxiv.org/abs/1905.12712
Isocitric acid,2TMS,#4	C[Si](C)(C)OC(=O)CC(C(=O)O[Si](C)(C)C)C(O)C(=O)O	1755.5	Semi standard non polar	https://arxiv.org/abs/1905.12712
Isocitric acid,2TMS,#5	C[Si](C)(C)OC(=O)CC(C(=O)O)C(O)C(=O)O[Si](C)(C)C	1737.8	Semi standard non polar	https://arxiv.org/abs/1905.12712
Isocitric acid,2TMS,#6	C[Si](C)(C)OC(=O)C(O)C(CC(=O)O)C(=O)O[Si](C)(C)C	1754.5	Semi standard non polar	https://arxiv.org/abs/1905.12712
Isocitric acid,3TMS,#1	C[Si](C)(C)OC(=O)CC(C(=O)O)C(O[Si](C)(C)C)C(=O)O[Si](C)(C)C	1791.9	Semi standard non polar	https://arxiv.org/abs/1905.12712
Isocitric acid,3TMS,#2	C[Si](C)(C)OC(=O)C(CC(=O)O)C(O[Si](C)(C)C)C(=O)O[Si](C)(C)C	1794.3	Semi standard non polar	https://arxiv.org/abs/1905.12712
Isocitric acid,3TMS,#3	C[Si](C)(C)OC(=O)CC(C(=O)O[Si](C)(C)C)C(O[Si](C)(C)C)C(=O)O	1795.8	Semi standard non polar	https://arxiv.org/abs/1905.12712
Isocitric acid,3TMS,#4	C[Si](C)(C)OC(=O)CC(C(=O)O[Si](C)(C)C)C(O)C(=O)O[Si](C)(C)C	1776.9	Semi standard non polar	https://arxiv.org/abs/1905.12712
Isocitric acid,4TMS,#1	C[Si](C)(C)OC(=O)CC(C(=O)O[Si](C)(C)C)C(O[Si](C)(C)C)C(=O)O[Si](C)(C)C	1864.1	Semi standard non polar	https://arxiv.org/abs/1905.12712
Isocitric acid,1TBDMS,#1	CC(C)(C)[Si](C)(C)OC(C(=O)O)C(CC(=O)O)C(=O)O	1978.9	Semi standard non polar	https://arxiv.org/abs/1905.12712
Isocitric acid,1TBDMS,#2	CC(C)(C)[Si](C)(C)OC(=O)CC(C(=O)O)C(O)C(=O)O	1971.6	Semi standard non polar	https://arxiv.org/abs/1905.12712
Isocitric acid,1TBDMS,#3	CC(C)(C)[Si](C)(C)OC(=O)C(CC(=O)O)C(O)C(=O)O	1972.5	Semi standard non polar	https://arxiv.org/abs/1905.12712
Isocitric acid,1TBDMS,#4	CC(C)(C)[Si](C)(C)OC(=O)C(O)C(CC(=O)O)C(=O)O	1960.3	Semi standard non polar	https://arxiv.org/abs/1905.12712
Isocitric acid,2TBDMS,#1	CC(C)(C)[Si](C)(C)OC(=O)C(O[Si](C)(C)C(C)(C)C)C(CC(=O)O)C(=O)O	2198.1	Semi standard non polar	https://arxiv.org/abs/1905.12712
Isocitric acid,2TBDMS,#2	CC(C)(C)[Si](C)(C)OC(=O)CC(C(=O)O)C(O[Si](C)(C)C(C)(C)C)C(=O)O	2193.1	Semi standard non polar	https://arxiv.org/abs/1905.12712
Isocitric acid,2TBDMS,#3	CC(C)(C)[Si](C)(C)OC(=O)C(CC(=O)O)C(O[Si](C)(C)C(C)(C)C)C(=O)O	2210.3	Semi standard non polar	https://arxiv.org/abs/1905.12712
Isocitric acid,2TBDMS,#4	CC(C)(C)[Si](C)(C)OC(=O)CC(C(=O)O[Si](C)(C)C(C)(C)C)C(O)C(=O)O	2216.3	Semi standard non polar	https://arxiv.org/abs/1905.12712
Isocitric acid,2TBDMS,#5	CC(C)(C)[Si](C)(C)OC(=O)CC(C(=O)O)C(O)C(=O)O[Si](C)(C)C(C)(C)C	2202.8	Semi standard non polar	https://arxiv.org/abs/1905.12712
Isocitric acid,2TBDMS,#6	CC(C)(C)[Si](C)(C)OC(=O)C(O)C(CC(=O)O)C(=O)O[Si](C)(C)C(C)(C)C	2207.8	Semi standard non polar	https://arxiv.org/abs/1905.12712
Isocitric acid,3TBDMS,#1	CC(C)(C)[Si](C)(C)OC(=O)CC(C(=O)O)C(O[Si](C)(C)C(C)(C)C)C(=O)O[Si](C)(C)C(C)(C)C	2433.8	Semi standard non polar	https://arxiv.org/abs/1905.12712
Isocitric acid,3TBDMS,#2	CC(C)(C)[Si](C)(C)OC(=O)C(CC(=O)O)C(O[Si](C)(C)C(C)(C)C)C(=O)O[Si](C)(C)C(C)(C)C	2449.2	Semi standard non polar	https://arxiv.org/abs/1905.12712
Isocitric acid,3TBDMS,#3	CC(C)(C)[Si](C)(C)OC(=O)CC(C(=O)O[Si](C)(C)C(C)(C)C)C(O[Si](C)(C)C(C)(C)C)C(=O)O	2451.0	Semi standard non polar	https://arxiv.org/abs/1905.12712
Isocitric acid,3TBDMS,#4	CC(C)(C)[Si](C)(C)OC(=O)CC(C(=O)O[Si](C)(C)C(C)(C)C)C(O)C(=O)O[Si](C)(C)C(C)(C)C	2434.5	Semi standard non polar	https://arxiv.org/abs/1905.12712
Isocitric acid,4TBDMS,#1	CC(C)(C)[Si](C)(C)OC(=O)CC(C(=O)O[Si](C)(C)C(C)(C)C)C(O[Si](C)(C)C(C)(C)C)C(=O)O[Si](C)(C)C(C)(C)C	2625.5	Semi standard non polar	https://arxiv.org/abs/1905.12712

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Experimental GC-MS	GC-MS Spectrum - Isocitric acid GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies) (4 TMS)	splash10-0002-1952000000-7c34751686a6bdb54cab	2014-06-16	HMDB team, MONA, MassBank	View Spectrum
Experimental GC-MS	GC-MS Spectrum - Isocitric acid GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies) (4 TMS)	splash10-0002-0963000000-459b45ff9246b5f55914	2014-06-16	HMDB team, MONA, MassBank	View Spectrum
Experimental GC-MS	GC-MS Spectrum - Isocitric acid GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies) (Non-derivatized)	splash10-0002-0942000000-61204d02a28e43d21607	2014-06-16	HMDB team, MONA, MassBank	View Spectrum
Experimental GC-MS	GC-MS Spectrum - Isocitric acid GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies) (4 TMS)	splash10-00di-9420000000-4e1a59fe735855d52ce2	2014-06-16	HMDB team, MONA, MassBank	View Spectrum
Experimental GC-MS	GC-MS Spectrum - Isocitric acid GC-MS (4 TMS)	splash10-00ea-3793000000-84858fa896697420275f	2014-06-16	HMDB team, MONA, MassBank	View Spectrum
Experimental GC-MS	GC-MS Spectrum - Isocitric acid GC-EI-TOF (Non-derivatized)	splash10-0002-1952000000-7c34751686a6bdb54cab	2017-09-12	HMDB team, MONA, MassBank	View Spectrum
Experimental GC-MS	GC-MS Spectrum - Isocitric acid GC-EI-TOF (Non-derivatized)	splash10-0002-0963000000-459b45ff9246b5f55914	2017-09-12	HMDB team, MONA, MassBank	View Spectrum
Experimental GC-MS	GC-MS Spectrum - Isocitric acid GC-EI-TOF (Non-derivatized)	splash10-00di-9420000000-4e1a59fe735855d52ce2	2017-09-12	HMDB team, MONA, MassBank	View Spectrum
Experimental GC-MS	GC-MS Spectrum - Isocitric acid GC-MS (Non-derivatized)	splash10-00ea-3793000000-84858fa896697420275f	2017-09-12	HMDB team, MONA, MassBank	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Isocitric acid GC-MS (Non-derivatized) - 70eV, Positive	splash10-00ba-7900000000-96194d87d52b155cf1b9	2016-09-22	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Isocitric acid GC-MS (4 TMS) - 70eV, Positive	splash10-02vi-7029500000-2bb65fc897e48cc21750	2017-10-06	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Isocitric acid GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum

MS/MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Experimental LC-MS/MS	LC-MS/MS Spectrum - Isocitric acid Quattro_QQQ 10V, Positive-QTOF (Annotated)	splash10-0udi-1900000000-8e1185b0504ea1547715	2012-07-24	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Isocitric acid Quattro_QQQ 25V, Positive-QTOF (Annotated)	splash10-05fr-7900000000-0855c1ceb168d556b7f2	2012-07-24	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Isocitric acid Quattro_QQQ 40V, Positive-QTOF (Annotated)	splash10-0bu1-9500000000-140b46d0f1dc8fcd9e49	2012-07-24	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Isocitric acid LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Positive-QTOF	splash10-00fu-0940000000-033739944b190c47c6a7	2012-08-31	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Isocitric acid LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Positive-QTOF	splash10-053r-1900000000-89ff897aa220452bfa16	2012-08-31	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Isocitric acid LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Positive-QTOF	splash10-00di-0900000000-36aeb28d857c9039938b	2012-08-31	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Isocitric acid LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Positive-QTOF	splash10-03di-1900000000-53373dc0755caa954310	2012-08-31	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Isocitric acid LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Negative-QTOF	splash10-0006-0901310000-883764bf7b686ca7fd17	2012-08-31	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Isocitric acid LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Negative-QTOF	splash10-03di-0900000000-66d03405eeb126c6ad9d	2012-08-31	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Isocitric acid LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Negative-QTOF	splash10-00di-0900000000-cdad17a11f419421c787	2012-08-31	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Isocitric acid LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Negative-QTOF	splash10-0udi-0009000000-d3440c84a488b3e22212	2012-08-31	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Isocitric acid LC-ESI-QQ (API3000, Applied Biosystems) 10V, Negative-QTOF	splash10-0006-0900000000-3aa263561a7a49df7d3d	2012-08-31	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Isocitric acid LC-ESI-QQ (API3000, Applied Biosystems) 20V, Negative-QTOF	splash10-0006-1900000000-3636f87026e4206a1638	2012-08-31	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Isocitric acid LC-ESI-QQ (API3000, Applied Biosystems) 30V, Negative-QTOF	splash10-01w3-9600000000-ab1a2b9a29528a623d0b	2012-08-31	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Isocitric acid LC-ESI-QQ (API3000, Applied Biosystems) 40V, Negative-QTOF	splash10-0079-9000000000-3c33cefeb87f85efd5de	2012-08-31	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Isocitric acid LC-ESI-QQ (API3000, Applied Biosystems) 50V, Negative-QTOF	splash10-059m-9000000000-34775db8bbc008018633	2012-08-31	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Isocitric acid LC-ESI-QQ , negative-QTOF	splash10-0006-0900000000-3aa263561a7a49df7d3d	2017-09-14	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Isocitric acid LC-ESI-QQ , negative-QTOF	splash10-0006-1900000000-3636f87026e4206a1638	2017-09-14	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Isocitric acid LC-ESI-QQ , negative-QTOF	splash10-01w3-9600000000-ab1a2b9a29528a623d0b	2017-09-14	HMDB team, MONA	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Isocitric acid 10V, Positive-QTOF	splash10-004j-0900000000-a75a4b486df1552d6d93	2016-09-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Isocitric acid 20V, Positive-QTOF	splash10-0gla-4900000000-d04fec4218cafd6195df	2016-09-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Isocitric acid 40V, Positive-QTOF	splash10-0fk9-8900000000-4e5fbbb415df9fbc8f31	2016-09-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Isocitric acid 10V, Negative-QTOF	splash10-00ke-1900000000-c364bae4640e201c366d	2016-09-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Isocitric acid 20V, Negative-QTOF	splash10-0v4j-4900000000-d00f263a75673b7981c7	2016-09-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Isocitric acid 40V, Negative-QTOF	splash10-0pk9-9200000000-156693398229f972d717	2016-09-12	Wishart Lab	View Spectrum

NMR Spectra

Spectrum Type	Description	Deposition Date	Source	View
Predicted 1D NMR	¹³C NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Experimental 2D NMR	[¹H, ¹³C]-HSQC NMR Spectrum (2D, 600 MHz, H₂O, experimental)	2012-12-05	Wishart Lab	View Spectrum

Biological Properties

Cellular Locations

Cytoplasm
Mitochondria
Peroxisome

Biospecimen Locations

Blood
Cellular Cytoplasm
Cerebrospinal Fluid (CSF)
Feces
Saliva
Semen
Urine

Tissue Locations

Adrenal Gland

Pathways

Name	SMPDB/PathBank	KEGG
Citric Acid Cycle
Congenital lactic acidosis		Not Available
Fumarase deficiency		Not Available
Mitochondrial complex II deficiency		Not Available
2-ketoglutarate dehydrogenase complex deficiency		Not Available

Normal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Blood	Detected and Quantified	6.0 (0.0-10.0) uM	Adult (>18 years old)	Both	Normal	8412012	details
Blood	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Both	Normal	32966057	details
Cellular Cytoplasm	Detected and Quantified	38 (23-53) uM	Adult (>18 years old)	Both	Normal	8579834	details
Cerebrospinal Fluid (CSF)	Detected and Quantified	10.0 +/- 9.0 uM	Adult (>18 years old)	Not Specified	Normal	8412012	details
Feces	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Both	Normal	29808030	details
Saliva	Detected and Quantified	4.17 +/- 1.75 uM	Adult (>18 years old)	Female	Normal	23857558	details
Saliva	Detected and Quantified	0.988 +/- 0.531 uM	Adult (>18 years old)	Not Specified	Normal	Sugimoto et al. (...	details
Saliva	Detected and Quantified	0.294 +/- 0.267 uM	Adult (>18 years old)	Female	Normal	Sugimoto et al. (...	details
Saliva	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Both	Normal	Zerihun T. Dame, ...	details
Saliva	Detected and Quantified	0.616 +/- 0.351 uM	Adult (>18 years old)	Female	Normal	Sugimoto et al. (...	details
Saliva	Detected and Quantified	0.616 +/- 0.351 uM	Adult (>18 years old)	Not Specified	Normal	Sugimoto et al. (...	details
Semen	Detected and Quantified	400 - 1500 uM	Adult (>18 years old)	Both	Normal	8115279	details
Urine	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Both	Normal	25733631	details
Urine	Detected and Quantified	52.403 +/- 28.756 umol/mmol creatinine	Children (1 - 13 years old)	Not Specified	Normal	Mordechai, Hien, ...	details
Urine	Detected and Quantified	56.8(19.4-119.1) umol/mmol creatinine	Adult (>18 years old)	Both	Normal	24023812	details
Urine	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Both	Normal	24023812	details
Urine	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Both	Normal	21389975	details
Urine	Detected and Quantified	30-57 umol/mmol creatinine	Adult (>18 years old)	Female	Normal	27012787	details
Urine	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Both	Normal	28157703	details
Urine	Detected and Quantified	94.3 (29.8-154.4) umol/mmol creatinine	Newborn (0-30 days old)	Both	Normal	8087979	details
Urine	Detected and Quantified	120.1 (101.1-265.3) umol/mmol creatinine	Infant (0-1 year old)	Both	Normal	8087979	details
Urine	Detected and Quantified	53.7 (31.9-83.1) umol/mmol creatinine	Children (1-13 years old)	Both	Normal	8087979	details
Urine	Detected and Quantified	45.0 (18.0-69.9) umol/mmol creatinine	Children (1-13 years old)	Both	Normal	8087979	details
Urine	Detected and Quantified	38.9 (16.0-118.0) umol/mmol creatinine	Adult (>18 years old)	Both	Normal	8087979	details
Urine	Detected and Quantified	19.0 (5.0-34.0) umol/mmol creatinine	Newborn (0-30 days old)	Both	Normal	Geigy Scientific ...	details
Urine	Detected and Quantified	7.7 (5.0-12.0) umol/mmol creatinine	Adult (>18 years old)	Both	Normal	Geigy Scientific ...	details
Urine	Detected and Quantified	24.52 umol/mmol creatinine	Adult (>18 years old)	Male	Normal	Shaykhutdinov RA,...	details
Urine	Detected and Quantified	58 (36-84) umol/mmol creatinine	Adult (>18 years old)	Both	Normal	2702744	details
Urine	Detected and Quantified	46.9 (20.4-89.2) umol/mmol creatinine	Adult (>18 years old)	Both	Normal	24023812	details
Urine	Detected and Quantified	19.08 (5.26 - 42.76) umol/mmol creatinine	Adult (>18 years old)	Both	Normal	657545	details
Urine	Detected and Quantified	22.0 +/- 13.8 umol/mmol creatinine	Adult (>18 years old)	Both	Normal	15992788	details
Urine	Detected and Quantified	27-43 umol/mmol creatinine	Adult (>18 years old)	Male	Normal	27012787	details
Urine	Detected and Quantified	14.7 umol/mmol creatinine	Adult (>18 years old)	Both	Normal	21388201	details

Abnormal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Cellular Cytoplasm	Detected and Quantified	15 (14.8-15.2) uM	Adult (>18 years old)	Both	Anoxia	8579834	details
Saliva	Detected and Quantified	3.75 +/- 2.89 uM	Adult (>18 years old)	Male	Alzheimer's disease	23857558	details
Saliva	Detected and Quantified	3.28 +/- 1.43 uM	Adult (>18 years old)	Male	Frontotemporal lobe dementia	23857558	details
Saliva	Detected and Quantified	3.98 +/- 0.15 uM	Adult (>18 years old)	Both	Lewy body disease	23857558	details
Urine	Detected and Quantified	90.008 +/- 97.639 umol/mmol creatinine	Children (1 - 13 years old)	Not Specified	Eosinophilic esophagitis	Mordechai, Hien, ...	details
Urine	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Both	Bladder cancer	28157703	details
Urine	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Both	Autosomal dominant polycystic kidney disease (ADPKD)	21389975	details

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 ]
Alzheimer's disease
Tsuruoka M, Hara J, Hirayama A, Sugimoto M, Soga T, Shankle WR, Tomita M: Capillary electrophoresis-mass spectrometry-based metabolome analysis of serum and saliva from neurodegenerative dementia patients. Electrophoresis. 2013 Oct;34(19):2865-72. doi: 10.1002/elps.201300019. Epub 2013 Sep 6. [PubMed:23857558 ]
Frontotemporal dementia
Tsuruoka M, Hara J, Hirayama A, Sugimoto M, Soga T, Shankle WR, Tomita M: Capillary electrophoresis-mass spectrometry-based metabolome analysis of serum and saliva from neurodegenerative dementia patients. Electrophoresis. 2013 Oct;34(19):2865-72. doi: 10.1002/elps.201300019. Epub 2013 Sep 6. [PubMed:23857558 ]
Lewy body disease
Tsuruoka M, Hara J, Hirayama A, Sugimoto M, Soga T, Shankle WR, Tomita M: Capillary electrophoresis-mass spectrometry-based metabolome analysis of serum and saliva from neurodegenerative dementia patients. Electrophoresis. 2013 Oct;34(19):2865-72. doi: 10.1002/elps.201300019. Epub 2013 Sep 6. [PubMed:23857558 ]
Autosomal dominant polycystic kidney disease
Gronwald W, Klein MS, Zeltner R, Schulze BD, Reinhold SW, Deutschmann M, Immervoll AK, Boger CA, Banas B, Eckardt KU, Oefner PJ: Detection of autosomal dominant polycystic kidney disease by NMR spectroscopic fingerprinting of urine. Kidney Int. 2011 Jun;79(11):1244-53. doi: 10.1038/ki.2011.30. Epub 2011 Mar 9. [PubMed:21389975 ]
Eosinophilic esophagitis
(). Mordechai, Hien, and David S. Wishart. .

Associated OMIM IDs

104300 (Alzheimer's disease)
600274 (Frontotemporal dementia)
601313 (Autosomal dominant polycystic kidney disease)
610247 (Eosinophilic esophagitis)

External Links

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

KNApSAcK ID

Chemspider ID

KEGG Compound ID

BioCyc ID

BiGG ID

Wikipedia Link

METLIN ID

PubChem Compound

PDB ID

Not Available

ChEBI ID

30887

Food Biomarker Ontology

Not Available

VMH ID

ICIT

MarkerDB ID

Not Available

Good Scents ID

Not Available

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

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 ]
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 ]
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 ]
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 ]
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 ]
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 ]
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 ]
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 ]
Mikosha AS, Monissarenko VP, Bychkovskaia LA: [Properties of adrenocortical isocitrate dehydrogenase]. Vopr Med Khim. 1981 Nov-Dec;27(6):736-9. [PubMed:7336646 ]
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

Enzyme Details

1. Aconitate hydratase, mitochondrial

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 acid	details
Isocitric acid → cis-Aconitic acid + Water	details

Enzyme Details

2. Cytoplasmic aconitate hydratase

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 acid	details
Isocitric acid → cis-Aconitic acid + Water	details

Enzyme Details

3. Isocitrate dehydrogenase [NADP], mitochondrial

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) + NADPH	details
Isocitric acid + NADP → Oxoglutaric acid + Carbon dioxide + NADPH + Hydrogen Ion	details
Isocitric acid + NADP → Oxalosuccinic acid + NADPH + Hydrogen Ion	details

Enzyme Details

4. Isocitrate dehydrogenase [NAD] subunit beta, mitochondrial

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) + NADH	details
Isocitric acid + NAD → Oxoglutaric acid + Carbon dioxide + NADH + Hydrogen Ion	details

Enzyme Details

5. Isocitrate dehydrogenase [NADP] cytoplasmic

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) + NADPH	details
Isocitric acid + NADP → Oxoglutaric acid + Carbon dioxide + NADPH + Hydrogen Ion	details
Isocitric acid + NADP → Oxalosuccinic acid + NADPH + Hydrogen Ion	details

Enzyme Details

6. Isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial

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) + NADH	details
Isocitric acid + NAD → Oxoglutaric acid + Carbon dioxide + NADH + Hydrogen Ion	details

Enzyme Details

7. Isocitrate dehydrogenase [NAD] subunit gamma, mitochondrial

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) + NADH	details
Isocitric acid + NAD → Oxoglutaric acid + Carbon dioxide + NADH + Hydrogen Ion	details

Showing metabocard for Isocitric acid (HMDB0000193)

MOL for HMDB0000193 (Isocitric acid)

3D MOL for HMDB0000193 (Isocitric acid)

3D SDF for HMDB0000193 (Isocitric acid)

3D-SDF for HMDB0000193 (Isocitric acid)

PDB for HMDB0000193 (Isocitric acid)

3D PDB for HMDB0000193 (Isocitric acid)

SMILES for HMDB0000193 (Isocitric acid)

INCHI for HMDB0000193 (Isocitric acid)

Structure for HMDB0000193 (Isocitric acid)

3D Structure for HMDB0000193 (Isocitric acid)

Experimental Collision Cross Sections

Predicted Collision Cross Sections

Predicted Kovats Retention Indices

Derivatized

GC-MS Spectra

MS/MS Spectra

NMR Spectra

Enzymes

Reactions

Reactions

Reactions

Reactions

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Reactions