Showing metabocard for Malonic acid (MMDBc0000138)

Record Information
Version1.0
StatusDetected and Quantified
Creation Date2020-10-27 23:37:15 UTC
Update Date2024-09-29 08:11:48 UTC
Metabolite IDMMDBc0000138
Metabolite Identification
Common NameMalonic acid
DescriptionMalonic acid (IUPAC systematic name: propanedioic acid) is a dicarboxylic acid with structure CH2(COOH)2. The ionised form of malonic acid, as well as its esters and salts, are known as malonates. For example, diethyl malonate is malonic acid's ethyl ester. The name originates from Latin malum, meaning apple. Malonic acid is the archetypal example of a competitive inhibitor: it acts against succinate dehydrogenase (complex II) in the respiratory electron transport chain. Malonic acid is found to be associated with malonyl-CoA decarboxylase deficiency, which is an inborn error of metabolism.
Structure
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for #<Metabolite:0x00007f9250da6648>


  Mrv1652309042000052D          

  7  6  0  0  0  0            999 V2000
    2.0479    0.0957    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3332    0.5082    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3332    1.3333    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.6187    0.0957    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0957    0.5082    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8103    0.0957    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0957    1.3333    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  2  0  0  0  0
  2  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  5  7  2  0  0  0  0
M  END
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3D MOL for #<Metabolite:0x00007f9250da6648>

HMDB0000691
     RDKit          3D
Malonic acid
 11 10  0  0  0  0  0  0  0  0999 V2000
    0.7434    1.6322    0.2780 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.0764    0.4389    0.0389 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4163    0.1386   -0.1503 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1037   -0.6719   -0.0517 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2864   -0.2021    0.1718 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2023   -1.0621    0.1182 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6448    1.1045    0.4329 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6976   -0.3940   -0.9816 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1304   -1.1073   -1.0770 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3870   -1.4391    0.7268 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4212    1.5622   -0.0365 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  2  0
  5  7  1  0
  3  8  1  0
  4  9  1  0
  4 10  1  0
  7 11  1  0
M  END
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3D SDF for #<Metabolite:0x00007f9250da6648>


  Mrv1652309042000052D          

  7  6  0  0  0  0            999 V2000
    2.0479    0.0957    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3332    0.5082    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3332    1.3333    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.6187    0.0957    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0957    0.5082    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8103    0.0957    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0957    1.3333    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  2  0  0  0  0
  2  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  5  7  2  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0000138

> <DATABASE_NAME>
MIME

> <SMILES>
OC(=O)CC(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C3H4O4/c4-2(5)1-3(6)7/h1H2,(H,4,5)(H,6,7)

> <INCHI_KEY>
OFOBLEOULBTSOW-UHFFFAOYSA-N

> <FORMULA>
C3H4O4

> <MOLECULAR_WEIGHT>
104.0615

> <EXACT_MASS>
104.010958616

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
11

> <JCHEM_AVERAGE_POLARIZABILITY>
8.127328970673815

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
propanedioic acid

> <ALOGPS_LOGP>
-0.60

> <JCHEM_LOGP>
-0.3311172683333333

> <ALOGPS_LOGS>
0.28

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
5.919487044057661

> <JCHEM_PKA_STRONGEST_ACIDIC>
2.4284239631132736

> <JCHEM_POLAR_SURFACE_AREA>
74.6

> <JCHEM_REFRACTIVITY>
18.9878

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.97e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
malonic acid

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for #<Metabolite:0x00007f9250da6648>

HMDB0000691
     RDKit          3D
Malonic acid
 11 10  0  0  0  0  0  0  0  0999 V2000
    0.7434    1.6322    0.2780 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.0764    0.4389    0.0389 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4163    0.1386   -0.1503 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1037   -0.6719   -0.0517 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2864   -0.2021    0.1718 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2023   -1.0621    0.1182 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6448    1.1045    0.4329 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6976   -0.3940   -0.9816 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1304   -1.1073   -1.0770 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3870   -1.4391    0.7268 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4212    1.5622   -0.0365 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  2  0
  5  7  1  0
  3  8  1  0
  4  9  1  0
  4 10  1  0
  7 11  1  0
M  END
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PDB for #<Metabolite:0x00007f9250da6648>

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       3.823   0.179   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0       2.489   0.949   0.000  0.00  0.00           C+0
HETATM    3  O   UNK     0       2.489   2.489   0.000  0.00  0.00           O+0
HETATM    4  C   UNK     0       1.155   0.179   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -0.179   0.949   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0      -1.513   0.179   0.000  0.00  0.00           O+0
HETATM    7  O   UNK     0      -0.179   2.489   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    4                                                  
CONECT    3    2                                                            
CONECT    4    2    5                                                       
CONECT    5    4    6    7                                                  
CONECT    6    5                                                            
CONECT    7    5                                                            
MASTER        0    0    0    0    0    0    0    0    7    0   12    0
END
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3D PDB for #<Metabolite:0x00007f9250da6648>

COMPND    HMDB0000691
HETATM    1  O1  UNL     1       0.743   1.632   0.278  1.00  0.00           O  
HETATM    2  C1  UNL     1       1.076   0.439   0.039  1.00  0.00           C  
HETATM    3  O2  UNL     1       2.416   0.139  -0.150  1.00  0.00           O  
HETATM    4  C2  UNL     1       0.104  -0.672  -0.052  1.00  0.00           C  
HETATM    5  C3  UNL     1      -1.286  -0.202   0.172  1.00  0.00           C  
HETATM    6  O3  UNL     1      -2.202  -1.062   0.118  1.00  0.00           O  
HETATM    7  O4  UNL     1      -1.645   1.104   0.433  1.00  0.00           O  
HETATM    8  H1  UNL     1       2.698  -0.394  -0.982  1.00  0.00           H  
HETATM    9  H2  UNL     1       0.130  -1.107  -1.077  1.00  0.00           H  
HETATM   10  H3  UNL     1       0.387  -1.439   0.727  1.00  0.00           H  
HETATM   11  H4  UNL     1      -2.421   1.562  -0.037  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3    4
CONECT    3    8
CONECT    4    5    9   10
CONECT    5    6    6    7
CONECT    7   11
END
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SMILES for #<Metabolite:0x00007f9250da6648>

OC(=O)CC(O)=O
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INCHI for #<Metabolite:0x00007f9250da6648>

InChI=1S/C3H4O4/c4-2(5)1-3(6)7/h1H2,(H,4,5)(H,6,7)
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Synonyms
ValueSource
H2MaloChEBI
HOOC-CH2-COOHChEBI
Propanedioic acidChEBI
PropanedioateGenerator
MalonateGenerator
alpha,Omega-dicarboxylic acidHMDB
Carboxyacetic acidHMDB
DicarboxylateHMDB
Dicarboxylic acidHMDB
DicarboxymethaneHMDB
Kyselina malonovaHMDB
Malonate dicarboxylic acidHMDB
Metahnedicarboxylic acidHMDB
Methanedicarbonic acidHMDB
Methanedicarboxylic acidHMDB
Propanedioic acid dithallium saltHMDB
Propanediolic acidHMDB
Thallium malonateHMDB
Malonic acid, 2-(14)C-labeledHMDB
Malonic acid, monocalcium saltHMDB
Malonic acid, 1,3-(14)C2-labeledHMDB
Malonic acid, diammonium saltHMDB
Malonic acid, disodium saltHMDB
Malonic acid, dithallium saltHMDB
Malonic acid, dipotassium saltHMDB
Malonic acid, disodium salt, 1-(14)C-labeledHMDB
Malonic acid, monosodium saltHMDB
Malonic acid, potassium saltHMDB
Malonic acid, sodium saltHMDB
Thallous malonateHMDB
Dithallium malonateHMDB
Monosodium malonateHMDB
Malonic acidGenerator
Molecular FormulaC3H4O4
Average Mass104.0615
Monoisotopic Mass104.010958616
IUPAC Namepropanedioic acid
Traditional Namemalonic acid
CAS Registry Number141-82-2
SMILES
OC(=O)CC(O)=O
InChI Identifier
InChI=1S/C3H4O4/c4-2(5)1-3(6)7/h1H2,(H,4,5)(H,6,7)
InChI KeyOFOBLEOULBTSOW-UHFFFAOYSA-N