Showing metabocard for (2R)-Homocitric acid (MMDBc0032919)

Record Information
Version1.0
StatusDetected and Quantified
Creation Date2021-11-19 04:27:22 UTC
Update Date2024-04-30 19:54:59 UTC
Metabolite IDMMDBc0032919
Metabolite Identification
Common Name(2R)-Homocitric acid
DescriptionHomocitric acid (CAS: 3562-74-1) is a normal urinary organic acid (PMID: 14708889 ). Homocitric acid is a citric acid analogue found as a minor metabolite in urine samples from patients with propionic acidaemia. Homocitric acid is formed by citrate synthase due to propionyl-CoA carboxylase deficiency (by the citrate synthase condensation reaction of alpha-ketoglutarate with acetyl coenzyme A and propionyl coenzyme A) (PMID: 7850997 ). Homocitric acid has been identified in the human placenta (PMID: 32033212 ).
Structure
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for #<Metabolite:0x00007f92505e3e10>


  Mrv1652310231917012D          

 14 13  0  0  0  0            999 V2000
 9993.1424 9992.7759    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
 9992.4284 9993.1882    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9991.7139 9992.7759    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9990.9992 9993.1882    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9990.2846 9992.7759    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9990.9992 9994.0128    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9993.8577 9993.1882    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9994.5730 9992.7759    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9995.2863 9993.1882    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9994.5730 9991.9517    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9993.1424 9991.9517    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9993.8577 9991.5381    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9992.4284 9991.5381    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9993.8577 9992.3634    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  7  1  0  0  0  0
  1 11  1  0  0  0  0
  1 14  1  6  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  4  6  2  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  8 10  2  0  0  0  0
 11 12  1  0  0  0  0
 11 13  2  0  0  0  0
M  END
Download

3D MOL for #<Metabolite:0x00007f92505e3e10>

HMDB0003518
     RDKit          3D
Homocitric acid
 24 23  0  0  0  0  0  0  0  0999 V2000
   -2.0339   -1.6096    1.0258 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6251   -0.8926    0.2195 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0407   -0.8951    0.3404 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9376   -0.0898   -0.7937 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8503    0.7737   -0.3314 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3548    0.2215    0.3175 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.1842   -0.4845    1.4734 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1507   -0.5914   -0.6923 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3811   -1.1717   -0.1281 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0964   -1.8676   -0.9219 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8260   -1.0314    1.1712 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2332    1.4328    0.6070 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6610    1.6239    1.7512 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.5361    2.3070   -0.4480 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5274    0.0053    0.1841 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7403    0.5405   -1.3045 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5835   -0.8063   -1.5899 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2916    1.5241    0.3917 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4819    1.3612   -1.2278 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6059   -1.3585    1.5137 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5230   -1.3908   -1.1367 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4708    0.1346   -1.4728 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8124   -1.0179    1.3868 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2769    3.2825   -0.3352 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  1  1
  6  8  1  0
  8  9  1  0
  9 10  2  0
  9 11  1  0
  6 12  1  0
 12 13  2  0
 12 14  1  0
  3 15  1  0
  4 16  1  0
  4 17  1  0
  5 18  1  0
  5 19  1  0
  7 20  1  0
  8 21  1  0
  8 22  1  0
 11 23  1  0
 14 24  1  0
M  END
Download

3D SDF for #<Metabolite:0x00007f92505e3e10>


  Mrv1652310231917012D          

 14 13  0  0  0  0            999 V2000
 9993.1424 9992.7759    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
 9992.4284 9993.1882    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9991.7139 9992.7759    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9990.9992 9993.1882    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9990.2846 9992.7759    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9990.9992 9994.0128    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9993.8577 9993.1882    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9994.5730 9992.7759    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9995.2863 9993.1882    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9994.5730 9991.9517    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9993.1424 9991.9517    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9993.8577 9991.5381    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9992.4284 9991.5381    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9993.8577 9992.3634    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  7  1  0  0  0  0
  1 11  1  0  0  0  0
  1 14  1  6  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  4  6  2  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  8 10  2  0  0  0  0
 11 12  1  0  0  0  0
 11 13  2  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0032919

> <DATABASE_NAME>
MIME

> <SMILES>
OC(=O)CC[C@@](O)(CC(O)=O)C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C7H10O7/c8-4(9)1-2-7(14,6(12)13)3-5(10)11/h14H,1-3H2,(H,8,9)(H,10,11)(H,12,13)/t7-/m1/s1

> <INCHI_KEY>
XKJVEVRQMLKSMO-SSDOTTSWSA-N

> <FORMULA>
C7H10O7

> <MOLECULAR_WEIGHT>
206.1501

> <EXACT_MASS>
206.042652674

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_ATOM_COUNT>
24

> <JCHEM_AVERAGE_POLARIZABILITY>
17.44345390081851

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2R)-2-hydroxybutane-1,2,4-tricarboxylic acid

> <ALOGPS_LOGP>
-1.50

> <JCHEM_LOGP>
-1.0340262470000003

> <ALOGPS_LOGS>
-0.03

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-3

> <JCHEM_PKA>
3.9251914717112886

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.086703991163821

> <JCHEM_PKA_STRONGEST_BASIC>
-4.0751445556736625

> <JCHEM_POLAR_SURFACE_AREA>
132.13

> <JCHEM_REFRACTIVITY>
40.37890000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.91e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(R)-homocitric acid

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for #<Metabolite:0x00007f92505e3e10>

HMDB0003518
     RDKit          3D
Homocitric acid
 24 23  0  0  0  0  0  0  0  0999 V2000
   -2.0339   -1.6096    1.0258 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6251   -0.8926    0.2195 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0407   -0.8951    0.3404 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9376   -0.0898   -0.7937 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8503    0.7737   -0.3314 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3548    0.2215    0.3175 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.1842   -0.4845    1.4734 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1507   -0.5914   -0.6923 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3811   -1.1717   -0.1281 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0964   -1.8676   -0.9219 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8260   -1.0314    1.1712 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2332    1.4328    0.6070 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6610    1.6239    1.7512 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.5361    2.3070   -0.4480 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5274    0.0053    0.1841 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7403    0.5405   -1.3045 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5835   -0.8063   -1.5899 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2916    1.5241    0.3917 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4819    1.3612   -1.2278 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6059   -1.3585    1.5137 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5230   -1.3908   -1.1367 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4708    0.1346   -1.4728 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8124   -1.0179    1.3868 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2769    3.2825   -0.3352 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  1  1
  6  8  1  0
  8  9  1  0
  9 10  2  0
  9 11  1  0
  6 12  1  0
 12 13  2  0
 12 14  1  0
  3 15  1  0
  4 16  1  0
  4 17  1  0
  5 18  1  0
  5 19  1  0
  7 20  1  0
  8 21  1  0
  8 22  1  0
 11 23  1  0
 14 24  1  0
M  END
Download

PDB for #<Metabolite:0x00007f92505e3e10>

HEADER    PROTEIN                                 23-OCT-19   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   23-OCT-19         0                                  
HETATM    1  C   UNK     0    8653.8668653.182   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0    8652.5338653.951   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0    8651.1998653.182   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0    8649.8658653.951   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0    8648.5318653.182   0.000  0.00  0.00           O+0
HETATM    6  O   UNK     0    8649.8658655.491   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0    8655.2018653.951   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0    8656.5368653.182   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0    8657.8688653.951   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0    8656.5368651.643   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0    8653.8668651.643   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0    8655.2018650.871   0.000  0.00  0.00           O+0
HETATM   13  O   UNK     0    8652.5338650.871   0.000  0.00  0.00           O+0
HETATM   14  O   UNK     0    8655.2018652.412   0.000  0.00  0.00           O+0
CONECT    1    2    7   11   14                                             
CONECT    2    1    3                                                       
CONECT    3    2    4                                                       
CONECT    4    3    5    6                                                  
CONECT    5    4                                                            
CONECT    6    4                                                            
CONECT    7    1    8                                                       
CONECT    8    7    9   10                                                  
CONECT    9    8                                                            
CONECT   10    8                                                            
CONECT   11    1   12   13                                                  
CONECT   12   11                                                            
CONECT   13   11                                                            
CONECT   14    1                                                            
MASTER        0    0    0    0    0    0    0    0   14    0   26    0
END
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3D PDB for #<Metabolite:0x00007f92505e3e10>

COMPND    HMDB0003518
HETATM    1  O1  UNL     1      -2.034  -1.610   1.026  1.00  0.00           O  
HETATM    2  C1  UNL     1      -2.625  -0.893   0.220  1.00  0.00           C  
HETATM    3  O2  UNL     1      -4.041  -0.895   0.340  1.00  0.00           O  
HETATM    4  C2  UNL     1      -1.938  -0.090  -0.794  1.00  0.00           C  
HETATM    5  C3  UNL     1      -0.850   0.774  -0.331  1.00  0.00           C  
HETATM    6  C4  UNL     1       0.355   0.222   0.318  1.00  0.00           C  
HETATM    7  O3  UNL     1       0.184  -0.485   1.473  1.00  0.00           O  
HETATM    8  C5  UNL     1       1.151  -0.591  -0.692  1.00  0.00           C  
HETATM    9  C6  UNL     1       2.381  -1.172  -0.128  1.00  0.00           C  
HETATM   10  O4  UNL     1       3.096  -1.868  -0.922  1.00  0.00           O  
HETATM   11  O5  UNL     1       2.826  -1.031   1.171  1.00  0.00           O  
HETATM   12  C7  UNL     1       1.233   1.433   0.607  1.00  0.00           C  
HETATM   13  O6  UNL     1       1.661   1.624   1.751  1.00  0.00           O  
HETATM   14  O7  UNL     1       1.536   2.307  -0.448  1.00  0.00           O  
HETATM   15  H1  UNL     1      -4.527   0.005   0.184  1.00  0.00           H  
HETATM   16  H2  UNL     1      -2.740   0.541  -1.305  1.00  0.00           H  
HETATM   17  H3  UNL     1      -1.583  -0.806  -1.590  1.00  0.00           H  
HETATM   18  H4  UNL     1      -1.292   1.524   0.392  1.00  0.00           H  
HETATM   19  H5  UNL     1      -0.482   1.361  -1.228  1.00  0.00           H  
HETATM   20  H6  UNL     1       0.606  -1.358   1.514  1.00  0.00           H  
HETATM   21  H7  UNL     1       0.523  -1.391  -1.137  1.00  0.00           H  
HETATM   22  H8  UNL     1       1.471   0.135  -1.473  1.00  0.00           H  
HETATM   23  H9  UNL     1       3.812  -1.018   1.387  1.00  0.00           H  
HETATM   24  H10 UNL     1       1.277   3.283  -0.335  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3    4
CONECT    3   15
CONECT    4    5   16   17
CONECT    5    6   18   19
CONECT    6    7    8   12
CONECT    7   20
CONECT    8    9   21   22
CONECT    9   10   10   11
CONECT   11   23
CONECT   12   13   13   14
CONECT   14   24
END
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SMILES for #<Metabolite:0x00007f92505e3e10>

OC(=O)CC[C@@](O)(CC(O)=O)C(O)=O
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INCHI for #<Metabolite:0x00007f92505e3e10>

InChI=1S/C7H10O7/c8-4(9)1-2-7(14,6(12)13)3-5(10)11/h14H,1-3H2,(H,8,9)(H,10,11)(H,12,13)/t7-/m1/s1
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Synonyms
ValueSource
(R)-2-Hydroxy-1,2,4-butanetricarboxylic acidChEBI
(R)-2-Hydroxybutane-1,2,4-tricarboxylic acidChEBI
(R)-Homocitric acidChEBI
3-Hydroxy-3-carboxyadipic acidChEBI
HomocitrateChEBI
(R)-2-Hydroxy-1,2,4-butanetricarboxylateGenerator
(R)-2-Hydroxybutane-1,2,4-tricarboxylateGenerator
(R)-HomocitrateGenerator
3-Hydroxy-3-carboxyadipateGenerator
2-Hydroxybutane-1,2,4-tricarboxylateHMDB
(2R)-2-Hydroxy-1,2,4-butanetricarboxylateHMDB
(2R)-2-Hydroxy-1,2,4-butanetricarboxylic acidHMDB
(±)-homocitrateHMDB
(±)-homocitric acidHMDB
2-Hydroxy-1,2,4-butanetricarboxylateHMDB
2-Hydroxy-1,2,4-butanetricarboxylic acidHMDB
Homocitric acidHMDB
Molecular FormulaC7H10O7
Average Mass206.1501
Monoisotopic Mass206.042652674
IUPAC Name(2R)-2-hydroxybutane-1,2,4-tricarboxylic acid
Traditional Name(R)-homocitric acid
CAS Registry Number3562-74-1
SMILES
OC(=O)CC[C@@](O)(CC(O)=O)C(O)=O
InChI Identifier
InChI=1S/C7H10O7/c8-4(9)1-2-7(14,6(12)13)3-5(10)11/h14H,1-3H2,(H,8,9)(H,10,11)(H,12,13)/t7-/m1/s1
InChI KeyXKJVEVRQMLKSMO-SSDOTTSWSA-N