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Showing metabocard for D-threo-Isocitric acid (HMDB0001874)

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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2006-02-23 12:38:32 UTC
Update Date2023-02-21 17:15:53 UTC
HMDB IDHMDB0001874
Secondary Accession Numbers
  • HMDB01874
Metabolite Identification
Common NameD-threo-Isocitric acid
DescriptionD-threo-Isocitric acid, also known as isocitrate or isocitrIC ACID, belongs to the class of organic compounds known as tricarboxylic acids and derivatives. These are carboxylic acids containing exactly three carboxyl groups. D-threo-Isocitric acid exists in all living species, ranging from bacteria to plants to humans. D-threo-Isocitric acid has been detected, but not quantified in, several different foods, such as salmonberries (Rubus spectabilis), black elderberries (Sambucus nigra), common peas (Pisum sativum), nectarines (Prunus persica var. nucipersica), and olives (Olea europaea). This could make D-threo-isocitric acid a potential biomarker for the consumption of these foods. D-threo-Isocitric acid is a primary metabolite. Primary metabolites are metabolically or physiologically essential metabolites. They are directly involved in an organism’s growth, development or reproduction. Based on a literature review a significant number of articles have been published on D-threo-Isocitric acid.
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0001874 (D-threo-Isocitric acid)

  Mrv1652309042000252D          

 13 12  0  0  1  0            999 V2000
    4.3862   -4.6980    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.1007   -4.2855    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    5.8152   -4.6980    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    6.5297   -4.2855    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.2441   -4.6980    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.5297   -3.4605    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.8152   -5.5230    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.1007   -3.4604    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.8152   -3.0480    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.3862   -3.0479    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.6718   -4.2854    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9572   -4.6980    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.6718   -3.4604    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  0  0  0  0
  3  2  1  0  0  0  0
  4  3  1  0  0  0  0
  5  4  1  0  0  0  0
  6  4  2  0  0  0  0
  3  7  1  6  0  0  0
  2  8  1  6  0  0  0
  9  8  1  0  0  0  0
 10  8  2  0  0  0  0
 11  1  1  0  0  0  0
 12 11  1  0  0  0  0
 13 11  2  0  0  0  0
M  END
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3D MOL for HMDB0001874 (D-threo-Isocitric acid)

HMDB0001874
     RDKit          3D
D-threo-Isocitric acid
 21 20  0  0  0  0  0  0  0  0999 V2000
   -0.1530   -2.4846    0.7083 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8711   -1.8882   -0.1290 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5097   -2.7156   -1.0680 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1178   -0.4589   -0.2410 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2690    0.4495    0.5756 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.8482    1.8366    0.2967 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1265    2.7085   -0.2059 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1602    2.1329    0.5949 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1589    0.6144    0.0589 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.7366    1.4879    1.0307 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9757   -0.5604   -0.0481 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8280   -0.8524    0.8189 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.8438   -1.4099   -1.1338 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4945   -2.6170   -1.2907 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2128   -0.2929   -0.0202 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9796   -0.1634   -1.3188 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3209    0.3206    1.6550 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3531    2.4106    1.5656 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0783    1.1728   -0.9035 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1864    2.2494    0.5793 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6087   -1.9399   -1.5250 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  1
  8 18  1  0
  9 19  1  6
 10 20  1  0
 13 21  1  0
M  END
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3D SDF for HMDB0001874 (D-threo-Isocitric acid)

  Mrv1652309042000252D          

 13 12  0  0  1  0            999 V2000
    4.3862   -4.6980    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.1007   -4.2855    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    5.8152   -4.6980    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    6.5297   -4.2855    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.2441   -4.6980    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.5297   -3.4605    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.8152   -5.5230    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.1007   -3.4604    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.8152   -3.0480    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.3862   -3.0479    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.6718   -4.2854    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9572   -4.6980    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.6718   -3.4604    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  0  0  0  0
  3  2  1  0  0  0  0
  4  3  1  0  0  0  0
  5  4  1  0  0  0  0
  6  4  2  0  0  0  0
  3  7  1  6  0  0  0
  2  8  1  6  0  0  0
  9  8  1  0  0  0  0
 10  8  2  0  0  0  0
 11  1  1  0  0  0  0
 12 11  1  0  0  0  0
 13 11  2  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0001874

> <DATABASE_NAME>
hmdb

> <SMILES>
O[C@H]([C@H](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)/t2-,4+/m0/s1

> <INCHI_KEY>
ODBLHEXUDAPZAU-ZAFYKAAXSA-N

> <FORMULA>
C6H8O7

> <MOLECULAR_WEIGHT>
192.1235

> <EXACT_MASS>
192.02700261

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_ATOM_COUNT>
21

> <JCHEM_AVERAGE_POLARIZABILITY>
15.536697322949372

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(1R,2S)-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>
4.676758742531204

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.068323851495592

> <JCHEM_PKA_STRONGEST_BASIC>
-4.021353286822632

> <JCHEM_POLAR_SURFACE_AREA>
132.13000000000002

> <JCHEM_REFRACTIVITY>
35.716100000000004

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
5.25e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
threo-DS(+)-isocitrate

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for HMDB0001874 (D-threo-Isocitric acid)

HMDB0001874
     RDKit          3D
D-threo-Isocitric acid
 21 20  0  0  0  0  0  0  0  0999 V2000
   -0.1530   -2.4846    0.7083 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8711   -1.8882   -0.1290 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5097   -2.7156   -1.0680 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1178   -0.4589   -0.2410 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2690    0.4495    0.5756 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.8482    1.8366    0.2967 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1265    2.7085   -0.2059 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1602    2.1329    0.5949 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1589    0.6144    0.0589 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.7366    1.4879    1.0307 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9757   -0.5604   -0.0481 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8280   -0.8524    0.8189 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.8438   -1.4099   -1.1338 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4945   -2.6170   -1.2907 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2128   -0.2929   -0.0202 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9796   -0.1634   -1.3188 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3209    0.3206    1.6550 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3531    2.4106    1.5656 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0783    1.1728   -0.9035 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1864    2.2494    0.5793 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6087   -1.9399   -1.5250 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  1
  8 18  1  0
  9 19  1  6
 10 20  1  0
 13 21  1  0
M  END
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PDB for HMDB0001874 (D-threo-Isocitric acid)

HEADER    PROTEIN                                 04-SEP-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   04-SEP-20         0                                  
HETATM    1  C   UNK     0       8.188  -8.770   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       9.521  -8.000   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      10.855  -8.770   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      12.189  -8.000   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0      13.522  -8.770   0.000  0.00  0.00           O+0
HETATM    6  O   UNK     0      12.189  -6.460   0.000  0.00  0.00           O+0
HETATM    7  O   UNK     0      10.855 -10.310   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0       9.521  -6.459   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0      10.855  -5.690   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0       8.188  -5.689   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0       6.854  -7.999   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0       5.520  -8.770   0.000  0.00  0.00           O+0
HETATM   13  O   UNK     0       6.854  -6.459   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 HMDB0001874 (D-threo-Isocitric acid)

COMPND    HMDB0001874
HETATM    1  O1  UNL     1      -0.153  -2.485   0.708  1.00  0.00           O  
HETATM    2  C1  UNL     1      -0.871  -1.888  -0.129  1.00  0.00           C  
HETATM    3  O2  UNL     1      -1.510  -2.716  -1.068  1.00  0.00           O  
HETATM    4  C2  UNL     1      -1.118  -0.459  -0.241  1.00  0.00           C  
HETATM    5  C3  UNL     1      -0.269   0.450   0.576  1.00  0.00           C  
HETATM    6  C4  UNL     1      -0.848   1.837   0.297  1.00  0.00           C  
HETATM    7  O3  UNL     1      -0.126   2.709  -0.206  1.00  0.00           O  
HETATM    8  O4  UNL     1      -2.160   2.133   0.595  1.00  0.00           O  
HETATM    9  C5  UNL     1       1.159   0.614   0.059  1.00  0.00           C  
HETATM   10  O5  UNL     1       1.737   1.488   1.031  1.00  0.00           O  
HETATM   11  C6  UNL     1       1.976  -0.560  -0.048  1.00  0.00           C  
HETATM   12  O6  UNL     1       2.828  -0.852   0.819  1.00  0.00           O  
HETATM   13  O7  UNL     1       1.844  -1.410  -1.134  1.00  0.00           O  
HETATM   14  H1  UNL     1      -2.494  -2.617  -1.291  1.00  0.00           H  
HETATM   15  H2  UNL     1      -2.213  -0.293  -0.020  1.00  0.00           H  
HETATM   16  H3  UNL     1      -0.980  -0.163  -1.319  1.00  0.00           H  
HETATM   17  H4  UNL     1      -0.321   0.321   1.655  1.00  0.00           H  
HETATM   18  H5  UNL     1      -2.353   2.411   1.566  1.00  0.00           H  
HETATM   19  H6  UNL     1       1.078   1.173  -0.904  1.00  0.00           H  
HETATM   20  H7  UNL     1       2.186   2.249   0.579  1.00  0.00           H  
HETATM   21  H8  UNL     1       2.609  -1.940  -1.525  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 HMDB0001874 (D-threo-Isocitric acid)

O[C@H]([C@H](CC(O)=O)C(O)=O)C(O)=O
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INCHI for HMDB0001874 (D-threo-Isocitric acid)

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)/t2-,4+/m0/s1
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View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
Chemical FormulaC6H8O7
Average Molecular Weight192.1235
Monoisotopic Molecular Weight192.02700261
IUPAC Name(1R,2S)-1-hydroxypropane-1,2,3-tricarboxylic acid
Traditional Namethreo-DS(+)-isocitrate
CAS Registry Number6061-97-8
SMILES
O[C@H]([C@H](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)/t2-,4+/m0/s1
InChI KeyODBLHEXUDAPZAU-ZAFYKAAXSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as tricarboxylic acids and derivatives. These are carboxylic acids containing exactly three carboxyl groups.
KingdomOrganic compounds
Super ClassOrganic acids and derivatives
ClassCarboxylic acids and derivatives
Sub ClassTricarboxylic acids and derivatives
Direct ParentTricarboxylic acids and derivatives
Alternative Parents
Substituents
  • Tricarboxylic acid or derivatives
  • Beta-hydroxy acid
  • Monosaccharide
  • Hydroxy acid
  • Alpha-hydroxy acid
  • Secondary alcohol
  • Carboxylic acid
  • Organic oxygen compound
  • Organic oxide
  • Hydrocarbon derivative
  • Organooxygen compound
  • Carbonyl group
  • Alcohol
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Ontology
Physiological effectNot Available
Disposition
Biological locationRoute of exposureSource
Process
Naturally occurring process
RoleNot Available
Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
Predicted Chromatographic Properties
Spectra
Biological Properties
Cellular Locations
  • Mitochondria
  • Peroxisome
Biospecimen Locations
  • Blood
Tissue LocationsNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodExpected but not QuantifiedNot QuantifiedNot AvailableNot Available
Normal
      Not Available
 details
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB012771
KNApSAcK IDC00001188
Chemspider ID4477081
KEGG Compound IDC00451
BioCyc IDTHREO-DS-ISO-CITRATE
BiGG ID34579
Wikipedia LinkNot Available
METLIN ID3328
PubChem Compound5318532
PDB IDNot Available
ChEBI ID151
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceWong, Chi Huey; Whitesides, George M. Enzyme-catalyzed transhydrogenation between nicotinamide cofactors and its application in organic synthesis. Journal of the American Chemical Society (1982), 104(12), 3542-4.
Material Safety Data Sheet (MSDS)Not Available
General ReferencesNot Available