Showing metabocard for cis-Aconitic acid (MMDBc0000021)

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Record Information
Version1.0
StatusDetected and Quantified
Creation Date2020-10-27 23:27:29 UTC
Update Date2024-04-30 19:30:52 UTC
Metabolite IDMMDBc0000021
Metabolite Identification
Common Namecis-Aconitic acid
Descriptioncis-Aconitic acid is an intermediate in the tricarboxylic acid cycle produced by the dehydration of citric acid. The enzyme aconitase (aconitate hydratase; EC 4.2.1.3) catalyses the stereo-specific isomerization of citrate to isocitrate via cis-aconitate in the tricarboxylic acid cycle.
Structure
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for #<Metabolite:0x00007f5341ad8108>

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 #<Metabolite:0x00007f5341ad8108>

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 #<Metabolite:0x00007f5341ad8108>

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>
MMDBc0000021

> <DATABASE_NAME>
MIME

> <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 #<Metabolite:0x00007f5341ad8108>

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
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PDB for #<Metabolite:0x00007f5341ad8108>

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 #<Metabolite:0x00007f5341ad8108>

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 #<Metabolite:0x00007f5341ad8108>

OC(=O)C\C(=C\C(O)=O)C(O)=O
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INCHI for #<Metabolite:0x00007f5341ad8108>

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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Synonyms
Molecular FormulaC6H6O6
Average Mass174.1082
Monoisotopic Mass174.016437924
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