Showing metabocard for Isocitric acid (MMDBc0029787)

Record Information
Version1.0
StatusDetected and Quantified
Creation Date2021-11-17 23:41:39 UTC
Update Date2024-04-30 19:41:57 UTC
Metabolite IDMMDBc0029787
Metabolite Identification
Common NameIsocitric acid
DescriptionIsocitric acid is a protonated form of isocitrate, which is a substrate of the citric acid cycle. Isocitrate is formed from citrate with the help of the enzyme aconitase, and is acted upon by isocitrate dehydrogenase. Salts and esters of isocitric acid are known as isocitrates. (Wikipedia )
Structure
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for #<Metabolite:0x00007f9220013330>


  Mrv1652305271900172D          

 13 12  0  0  0  0            999 V2000
    4.6184    1.8414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9039    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1895    1.8414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4750    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7605    1.8414    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4750    0.6039    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.1895    2.6664    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.9039    0.6039    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1895    0.1914    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.6184    0.1914    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.3329    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.0474    1.8414    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.3329    0.6039    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  2  0  0  0  0
  4  6  1  0  0  0  0
  3  7  1  0  0  0  0
  2  8  1  0  0  0  0
  8  9  2  0  0  0  0
  8 10  1  0  0  0  0
  1 11  1  0  0  0  0
 11 12  2  0  0  0  0
 11 13  1  0  0  0  0
M  END
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3D MOL for #<Metabolite:0x00007f9220013330>

HMDB0000193
     RDKit          3D
Isocitric acid
 21 20  0  0  0  0  0  0  0  0999 V2000
   -2.4382    0.1096    1.2675 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0067    0.8823    0.3844 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9014    1.9199    0.0407 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6996    0.7439   -0.2482 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0549   -0.4730    0.1416 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6645   -1.6952   -0.2364 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1383   -2.4499   -1.1259 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8562   -2.1206    0.2680 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4414   -0.5255   -0.5027 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9802   -1.7409   -0.0162 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.3216    0.5620   -0.0429 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3025    0.2693    0.6803 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1349    1.8906   -0.3598 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9676    2.7432    0.6381 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8780    0.7684   -1.3621 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1390    1.6896   -0.0466 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2896   -0.4718    1.2569 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5374   -2.5482   -0.3437 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3726   -0.5652   -1.6158 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9339   -1.6526    0.9888 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3952    2.6642    0.2341 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  1  0
  5  6  1  0
  6  7  2  0
  6  8  1  0
  5  9  1  0
  9 10  1  0
  9 11  1  0
 11 12  2  0
 11 13  1  0
  3 14  1  0
  4 15  1  0
  4 16  1  0
  5 17  1  0
  8 18  1  0
  9 19  1  0
 10 20  1  0
 13 21  1  0
M  END
Download

3D SDF for #<Metabolite:0x00007f9220013330>


  Mrv1652305271900172D          

 13 12  0  0  0  0            999 V2000
    4.6184    1.8414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9039    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1895    1.8414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4750    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7605    1.8414    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4750    0.6039    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.1895    2.6664    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.9039    0.6039    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1895    0.1914    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.6184    0.1914    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.3329    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.0474    1.8414    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.3329    0.6039    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  2  0  0  0  0
  4  6  1  0  0  0  0
  3  7  1  0  0  0  0
  2  8  1  0  0  0  0
  8  9  2  0  0  0  0
  8 10  1  0  0  0  0
  1 11  1  0  0  0  0
 11 12  2  0  0  0  0
 11 13  1  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0029787

> <DATABASE_NAME>
MIME

> <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

> <FORMULA>
C6H8O7

> <MOLECULAR_WEIGHT>
192.1235

> <EXACT_MASS>
192.02700261

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_ATOM_COUNT>
21

> <JCHEM_AVERAGE_POLARIZABILITY>
15.55020163539311

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
1-hydroxypropane-1,2,3-tricarboxylic acid

> <ALOGPS_LOGP>
-0.35

> <JCHEM_LOGP>
-1.4463282496666667

> <ALOGPS_LOGS>
-0.56

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-3

> <JCHEM_PKA>
4.676758742531203

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.068323851495594

> <JCHEM_PKA_STRONGEST_BASIC>
-4.021353286822632

> <JCHEM_POLAR_SURFACE_AREA>
132.13

> <JCHEM_REFRACTIVITY>
35.7161

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
5.25e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
isocitric acid

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for #<Metabolite:0x00007f9220013330>

HMDB0000193
     RDKit          3D
Isocitric acid
 21 20  0  0  0  0  0  0  0  0999 V2000
   -2.4382    0.1096    1.2675 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0067    0.8823    0.3844 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9014    1.9199    0.0407 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6996    0.7439   -0.2482 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0549   -0.4730    0.1416 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6645   -1.6952   -0.2364 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1383   -2.4499   -1.1259 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8562   -2.1206    0.2680 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4414   -0.5255   -0.5027 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9802   -1.7409   -0.0162 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.3216    0.5620   -0.0429 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3025    0.2693    0.6803 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1349    1.8906   -0.3598 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9676    2.7432    0.6381 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8780    0.7684   -1.3621 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1390    1.6896   -0.0466 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2896   -0.4718    1.2569 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5374   -2.5482   -0.3437 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3726   -0.5652   -1.6158 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9339   -1.6526    0.9888 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3952    2.6642    0.2341 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  1  0
  5  6  1  0
  6  7  2  0
  6  8  1  0
  5  9  1  0
  9 10  1  0
  9 11  1  0
 11 12  2  0
 11 13  1  0
  3 14  1  0
  4 15  1  0
  4 16  1  0
  5 17  1  0
  8 18  1  0
  9 19  1  0
 10 20  1  0
 13 21  1  0
M  END
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PDB for #<Metabolite:0x00007f9220013330>

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
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3D PDB for #<Metabolite:0x00007f9220013330>

COMPND    HMDB0000193
HETATM    1  O1  UNL     1      -2.438   0.110   1.267  1.00  0.00           O  
HETATM    2  C1  UNL     1      -2.007   0.882   0.384  1.00  0.00           C  
HETATM    3  O2  UNL     1      -2.901   1.920   0.041  1.00  0.00           O  
HETATM    4  C2  UNL     1      -0.700   0.744  -0.248  1.00  0.00           C  
HETATM    5  C3  UNL     1       0.055  -0.473   0.142  1.00  0.00           C  
HETATM    6  C4  UNL     1      -0.665  -1.695  -0.236  1.00  0.00           C  
HETATM    7  O3  UNL     1      -0.138  -2.450  -1.126  1.00  0.00           O  
HETATM    8  O4  UNL     1      -1.856  -2.121   0.268  1.00  0.00           O  
HETATM    9  C5  UNL     1       1.441  -0.526  -0.503  1.00  0.00           C  
HETATM   10  O5  UNL     1       1.980  -1.741  -0.016  1.00  0.00           O  
HETATM   11  C6  UNL     1       2.322   0.562  -0.043  1.00  0.00           C  
HETATM   12  O6  UNL     1       3.302   0.269   0.680  1.00  0.00           O  
HETATM   13  O7  UNL     1       2.135   1.891  -0.360  1.00  0.00           O  
HETATM   14  H1  UNL     1      -2.968   2.743   0.638  1.00  0.00           H  
HETATM   15  H2  UNL     1      -0.878   0.768  -1.362  1.00  0.00           H  
HETATM   16  H3  UNL     1      -0.139   1.690  -0.047  1.00  0.00           H  
HETATM   17  H4  UNL     1       0.290  -0.472   1.257  1.00  0.00           H  
HETATM   18  H5  UNL     1      -2.537  -2.548  -0.344  1.00  0.00           H  
HETATM   19  H6  UNL     1       1.373  -0.565  -1.616  1.00  0.00           H  
HETATM   20  H7  UNL     1       1.934  -1.653   0.989  1.00  0.00           H  
HETATM   21  H8  UNL     1       2.395   2.664   0.234  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3    4
CONECT    3   14
CONECT    4    5   15   16
CONECT    5    6    9   17
CONECT    6    7    7    8
CONECT    8   18
CONECT    9   10   11   19
CONECT   10   20
CONECT   11   12   12   13
CONECT   13   21
END
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SMILES for #<Metabolite:0x00007f9220013330>

OC(C(CC(O)=O)C(O)=O)C(O)=O
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INCHI for #<Metabolite:0x00007f9220013330>

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)
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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
Molecular FormulaC6H8O7
Average Mass192.1235
Monoisotopic Mass192.02700261
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