Showing metabocard for D-Malic acid (MMDBc0000275)

Record Information
Version1.0
StatusDetected and Quantified
Creation Date2020-10-27 23:48:27 UTC
Update Date2024-10-09 23:26:29 UTC
Metabolite IDMMDBc0000275
Metabolite Identification
Common NameD-Malic acid
DescriptionD-Malic acid is found in herbs and spices. This enantiomer of rare occurrence; reported from fruits and leaves of Hibiscus sabdariffa (roselle) although there are many more isolations of malic acid with no opt. rotn. given and some may be of the R-for
Structure
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for #<Metabolite:0x00007f920faf8270>


  Mrv1652309042000372D          

  9  8  0  0  1  0            999 V2000
    1.9520    1.9520    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9520    1.1270    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.2375    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5230    1.1270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1914    0.7145    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5230    1.9520    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6664    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3809    1.1270    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6664   -0.1105    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  1  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
  2  7  1  0  0  0  0
  7  8  1  0  0  0  0
  7  9  2  0  0  0  0
M  END
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3D MOL for #<Metabolite:0x00007f920faf8270>

HMDB0031518
     RDKit          3D
D-Malic acid
 15 14  0  0  0  0  0  0  0  0999 V2000
    2.0504    0.7596    1.1777 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.8937   -0.0449    0.2252 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0371   -0.5643   -0.3634 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5269   -0.4093   -0.2334 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5027    0.3175    0.6025 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.3496    1.6988    0.4911 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8655   -0.0597    0.2219 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6927    0.8055   -0.1350 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2942   -1.3801    0.2406 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.6754    0.0445   -0.8819 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4150   -0.2139   -1.3055 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3767   -1.4995   -0.0757 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3047    0.0747    1.6749 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7878    2.0657   -0.3069 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1780   -1.5946    0.7012 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
  5  7  1  0
  7  8  2  0
  7  9  1  0
  3 10  1  0
  4 11  1  0
  4 12  1  0
  5 13  1  1
  6 14  1  0
  9 15  1  0
M  END
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3D SDF for #<Metabolite:0x00007f920faf8270>


  Mrv1652309042000372D          

  9  8  0  0  1  0            999 V2000
    1.9520    1.9520    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9520    1.1270    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.2375    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5230    1.1270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1914    0.7145    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5230    1.9520    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6664    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3809    1.1270    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6664   -0.1105    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  1  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
  2  7  1  0  0  0  0
  7  8  1  0  0  0  0
  7  9  2  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0000275

> <DATABASE_NAME>
MIME

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

> <INCHI_IDENTIFIER>
InChI=1S/C4H6O5/c5-2(4(8)9)1-3(6)7/h2,5H,1H2,(H,6,7)(H,8,9)/t2-/m1/s1

> <INCHI_KEY>
BJEPYKJPYRNKOW-UWTATZPHSA-N

> <FORMULA>
C4H6O5

> <MOLECULAR_WEIGHT>
134.0874

> <EXACT_MASS>
134.021523302

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
15

> <JCHEM_AVERAGE_POLARIZABILITY>
10.926494198525464

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2R)-2-hydroxybutanedioic acid

> <ALOGPS_LOGP>
-0.87

> <JCHEM_LOGP>
-1.1136414279999998

> <ALOGPS_LOGS>
0.21

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
5.127730317344291

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.1983571934669475

> <JCHEM_PKA_STRONGEST_BASIC>
-3.913035238851454

> <JCHEM_POLAR_SURFACE_AREA>
94.83000000000001

> <JCHEM_REFRACTIVITY>
24.8752

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.18e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
.+-.-malic acid

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for #<Metabolite:0x00007f920faf8270>

HMDB0031518
     RDKit          3D
D-Malic acid
 15 14  0  0  0  0  0  0  0  0999 V2000
    2.0504    0.7596    1.1777 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.8937   -0.0449    0.2252 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0371   -0.5643   -0.3634 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5269   -0.4093   -0.2334 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5027    0.3175    0.6025 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.3496    1.6988    0.4911 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8655   -0.0597    0.2219 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6927    0.8055   -0.1350 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2942   -1.3801    0.2406 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.6754    0.0445   -0.8819 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4150   -0.2139   -1.3055 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3767   -1.4995   -0.0757 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3047    0.0747    1.6749 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7878    2.0657   -0.3069 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1780   -1.5946    0.7012 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
  5  7  1  0
  7  8  2  0
  7  9  1  0
  3 10  1  0
  4 11  1  0
  4 12  1  0
  5 13  1  1
  6 14  1  0
  9 15  1  0
M  END
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PDB for #<Metabolite:0x00007f920faf8270>

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  O   UNK     0       3.644   3.644   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0       3.644   2.104   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       2.310   1.334   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       0.976   2.104   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0      -0.357   1.334   0.000  0.00  0.00           O+0
HETATM    6  O   UNK     0       0.976   3.644   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0       4.977   1.334   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0       6.311   2.104   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0       4.977  -0.206   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    7                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5    6                                                  
CONECT    5    4                                                            
CONECT    6    4                                                            
CONECT    7    2    8    9                                                  
CONECT    8    7                                                            
CONECT    9    7                                                            
MASTER        0    0    0    0    0    0    0    0    9    0   16    0
END
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3D PDB for #<Metabolite:0x00007f920faf8270>

COMPND    HMDB0031518
HETATM    1  O1  UNL     1       2.050   0.760   1.178  1.00  0.00           O  
HETATM    2  C1  UNL     1       1.894  -0.045   0.225  1.00  0.00           C  
HETATM    3  O2  UNL     1       3.037  -0.564  -0.363  1.00  0.00           O  
HETATM    4  C2  UNL     1       0.527  -0.409  -0.233  1.00  0.00           C  
HETATM    5  C3  UNL     1      -0.503   0.318   0.603  1.00  0.00           C  
HETATM    6  O3  UNL     1      -0.350   1.699   0.491  1.00  0.00           O  
HETATM    7  C4  UNL     1      -1.866  -0.060   0.222  1.00  0.00           C  
HETATM    8  O4  UNL     1      -2.693   0.805  -0.135  1.00  0.00           O  
HETATM    9  O5  UNL     1      -2.294  -1.380   0.241  1.00  0.00           O  
HETATM   10  H1  UNL     1       3.675   0.044  -0.882  1.00  0.00           H  
HETATM   11  H2  UNL     1       0.415  -0.214  -1.305  1.00  0.00           H  
HETATM   12  H3  UNL     1       0.377  -1.499  -0.076  1.00  0.00           H  
HETATM   13  H4  UNL     1      -0.305   0.075   1.675  1.00  0.00           H  
HETATM   14  H5  UNL     1      -0.788   2.066  -0.307  1.00  0.00           H  
HETATM   15  H6  UNL     1      -3.178  -1.595   0.701  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3    4
CONECT    3   10
CONECT    4    5   11   12
CONECT    5    6    7   13
CONECT    6   14
CONECT    7    8    8    9
CONECT    9   15
END
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SMILES for #<Metabolite:0x00007f920faf8270>

O[C@H](CC(O)=O)C(O)=O
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INCHI for #<Metabolite:0x00007f920faf8270>

InChI=1S/C4H6O5/c5-2(4(8)9)1-3(6)7/h2,5H,1H2,(H,6,7)(H,8,9)/t2-/m1/s1
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Synonyms
ValueSource
(+)-D-Malic acidChEBI
(R)-2-Hydroxybutanedioic acidChEBI
2-HYDROXY-succinIC ACIDChEBI
D-MalateKegg
(+)-D-MalateGenerator
(R)-2-HydroxybutanedioateGenerator
2-HYDROXY-succinateGenerator
(R)-MalateHMDB
(R)-Hydroxybutanedioic acidHMDB
D-(+)-Malic acidHMDB
D-Hydroxybutanedioic acidHMDB
Hydroxy-(R)-butanedioic acidHMDB
R-Malic acidHMDB
D-Malic acidChEBI
Molecular FormulaC4H6O5
Average Mass134.0874
Monoisotopic Mass134.021523302
IUPAC Name(2R)-2-hydroxybutanedioic acid
Traditional Name.+-.-malic acid
CAS Registry Number636-61-3
SMILES
O[C@H](CC(O)=O)C(O)=O
InChI Identifier
InChI=1S/C4H6O5/c5-2(4(8)9)1-3(6)7/h2,5H,1H2,(H,6,7)(H,8,9)/t2-/m1/s1
InChI KeyBJEPYKJPYRNKOW-UWTATZPHSA-N