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Showing metabocard for cis-Aconitic acid (HMDB0000072)

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enzymes (2) Show 2 proteins
Record Information
Version5.0
StatusDetected and Quantified
Creation Date2005-11-16 15:48:42 UTC
Update Date2023-05-30 20:56:00 UTC
HMDB IDHMDB0000072
Secondary Accession Numbers
  • HMDB0000461
  • HMDB00072
  • HMDB00461
Metabolite Identification
Common Namecis-Aconitic acid
Descriptioncis-Aconitic acid, also known as cis-aconitate or acid, acontic, belongs to the class of organic compounds known as tricarboxylic acids and derivatives. These are carboxylic acids containing exactly three carboxyl groups. cis-Aconitic acid exists in all living species, ranging from bacteria to plants to humans. In humans, cis-aconitic acid is involved in the metabolic disorder called the glutaminolysis and cancer pathway. cis-Aconitic acid is a bland tasting compound. cis-Aconitic acid is found, on average, in the highest concentration within milk (cow). cis-Aconitic acid has also been detected, but not quantified in, several different foods, such as french plantains (Musa X paradisiaca), yams (Dioscorea), horseradishes (Armoracia rusticana), sweet potatos (Ipomoea batatas), and persimmons (Diospyros). This could make cis-aconitic acid a potential biomarker for the consumption of these foods. cis-Aconitic acid is a secondary metabolite. Secondary metabolites are metabolically or physiologically non-essential metabolites that may serve a role as defense or signalling molecules. In some cases they are simply molecules that arise from the incomplete metabolism of other secondary metabolites. Based on a literature review a significant number of articles have been published on cis-Aconitic acid.
Structure
Data?1676999669
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0000072 (cis-Aconitic acid)

cis-Aconitic acid.mol
  Mrv1652309032023512D          

 12 11  0  0  0  0            999 V2000
    1.4289   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289    0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434   -0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  2  0  0  0  0
  3  4  1  0  0  0  0
  3  5  1  0  0  0  0
  5  6  1  0  0  0  0
  1  7  2  0  0  0  0
  1  8  1  0  0  0  0
  4  9  2  0  0  0  0
  4 10  1  0  0  0  0
  6 11  2  0  0  0  0
  6 12  1  0  0  0  0
M  END
Download

3D MOL for HMDB0000072 (cis-Aconitic acid)

HMDB0000072
     RDKit          3D
cis-Aconitic acid
 18 17  0  0  0  0  0  0  0  0999 V2000
   -2.7888   -1.5143   -1.7892 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1240   -0.5858   -1.1948 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6224    0.6546   -1.3609 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9605   -0.9479   -0.4416 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1584   -0.1745    0.2255 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0013   -0.8291    0.9339 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2877   -0.3142    0.4506 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3324   -0.7860    0.9680 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4224    0.6514   -0.5321 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3162    1.2307    0.3189 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1773    1.9348   -0.1757 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.6361    1.9623    1.0839 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5941    0.8826   -1.5185 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7158   -2.0569   -0.4325 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9438   -0.5671    2.0316 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9579   -1.9222    0.8901 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4068    0.4152   -1.5331 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4691    1.9662    2.0758 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  2  4  1  0
  4  5  2  0
  5  6  1  0
  6  7  1  0
  7  8  2  0
  7  9  1  0
  5 10  1  0
 10 11  2  0
 10 12  1  0
  3 13  1  0
  4 14  1  0
  6 15  1  0
  6 16  1  0
  9 17  1  0
 12 18  1  0
M  END
Download

3D SDF for HMDB0000072 (cis-Aconitic acid)

cis-Aconitic acid.mol
  Mrv1652309032023512D          

 12 11  0  0  0  0            999 V2000
    1.4289   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289    0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434   -0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  2  0  0  0  0
  3  4  1  0  0  0  0
  3  5  1  0  0  0  0
  5  6  1  0  0  0  0
  1  7  2  0  0  0  0
  1  8  1  0  0  0  0
  4  9  2  0  0  0  0
  4 10  1  0  0  0  0
  6 11  2  0  0  0  0
  6 12  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0000072

> <DATABASE_NAME>
hmdb

> <SMILES>
OC(=O)C\C(=C\C(O)=O)C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C6H6O6/c7-4(8)1-3(6(11)12)2-5(9)10/h1H,2H2,(H,7,8)(H,9,10)(H,11,12)/b3-1-

> <INCHI_KEY>
GTZCVFVGUGFEME-IWQZZHSRSA-N

> <FORMULA>
C6H6O6

> <MOLECULAR_WEIGHT>
174.1082

> <EXACT_MASS>
174.016437924

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
18

> <JCHEM_AVERAGE_POLARIZABILITY>
14.15997033984106

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(1Z)-prop-1-ene-1,2,3-tricarboxylic acid

> <ALOGPS_LOGP>
-0.41

> <JCHEM_LOGP>
-0.521036942

> <ALOGPS_LOGS>
-1.41

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-3

> <JCHEM_PKA>
3.727127446992898

> <JCHEM_PKA_STRONGEST_ACIDIC>
2.106091815369544

> <JCHEM_POLAR_SURFACE_AREA>
111.89999999999999

> <JCHEM_REFRACTIVITY>
35.2305

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
6.72e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
cis-aconitic acid

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for HMDB0000072 (cis-Aconitic acid)

HMDB0000072
     RDKit          3D
cis-Aconitic acid
 18 17  0  0  0  0  0  0  0  0999 V2000
   -2.7888   -1.5143   -1.7892 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1240   -0.5858   -1.1948 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6224    0.6546   -1.3609 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9605   -0.9479   -0.4416 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1584   -0.1745    0.2255 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0013   -0.8291    0.9339 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2877   -0.3142    0.4506 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3324   -0.7860    0.9680 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4224    0.6514   -0.5321 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3162    1.2307    0.3189 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1773    1.9348   -0.1757 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.6361    1.9623    1.0839 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5941    0.8826   -1.5185 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7158   -2.0569   -0.4325 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9438   -0.5671    2.0316 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9579   -1.9222    0.8901 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4068    0.4152   -1.5331 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4691    1.9662    2.0758 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  2  4  1  0
  4  5  2  0
  5  6  1  0
  6  7  1  0
  7  8  2  0
  7  9  1  0
  5 10  1  0
 10 11  2  0
 10 12  1  0
  3 13  1  0
  4 14  1  0
  6 15  1  0
  6 16  1  0
  9 17  1  0
 12 18  1  0
M  END
Download

PDB for HMDB0000072 (cis-Aconitic acid)

HEADER    PROTEIN                                 03-SEP-20   NONE
TITLE     NULL                                                        
COMPND    MOLECULE: cis-Aconitic acid.mol                             
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   03-SEP-20         0                                  
HETATM    1  C   UNK     0       2.667  -0.770   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       1.334  -1.540   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.000  -0.770   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       0.000   0.770   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -1.334  -1.540   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -2.667  -0.770   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       2.667   0.770   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0       4.001  -1.540   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0      -1.334   1.540   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0       1.334   1.540   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0      -2.667   0.770   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0      -4.001  -1.540   0.000  0.00  0.00           O+0
CONECT    1    2    7    8                                                  
CONECT    2    1    3                                                       
CONECT    3    2    4    5                                                  
CONECT    4    3    9   10                                                  
CONECT    5    3    6                                                       
CONECT    6    5   11   12                                                  
CONECT    7    1                                                            
CONECT    8    1                                                            
CONECT    9    4                                                            
CONECT   10    4                                                            
CONECT   11    6                                                            
CONECT   12    6                                                            
MASTER        0    0    0    0    0    0    0    0   12    0   22    0
END
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3D PDB for HMDB0000072 (cis-Aconitic acid)

COMPND    HMDB0000072
HETATM    1  O1  UNL     1      -2.789  -1.514  -1.789  1.00  0.00           O  
HETATM    2  C1  UNL     1      -2.124  -0.586  -1.195  1.00  0.00           C  
HETATM    3  O2  UNL     1      -2.622   0.655  -1.361  1.00  0.00           O  
HETATM    4  C2  UNL     1      -0.961  -0.948  -0.442  1.00  0.00           C  
HETATM    5  C3  UNL     1      -0.158  -0.174   0.225  1.00  0.00           C  
HETATM    6  C4  UNL     1       1.001  -0.829   0.934  1.00  0.00           C  
HETATM    7  C5  UNL     1       2.288  -0.314   0.451  1.00  0.00           C  
HETATM    8  O3  UNL     1       3.332  -0.786   0.968  1.00  0.00           O  
HETATM    9  O4  UNL     1       2.422   0.651  -0.532  1.00  0.00           O  
HETATM   10  C6  UNL     1      -0.316   1.231   0.319  1.00  0.00           C  
HETATM   11  O5  UNL     1      -1.177   1.935  -0.176  1.00  0.00           O  
HETATM   12  O6  UNL     1       0.636   1.962   1.084  1.00  0.00           O  
HETATM   13  H1  UNL     1      -3.594   0.883  -1.518  1.00  0.00           H  
HETATM   14  H2  UNL     1      -0.716  -2.057  -0.432  1.00  0.00           H  
HETATM   15  H3  UNL     1       0.944  -0.567   2.032  1.00  0.00           H  
HETATM   16  H4  UNL     1       0.958  -1.922   0.890  1.00  0.00           H  
HETATM   17  H5  UNL     1       2.407   0.415  -1.533  1.00  0.00           H  
HETATM   18  H6  UNL     1       0.469   1.966   2.076  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3    4
CONECT    3   13
CONECT    4    5    5   14
CONECT    5    6   10
CONECT    6    7   15   16
CONECT    7    8    8    9
CONECT    9   17
CONECT   10   11   11   12
CONECT   12   18
END
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SMILES for HMDB0000072 (cis-Aconitic acid)

OC(=O)C\C(=C\C(O)=O)C(O)=O
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INCHI for HMDB0000072 (cis-Aconitic acid)

InChI=1S/C6H6O6/c7-4(8)1-3(6(11)12)2-5(9)10/h1H,2H2,(H,7,8)(H,9,10)(H,11,12)/b3-1-
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View in JSmolView Stereo Labels
Synonyms
ValueSource
(Z)-1-Propene-1,2,3-tricarboxylic acidChEBI
cis-1-Propene-1,2,3-tricarboxylic acidChEBI
(Z)-1-Propene-1,2,3-tricarboxylateGenerator
cis-1-Propene-1,2,3-tricarboxylateGenerator
cis-AconitateGenerator
(1Z)-1-Propene-1,2,3-tricarboxylateHMDB
(1Z)-1-Propene-1,2,3-tricarboxylic acidHMDB
(Z)-AconitateHMDB
(Z)-Aconitic acidHMDB
1-cis-2,3-PropenetricarboxylateHMDB
1-cis-2,3-Propenetricarboxylic acidHMDB
1-Propene-1,2,3-tricarboxylateHMDB
1-Propene-1,2,3-tricarboxylic acidHMDB
cis-AconateHMDB
cis-Aconic acidHMDB
cis-OxaloacetateHMDB
cis-Oxaloacetic acidHMDB
Acid, citridicHMDB
Acid, citridinicHMDB
Aconitic acidHMDB
Acontic acidHMDB
Adonic acidHMDB
Achilleic acidHMDB
Acid, aconticHMDB
Acid, equiseticHMDB
Citridinic acidHMDB
Acid, achilleicHMDB
AconitateHMDB
Citridic acidHMDB
Pyrocitric acidHMDB
Acid, aconiticHMDB
Acid, adonicHMDB
Acid, carboxyglutaconicHMDB
Acid, pyrocitricHMDB
Carboxyglutaconic acidHMDB
Equisetic acidHMDB
Chemical FormulaC6H6O6
Average Molecular Weight174.1082
Monoisotopic Molecular Weight174.016437924
IUPAC Name(1Z)-prop-1-ene-1,2,3-tricarboxylic acid
Traditional Namecis-aconitic acid
CAS Registry Number585-84-2
SMILES
OC(=O)C\C(=C\C(O)=O)C(O)=O
InChI Identifier
InChI=1S/C6H6O6/c7-4(8)1-3(6(11)12)2-5(9)10/h1H,2H2,(H,7,8)(H,9,10)(H,11,12)/b3-1-
InChI KeyGTZCVFVGUGFEME-IWQZZHSRSA-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
  • Carboxylic acid
  • Organic oxygen compound
  • Organic oxide
  • Hydrocarbon derivative
  • Organooxygen compound
  • Carbonyl group
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Ontology
Physiological effect
Organoleptic effect
Disposition
Biological locationSource
Process
Naturally occurring process
Role
Biological roleIndustrial application
Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting Point125 °CNot Available
Boiling Point542.00 to 543.00 °C. @ 760.00 mm HgThe Good Scents Company Information System
Water Solubility400 mg/mLNot Available
LogP-0.140The Good Scents Company Information System
Experimental Chromatographic Properties

Experimental Collision Cross Sections

Adduct TypeData SourceCCS Value (Å2)Reference
[M-H]-Astarita_neg124.730932474
[M-H]-Baker132.37830932474
[M+H]+Baker152.21430932474
[M-H]-Not Available132.378http://allccs.zhulab.cn/database/detail?ID=AllCCS00001769
[M+H]+Not Available152.214http://allccs.zhulab.cn/database/detail?ID=AllCCS00001769
Predicted Molecular Properties
PropertyValueSource
Water Solubility6.72 g/LALOGPS
logP-0.41ALOGPS
logP-0.52ChemAxon
logS-1.4ALOGPS
pKa (Strongest Acidic)2.11ChemAxon
Physiological Charge-3ChemAxon
Hydrogen Acceptor Count6ChemAxon
Hydrogen Donor Count3ChemAxon
Polar Surface Area111.9 ŲChemAxon
Rotatable Bond Count4ChemAxon
Refractivity35.23 m³·mol⁻¹ChemAxon
Polarizability14.16 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
DarkChem[M+H]+139.93431661259
DarkChem[M-H]-134.33231661259
AllCCS[M+H]+137.8732859911
AllCCS[M-H]-129.60832859911
DeepCCS[M+H]+132.41330932474
DeepCCS[M-H]-128.68830932474
DeepCCS[M-2H]-166.27530932474
DeepCCS[M+Na]+141.81430932474
AllCCS[M+H]+137.932859911
AllCCS[M+H-H2O]+134.032859911
AllCCS[M+NH4]+141.532859911
AllCCS[M+Na]+142.532859911
AllCCS[M-H]-129.632859911
AllCCS[M+Na-2H]-131.032859911
AllCCS[M+HCOO]-132.632859911

Predicted Retention Times

Underivatized

Chromatographic MethodRetention TimeReference
Measured using a Waters Acquity ultraperformance liquid chromatography (UPLC) ethylene-bridged hybrid (BEH) C18 column (100 mm × 2.1 mm; 1.7 μmparticle diameter). Predicted by Afia on May 17, 2022. Predicted by Afia on May 17, 2022.2.35 minutes32390414
Predicted by Siyang on May 30, 202210.6917 minutes33406817
Predicted by Siyang using ReTip algorithm on June 8, 20225.12 minutes32390414
AjsUoB = Accucore 150 Amide HILIC with 10mM Ammonium Formate, 0.1% Formic Acid167.7 seconds40023050
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid949.1 seconds40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid366.4 seconds40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid57.0 seconds40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid213.0 seconds40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid87.9 seconds40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid282.3 seconds40023050
BfG_NTS_RP1 =Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) with Water:ACN and 0.1% Formic Acid310.4 seconds40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)492.9 seconds40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid669.9 seconds40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid131.0 seconds40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid1018.7 seconds40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid237.5 seconds40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid284.3 seconds40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate935.7 seconds40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA250.0 seconds40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water554.0 seconds40023050

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
cis-Aconitic acidOC(=O)C\C(=C\C(O)=O)C(O)=O2781.8Standard polar33892256
cis-Aconitic acidOC(=O)C\C(=C\C(O)=O)C(O)=O1400.2Standard non polar33892256
cis-Aconitic acidOC(=O)C\C(=C\C(O)=O)C(O)=O1741.3Semi standard non polar33892256

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
cis-Aconitic acid,1TMS,isomer #1C[Si](C)(C)OC(=O)C/C(=C/C(=O)O)C(=O)O1718.6Semi standard non polar33892256
cis-Aconitic acid,1TMS,isomer #2C[Si](C)(C)OC(=O)/C=C(/CC(=O)O)C(=O)O1699.9Semi standard non polar33892256
cis-Aconitic acid,1TMS,isomer #3C[Si](C)(C)OC(=O)/C(=C\C(=O)O)CC(=O)O1670.3Semi standard non polar33892256
cis-Aconitic acid,2TMS,isomer #1C[Si](C)(C)OC(=O)/C=C(/CC(=O)O[Si](C)(C)C)C(=O)O1780.3Semi standard non polar33892256
cis-Aconitic acid,2TMS,isomer #2C[Si](C)(C)OC(=O)C/C(=C/C(=O)O)C(=O)O[Si](C)(C)C1742.9Semi standard non polar33892256
cis-Aconitic acid,2TMS,isomer #3C[Si](C)(C)OC(=O)/C=C(/CC(=O)O)C(=O)O[Si](C)(C)C1722.5Semi standard non polar33892256
cis-Aconitic acid,3TMS,isomer #1C[Si](C)(C)OC(=O)/C=C(/CC(=O)O[Si](C)(C)C)C(=O)O[Si](C)(C)C1745.8Semi standard non polar33892256
cis-Aconitic acid,1TBDMS,isomer #1CC(C)(C)[Si](C)(C)OC(=O)C/C(=C/C(=O)O)C(=O)O1965.7Semi standard non polar33892256
cis-Aconitic acid,1TBDMS,isomer #2CC(C)(C)[Si](C)(C)OC(=O)/C=C(/CC(=O)O)C(=O)O1950.7Semi standard non polar33892256
cis-Aconitic acid,1TBDMS,isomer #3CC(C)(C)[Si](C)(C)OC(=O)/C(=C\C(=O)O)CC(=O)O1943.6Semi standard non polar33892256
cis-Aconitic acid,2TBDMS,isomer #1CC(C)(C)[Si](C)(C)OC(=O)/C=C(/CC(=O)O[Si](C)(C)C(C)(C)C)C(=O)O2263.6Semi standard non polar33892256
cis-Aconitic acid,2TBDMS,isomer #2CC(C)(C)[Si](C)(C)OC(=O)C/C(=C/C(=O)O)C(=O)O[Si](C)(C)C(C)(C)C2205.9Semi standard non polar33892256
cis-Aconitic acid,2TBDMS,isomer #3CC(C)(C)[Si](C)(C)OC(=O)/C=C(/CC(=O)O)C(=O)O[Si](C)(C)C(C)(C)C2172.6Semi standard non polar33892256
cis-Aconitic acid,3TBDMS,isomer #1CC(C)(C)[Si](C)(C)OC(=O)/C=C(/CC(=O)O[Si](C)(C)C(C)(C)C)C(=O)O[Si](C)(C)C(C)(C)C2399.3Semi standard non polar33892256
Spectra
Biological Properties
Cellular Locations
  • Cytoplasm
Biospecimen Locations
  • Blood
  • Breast Milk
  • Cerebrospinal Fluid (CSF)
  • Saliva
  • Sweat
  • Urine
Tissue Locations
  • Prostate
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodDetected but not QuantifiedNot QuantifiedAdult (>18 years old)BothNormal details
Breast MilkDetected and Quantified10.1 +/- 3.1 uMAdult (>18 years old)Female
Normal		 details
Cerebrospinal Fluid (CSF)Detected and Quantified20.0 (13.0-27.0) uMAdult (>18 years old)BothNormal details
Cerebrospinal Fluid (CSF)Detected and Quantified2 uMChildren (1-13 years old)BothNormal details
SalivaDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Male
Normal		 details
SalivaDetected and Quantified0.363 +/- 0.169 uMAdult (>18 years old)Female
Normal
    • Sugimoto et al. (...
 details
SalivaDetected and Quantified0.358 +/- 0.198 uMAdult (>18 years old)Female
Normal
    • Sugimoto et al. (...
 details
SalivaDetected and Quantified0.176 +/- 0.107 uMAdult (>18 years old)Female
Normal
    • Sugimoto et al. (...
 details
SalivaDetected and Quantified0.172 +/- 0.179 uMAdult (>18 years old)Male
Normal
    • Sugimoto et al. (...
 details
SalivaDetected and Quantified3.17 +/- 1.17 uMAdult (>18 years old)FemaleNormal details
SalivaDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Male
Normal		 details
SalivaDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Male
Normal		 details
SalivaDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Male
Normal		 details
SalivaDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Male
Normal		 details
SalivaDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Male
Normal		 details
SalivaDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Male
Normal		 details
SalivaDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Male
Normal		 details
SalivaDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Male
Normal		 details
SalivaDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Male
Normal		 details
SweatDetected and Quantified< 10 uMAdult (40 years old)Male
Normal		 details
SweatDetected and Quantified< 10 uMAdult (60 years old)Male
Normal		 details
UrineDetected and Quantified45.72 +/- 2.82 umol/mmol creatinineNewborn (0-30 days old)Both
Normal
    • Analysis of 40 NI...
 details
UrineDetected and Quantified67.9 (14.3-100.7) umol/mmol creatinineNewborn (0-30 days old)BothNormal details
UrineDetected and Quantified8-40.7 umol/mmol creatinineInfant (0-1 year old)Female
Normal		 details
UrineDetected and Quantified8-26.0 umol/mmol creatinineInfant (0-1 year old)Male
Normal		 details
UrineDetected and Quantified7-30.6 umol/mmol creatinineInfant (0-1 year old)Male
Normal		 details
UrineDetected and Quantified2.0-23.6 umol/mmol creatinineInfant (0-1 year old)Female
Normal		 details
UrineDetected but not QuantifiedNot QuantifiedAdult (>18 years old)BothNormal details
UrineDetected and Quantified9.740-38.962 umol/mmol creatinineInfant (0-1 year old)Both
Normal		 details
UrineDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Normal		 details
UrineDetected and Quantified58-85 umol/mmol creatinineAdult (>18 years old)MaleNormal details
UrineDetected and Quantified48-103 umol/mmol creatinineAdult (>18 years old)FemaleNormal details
UrineDetected and Quantified<102.12 umol/mmol creatinineChildren (1 - 18 years old)Both
Normal
    • BC Children's Hos...
 details
UrineDetected and Quantified33.685 +/- 14.03 umol/mmol creatinineChildren (1 - 13 years old)Not Specified
Normal
    • Analysis of 30 no...
 details
UrineDetected and Quantified73.8 (64.0-130.3) umol/mmol creatinineInfant (0-1 year old)BothNormal details
UrineDetected and Quantified37.9 (17.3-63.3) umol/mmol creatinineChildren (1-13 years old)BothNormal details
UrineDetected and Quantified29.8 (14.7-93.1) umol/mmol creatinineAdolescent (13-18 years old)BothNormal details
UrineDetected and Quantified35.95 umol/mmol creatinineAdult (>18 years old)Male
Normal
    • Shaykhutdinov RA,...
 details
UrineDetected and Quantified13 (2.7-44) umol/mmol creatinineAdult (>18 years old)BothNormal details
UrineDetected and Quantified10.3(5.2-16.3) umol/mmol creatinineAdult (>18 years old)Both
Normal		 details
UrineDetected and Quantified20.9 (3.8-95.3) umol/mmol creatinineAdult (>18 years old)Both
Normal		 details
UrineDetected and Quantified54.5 (32.4-76.6) umol/mmol creatinineChildren (1-13 years old)BothNormal details
UrineDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Normal		 details
UrineDetected but not QuantifiedNot QuantifiedAdult (>18 years old)MaleNormal details
UrineDetected but not QuantifiedNot QuantifiedAdult (>18 years old)BothNormal details
Abnormal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
SalivaDetected and Quantified2.80 +/- 2.11 uMAdult (>18 years old)MaleAlzheimer's disease details
SalivaDetected and Quantified2.17 +/- 0.53 uMAdult (>18 years old)MaleFrontotemporal lobe dementia details
SalivaDetected and Quantified2.72 +/- 0.53 uMAdult (>18 years old)BothLewy body disease details
UrineDetected and Quantified32.0 (0.0-70.0) umol/mmol creatinineAdult (>18 years old)BothLung cancer details
UrineDetected and Quantified38.74 +/- 40.952 umol/mmol creatinineChildren (1 - 13 years old)Not Specified
Eosinophilic esophagitis
    • Analysis of 30 no...
 details
UrineDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Schizophrenia		 details
UrineDetected and Quantified6.494-293.514 umol/mmol creatinineInfant (0-1 year old)Both
Amish lethal microcephaly		 details
UrineDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Bladder cancer		 details
Associated Disorders and Diseases
Disease References
Alzheimer's disease
  1. 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
  1. 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
  1. 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 ]
Lung Cancer
  1. Wishart DS, Knox C, Guo AC, Eisner R, Young N, Gautam B, Hau DD, Psychogios N, Dong E, Bouatra S, Mandal R, Sinelnikov I, Xia J, Jia L, Cruz JA, Lim E, Sobsey CA, Shrivastava S, Huang P, Liu P, Fang L, Peng J, Fradette R, Cheng D, Tzur D, Clements M, Lewis A, De Souza A, Zuniga A, Dawe M, Xiong Y, Clive D, Greiner R, Nazyrova A, Shaykhutdinov R, Li L, Vogel HJ, Forsythe I: HMDB: a knowledgebase for the human metabolome. Nucleic Acids Res. 2009 Jan;37(Database issue):D603-10. doi: 10.1093/nar/gkn810. Epub 2008 Oct 25. [PubMed:18953024 ]
Eosinophilic esophagitis
  1. Slae, M., Huynh, H., Wishart, D.S. (2014). Analysis of 30 normal pediatric urine samples via NMR spectroscopy (unpublished work). NA.
Schizophrenia
  1. Yang J, Chen T, Sun L, Zhao Z, Qi X, Zhou K, Cao Y, Wang X, Qiu Y, Su M, Zhao A, Wang P, Yang P, Wu J, Feng G, He L, Jia W, Wan C: Potential metabolite markers of schizophrenia. Mol Psychiatry. 2013 Jan;18(1):67-78. doi: 10.1038/mp.2011.131. Epub 2011 Oct 25. [PubMed:22024767 ]
Amish lethal microcephaly
  1. Kelley RI, Robinson D, Puffenberger EG, Strauss KA, Morton DH: Amish lethal microcephaly: a new metabolic disorder with severe congenital microcephaly and 2-ketoglutaric aciduria. Am J Med Genet. 2002 Nov 1;112(4):318-26. doi: 10.1002/ajmg.10529. [PubMed:12376931 ]
Associated OMIM IDs
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB008306
KNApSAcK IDC00001177
Chemspider ID558863
KEGG Compound IDC00417
BioCyc IDCIS-ACONITATE
BiGG IDNot Available
Wikipedia LinkCitric acid cycle
METLIN ID5130
PubChem Compound643757
PDB IDNot Available
ChEBI ID32805
Food Biomarker OntologyNot Available
VMH IDHC00342
MarkerDB IDMDB00000038
Good Scents IDrw1057191
References
Synthesis ReferenceGutierrez, Eddie N.; Lamberti, Vincent. cis and trans Aconitic acids and their salts. U.S. (1978), 16 pp.
Material Safety Data Sheet (MSDS)Download (PDF)
General References
  1. Sreekumar A, Poisson LM, Rajendiran TM, Khan AP, Cao Q, Yu J, Laxman B, Mehra R, Lonigro RJ, Li Y, Nyati MK, Ahsan A, Kalyana-Sundaram S, Han B, Cao X, Byun J, Omenn GS, Ghosh D, Pennathur S, Alexander DC, Berger A, Shuster JR, Wei JT, Varambally S, Beecher C, Chinnaiyan AM: Metabolomic profiles delineate potential role for sarcosine in prostate cancer progression. Nature. 2009 Feb 12;457(7231):910-4. doi: 10.1038/nature07762. [PubMed:19212411 ]
  2. Boulat O, Gradwohl M, Matos V, Guignard JP, Bachmann C: Organic acids in the second morning urine in a healthy Swiss paediatric population. Clin Chem Lab Med. 2003 Dec;41(12):1642-58. [PubMed:14708889 ]
  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 ]
  4. Swart PJ, Kuipers EM, Smit C, Van Der Strate BW, Harmsen MC, Meijer DK: Lactoferrin. Antiviral activity of lactoferrin. Adv Exp Med Biol. 1998;443:205-13. [PubMed:9781360 ]
  5. 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 ]
  6. Redjems-Bennani N, Jeandel C, Lefebvre E, Blain H, Vidailhet M, Gueant JL: Abnormal substrate levels that depend upon mitochondrial function in cerebrospinal fluid from Alzheimer patients. Gerontology. 1998;44(5):300-4. [PubMed:9693263 ]
  7. Swart PJ, Kuipers ME, Smit C, Pauwels R, deBethune MP, de Clercq E, Meijer DK, Huisman JG: Antiviral effects of milk proteins: acylation results in polyanionic compounds with potent activity against human immunodeficiency virus types 1 and 2 in vitro. AIDS Res Hum Retroviruses. 1996 Jun 10;12(9):769-75. [PubMed:8738428 ]
  8. Matsuishi T, Urabe F, Percy AK, Komori H, Yamashita Y, Schultz RS, Ohtani Y, Kuriya N, Kato H: Abnormal carbohydrate metabolism in cerebrospinal fluid in Rett syndrome. J Child Neurol. 1994 Jan;9(1):26-30. [PubMed:8151077 ]

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 → cis-Aconitic acid + Waterdetails
Isocitric acid → cis-Aconitic acid + Waterdetails
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 → cis-Aconitic acid + Waterdetails
Isocitric acid → cis-Aconitic acid + Waterdetails