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Showing metabocard for (2R,3S)-2-methylisocitrate (HMDB0303970)

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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2021-09-24 06:05:05 UTC
Update Date2021-09-24 06:05:05 UTC
HMDB IDHMDB0303970
Secondary Accession NumbersNone
Metabolite Identification
Common Name(2R,3S)-2-methylisocitrate
Description(2r,3s)-2-methylisocitrate, also known as methylisocitric acid or (2s,3r)-3-hydroxybutane-1,2,3-tricarboxylate, belongs to tricarboxylic acids and derivatives class of compounds. Those are carboxylic acids containing exactly three carboxyl groups (2r,3s)-2-methylisocitrate is soluble (in water) and a weakly acidic compound (based on its pKa). (2r,3s)-2-methylisocitrate can be found in a number of food items such as green zucchini, cinnamon, fig, and nanking cherry, which makes (2r,3s)-2-methylisocitrate a potential biomarker for the consumption of these food products.
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0303970 ((2R,3S)-2-methylisocitrate)

  Mrv1533007131514022D          

 15 14  0  0  1  0            999 V2000
    1.4277   -0.9990    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9987    0.1982    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4267   -0.3963    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.7996   -0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6555   -1.1890    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6258   -0.1982    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    4.3716    0.5945    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.0284   -0.7926    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    2.0835   -1.7834    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.4564   -1.3871    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    0.2530   -0.5945    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5962    0.7926    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    1.8240    0.6027    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.2275   -0.5945    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  3  2  1  0  0  0  0
  4  2  1  0  0  0  0
  3  5  1  6  0  0  0
  7  1  1  1  0  0  0
  7  3  1  0  0  0  0
  7  6  1  0  0  0  0
  8  4  2  0  0  0  0
  9  4  1  0  0  0  0
 10  5  2  0  0  0  0
 11  5  1  0  0  0  0
 12  6  2  0  0  0  0
 13  6  1  0  0  0  0
  7 14  1  1  0  0  0
  3 15  1  1  0  0  0
M  CHG  3   9  -1  11  -1  13  -1
M  END
Download

3D MOL for HMDB0303970 ((2R,3S)-2-methylisocitrate)

HMDB0303970
     RDKit          3D
(2R,3S)-2-methylisocitrate
 21 20  0  0  0  0  0  0  0  0999 V2000
   -1.7750   -0.3376    1.1058 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6406    0.3468    0.3117 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.2647    1.4176    1.0700 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2930    0.8170   -0.9345 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7325    0.0324   -1.8056 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4205    2.1752   -1.1426 O   0  0  0  0  0  1  0  0  0  0  0  0
    0.4717   -0.6042    0.0620 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.5996   -0.0419   -0.7024 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3209    1.0644   -0.0825 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1580    1.4475    1.0901 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.2827    1.7875   -0.8163 O   0  0  0  0  0  1  0  0  0  0  0  0
   -0.0199   -1.8804   -0.5663 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7046   -2.7162    0.0501 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3157   -2.1097   -1.8814 O   0  0  0  0  0  1  0  0  0  0  0  0
   -2.5145    0.4996    1.2703 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4235   -0.7575    2.0494 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2891   -1.0536    0.4444 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5351    1.3506    2.0012 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8818   -0.8678    1.0950 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2121    0.2926   -1.7190 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3707   -0.8623   -0.8994 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  1
  2  4  1  0
  4  5  2  0
  4  6  1  0
  2  7  1  0
  7  8  1  0
  8  9  1  0
  9 10  2  0
  9 11  1  0
  7 12  1  0
 12 13  2  0
 12 14  1  0
  1 15  1  0
  1 16  1  0
  1 17  1  0
  3 18  1  0
  7 19  1  1
  8 20  1  0
  8 21  1  0
M  CHG  3   6  -1  11  -1  14  -1
M  END
Download

3D SDF for HMDB0303970 ((2R,3S)-2-methylisocitrate)

  Mrv1533007131514022D          

 15 14  0  0  1  0            999 V2000
    1.4277   -0.9990    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9987    0.1982    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4267   -0.3963    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.7996   -0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6555   -1.1890    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6258   -0.1982    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    4.3716    0.5945    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.0284   -0.7926    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    2.0835   -1.7834    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.4564   -1.3871    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    0.2530   -0.5945    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5962    0.7926    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    1.8240    0.6027    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.2275   -0.5945    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  3  2  1  0  0  0  0
  4  2  1  0  0  0  0
  3  5  1  6  0  0  0
  7  1  1  1  0  0  0
  7  3  1  0  0  0  0
  7  6  1  0  0  0  0
  8  4  2  0  0  0  0
  9  4  1  0  0  0  0
 10  5  2  0  0  0  0
 11  5  1  0  0  0  0
 12  6  2  0  0  0  0
 13  6  1  0  0  0  0
  7 14  1  1  0  0  0
  3 15  1  1  0  0  0
M  CHG  3   9  -1  11  -1  13  -1
M  END
> <DATABASE_ID>
HMDB0303970

> <DATABASE_NAME>
hmdb

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

> <INCHI_IDENTIFIER>
InChI=1S/C7H10O7/c1-7(14,6(12)13)3(5(10)11)2-4(8)9/h3,14H,2H2,1H3,(H,8,9)(H,10,11)(H,12,13)/p-3/t3-,7-/m1/s1

> <INCHI_KEY>
HHKPKXCSHMJWCF-WVBDSBKLSA-K

> <FORMULA>
C7H7O7

> <MOLECULAR_WEIGHT>
203.128

> <EXACT_MASS>
203.020823305

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_ATOM_COUNT>
21

> <JCHEM_AVERAGE_POLARIZABILITY>
16.025728450848295

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
-3

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(1R,2S)-1-hydroxy-1-methylpropane-1,2,3-tricarboxylate

> <ALOGPS_LOGP>
-0.42

> <JCHEM_LOGP>
-1.0135623636666664

> <ALOGPS_LOGS>
-0.83

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-3

> <JCHEM_PKA>
4.805179537739236

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.166870337568587

> <JCHEM_PKA_STRONGEST_BASIC>
-4.066922204255973

> <JCHEM_POLAR_SURFACE_AREA>
140.61999999999998

> <JCHEM_REFRACTIVITY>
72.9407

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
3.76e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2R,3S)2-methylisocitrate

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for HMDB0303970 ((2R,3S)-2-methylisocitrate)

HMDB0303970
     RDKit          3D
(2R,3S)-2-methylisocitrate
 21 20  0  0  0  0  0  0  0  0999 V2000
   -1.7750   -0.3376    1.1058 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6406    0.3468    0.3117 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.2647    1.4176    1.0700 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2930    0.8170   -0.9345 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7325    0.0324   -1.8056 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4205    2.1752   -1.1426 O   0  0  0  0  0  1  0  0  0  0  0  0
    0.4717   -0.6042    0.0620 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.5996   -0.0419   -0.7024 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3209    1.0644   -0.0825 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1580    1.4475    1.0901 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.2827    1.7875   -0.8163 O   0  0  0  0  0  1  0  0  0  0  0  0
   -0.0199   -1.8804   -0.5663 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7046   -2.7162    0.0501 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3157   -2.1097   -1.8814 O   0  0  0  0  0  1  0  0  0  0  0  0
   -2.5145    0.4996    1.2703 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4235   -0.7575    2.0494 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2891   -1.0536    0.4444 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5351    1.3506    2.0012 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8818   -0.8678    1.0950 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2121    0.2926   -1.7190 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3707   -0.8623   -0.8994 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  1
  2  4  1  0
  4  5  2  0
  4  6  1  0
  2  7  1  0
  7  8  1  0
  8  9  1  0
  9 10  2  0
  9 11  1  0
  7 12  1  0
 12 13  2  0
 12 14  1  0
  1 15  1  0
  1 16  1  0
  1 17  1  0
  3 18  1  0
  7 19  1  1
  8 20  1  0
  8 21  1  0
M  CHG  3   6  -1  11  -1  14  -1
M  END
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PDB for HMDB0303970 ((2R,3S)-2-methylisocitrate)

HEADER    PROTEIN                                 13-JUL-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   13-JUL-15         0                                  
HETATM    1  C   UNK     0       2.665  -1.865   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       5.598   0.370   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       4.530  -0.740   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       7.093  -0.000   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       4.957  -2.219   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       1.540   0.000   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       3.035  -0.370   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0       8.160   1.110   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0       7.520  -1.480   0.000  0.00  0.00           O-1
HETATM   10  O   UNK     0       3.889  -3.329   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0       6.452  -2.589   0.000  0.00  0.00           O-1
HETATM   12  O   UNK     0       0.472  -1.110   0.000  0.00  0.00           O+0
HETATM   13  O   UNK     0       1.113   1.480   0.000  0.00  0.00           O-1
HETATM   14  O   UNK     0       3.405   1.125   0.000  0.00  0.00           O+0
HETATM   15  H   UNK     0       6.025  -1.110   0.000  0.00  0.00           H+0
CONECT    1    7                                                            
CONECT    2    3    4                                                       
CONECT    3    2    5    7   15                                             
CONECT    4    2    8    9                                                  
CONECT    5    3   10   11                                                  
CONECT    6    7   12   13                                                  
CONECT    7    1    3    6   14                                             
CONECT    8    4                                                            
CONECT    9    4                                                            
CONECT   10    5                                                            
CONECT   11    5                                                            
CONECT   12    6                                                            
CONECT   13    6                                                            
CONECT   14    7                                                            
CONECT   15    3                                                            
MASTER        0    0    0    0    0    0    0    0   15    0   28    0
END
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3D PDB for HMDB0303970 ((2R,3S)-2-methylisocitrate)

COMPND    HMDB0303970
HETATM    1  C1  UNL     1      -1.775  -0.338   1.106  1.00  0.00           C  
HETATM    2  C2  UNL     1      -0.641   0.347   0.312  1.00  0.00           C  
HETATM    3  O1  UNL     1      -0.265   1.418   1.070  1.00  0.00           O  
HETATM    4  C3  UNL     1      -1.293   0.817  -0.934  1.00  0.00           C  
HETATM    5  O2  UNL     1      -1.732   0.032  -1.806  1.00  0.00           O  
HETATM    6  O3  UNL     1      -1.421   2.175  -1.143  1.00  0.00           O1-
HETATM    7  C4  UNL     1       0.472  -0.604   0.062  1.00  0.00           C  
HETATM    8  C5  UNL     1       1.600  -0.042  -0.702  1.00  0.00           C  
HETATM    9  C6  UNL     1       2.321   1.064  -0.083  1.00  0.00           C  
HETATM   10  O4  UNL     1       2.158   1.447   1.090  1.00  0.00           O  
HETATM   11  O5  UNL     1       3.283   1.787  -0.816  1.00  0.00           O1-
HETATM   12  C7  UNL     1      -0.020  -1.880  -0.566  1.00  0.00           C  
HETATM   13  O6  UNL     1      -0.705  -2.716   0.050  1.00  0.00           O  
HETATM   14  O7  UNL     1       0.316  -2.110  -1.881  1.00  0.00           O1-
HETATM   15  H1  UNL     1      -2.515   0.500   1.270  1.00  0.00           H  
HETATM   16  H2  UNL     1      -1.423  -0.758   2.049  1.00  0.00           H  
HETATM   17  H3  UNL     1      -2.289  -1.054   0.444  1.00  0.00           H  
HETATM   18  H4  UNL     1      -0.535   1.351   2.001  1.00  0.00           H  
HETATM   19  H5  UNL     1       0.882  -0.868   1.095  1.00  0.00           H  
HETATM   20  H6  UNL     1       1.212   0.293  -1.719  1.00  0.00           H  
HETATM   21  H7  UNL     1       2.371  -0.862  -0.899  1.00  0.00           H  
CONECT    1    2   15   16   17
CONECT    2    3    4    7
CONECT    3   18
CONECT    4    5    5    6
CONECT    7    8   12   19
CONECT    8    9   20   21
CONECT    9   10   10   11
CONECT   12   13   13   14
END
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SMILES for HMDB0303970 ((2R,3S)-2-methylisocitrate)

[H][C@@](CC([O-])=O)(C([O-])=O)[C@@](C)(O)C([O-])=O
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INCHI for HMDB0303970 ((2R,3S)-2-methylisocitrate)

InChI=1S/C7H10O7/c1-7(14,6(12)13)3(5(10)11)2-4(8)9/h3,14H,2H2,1H3,(H,8,9)(H,10,11)(H,12,13)/p-3/t3-,7-/m1/s1
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View in JSmolView Stereo Labels
Synonyms
ValueSource
(1R,2S)-1-Hydroxy-1-methylpropane-1,2,3-tricarboxylateChEBI
(1R,2S)-1-Hydroxy-1-methylpropane-1,2,3-tricarboxylic acidGenerator
(2S,3R)-3-Hydroxybutane-1,2,3-tricarboxylic acidGenerator
(2R,3S)-2-Methylisocitric acidGenerator
Chemical FormulaC7H7O7
Average Molecular Weight203.128
Monoisotopic Molecular Weight203.020823305
IUPAC Name(1R,2S)-1-hydroxy-1-methylpropane-1,2,3-tricarboxylate
Traditional Name(2R,3S)2-methylisocitrate
CAS Registry NumberNot Available
SMILES
[H][C@@](CC([O-])=O)(C([O-])=O)[C@@](C)(O)C([O-])=O
InChI Identifier
InChI=1S/C7H10O7/c1-7(14,6(12)13)3(5(10)11)2-4(8)9/h3,14H,2H2,1H3,(H,8,9)(H,10,11)(H,12,13)/p-3/t3-,7-/m1/s1
InChI KeyHHKPKXCSHMJWCF-WVBDSBKLSA-K
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
  • Tertiary alcohol
  • Carboxylic acid
  • Organic oxygen compound
  • Organic oxide
  • Hydrocarbon derivative
  • Organooxygen compound
  • Carbonyl group
  • Alcohol
  • Organic anion
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Ontology
Physiological effectNot Available
Disposition
Source
ProcessNot Available
RoleNot Available
Physical Properties
StateNot Available
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 LocationsNot Available
Biospecimen LocationsNot Available
Tissue LocationsNot Available
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB030112
KNApSAcK IDNot Available
Chemspider ID19951272
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound23615311
PDB IDNot Available
ChEBI ID57429
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General ReferencesNot Available