Showing metabocard for malonate (MMDBc0054554)

Microbial
Pharmaceutical
Xenobiotic
Record Information
Version2.0
StatusDetected and Quantified
Creation Date2022-06-05 23:17:37 UTC
Update Date2025-10-07 16:08:34 UTC
Metabolite IDMMDBc0054554
Metabolite Identification
Common Namemalonate
DescriptionMalonate is a dicarboxylic acid and a key metabolite in various biochemical pathways. Its chemical structure features two carboxyl groups (-COOH) attached to a three-carbon chain, making it a crucial intermediate in the citric acid cycle and fatty acid synthesis. Malonate acts as an inhibitor of succinate dehydrogenase, thereby influencing metabolic flux in cellular respiration. Additionally, malonate is utilized in synthetic organic chemistry, where it serves as a nucleophile in reactions such as Mo-catalyzed allylic alkylation, which couples malonate with allylic electrophiles (PMID:40968623 ). Recent studies have also explored the structural properties of malonate derivatives, such as L-phenylalanine L-phenylalaninium malonate, revealing unique hydrogen-bonded structures and optoelectronic characteristics (PMID:40975917 ). Furthermore, malonate's assimilation pathway has been engineered to enhance malonyl-CoA biosynthesis, significantly increasing production yields in microbial systems (PMID:40956660 ). This versatility in both biological and synthetic contexts underscores malonate's importance in chemistry and its potential applications in material science (PMID:41042218 ).
Structure
MOLSDFPDBSMILESInChI

MOL for #<Metabolite:0x00007faddc70ccb8>


  Mrv0541 02231216022D          

  7  6  0  0  0  0            999 V2000
    1.2375    2.1434    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    0.8250    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    1.4289    0.0000 O   0  0  0  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
    0.8250    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375   -0.7145    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    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  CHG  2   1  -1   6  -1
M  END
Download

3D MOL for #<Metabolite:0x00007faddc70ccb8>

Download
3D SDF for #<Metabolite:0x00007faddc70ccb8>

  Mrv0541 02231216022D          

  7  6  0  0  0  0            999 V2000
    1.2375    2.1434    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    0.8250    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    1.4289    0.0000 O   0  0  0  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
    0.8250    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375   -0.7145    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    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  CHG  2   1  -1   6  -1
M  END
> <DATABASE_ID>
MMDBc0054554

> <DATABASE_NAME>
MIME

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

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

> <INCHI_KEY>
OFOBLEOULBTSOW-UHFFFAOYSA-L

> <FORMULA>
C3H2O4

> <MOLECULAR_WEIGHT>
102.0456

> <EXACT_MASS>
101.995308552

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_AVERAGE_POLARIZABILITY>
7.334352879082738

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
-2

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
propanedioate

> <ALOGPS_LOGP>
-0.45

> <JCHEM_LOGP>
-0.3311172683333333

> <ALOGPS_LOGS>
0.53

> <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>
80.25999999999999

> <JCHEM_REFRACTIVITY>
40.662000000000006

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
4.67e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
malonate

> <JCHEM_VEBER_RULE>
0

$$$$

Download
3D-SDF for #<Metabolite:0x00007faddc70ccb8>
Download
PDB for #<Metabolite:0x00007faddc70ccb8>
HEADER    PROTEIN                                 23-FEB-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   23-FEB-12         0                                  
HETATM    1  O   UNK     0       2.310   4.001   0.000  0.00  0.00           O-1
HETATM    2  C   UNK     0       1.540   2.667   0.000  0.00  0.00           C+0
HETATM    3  O   UNK     0       0.000   2.667   0.000  0.00  0.00           O+0
HETATM    4  C   UNK     0       2.310   1.334   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       1.540   0.000   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0       2.310  -1.334   0.000  0.00  0.00           O-1
HETATM    7  O   UNK     0       0.000   0.000   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

Download
3D PDB for #<Metabolite:0x00007faddc70ccb8>
Download
SMILES for #<Metabolite:0x00007faddc70ccb8>
[O-]C(=O)CC([O-])=O
Download
INCHI for #<Metabolite:0x00007faddc70ccb8>
InChI=1S/C3H4O4/c4-2(5)1-3(6)7/h1H2,(H,4,5)(H,6,7)/p-2
Download
Synonyms
ValueSource
MaloChEBI
MalonateChEBI
Malonic acid, ion(2-)ChEBI
(-)OOC-CH2-COO(-)ChEBI
Propanedioic acid, ion(2-)ChEBI
Malonic acidGenerator
Malonate, ion(2-)Generator
Propanedioate, ion(2-)Generator
Malonic acid ionGenerator
Malonic acid, monocalcium saltMeSH
Thallium malonateMeSH
Malonic acid, disodium salt, 1-(14)C-labeledMeSH
Malonic acid, potassium saltMeSH
Malonic acid, sodium saltMeSH
Thallous malonateMeSH
Malonic acid, 1,3-(14)C2-labeledMeSH
Malonic acid, 2-(14)C-labeledMeSH
Malonic acid, diammonium saltMeSH
Malonic acid, dipotassium saltMeSH
Malonic acid, disodium saltMeSH
Malonic acid, dithallium saltMeSH
Malonic acid, monosodium saltMeSH
Dithallium malonateMeSH
Monosodium malonateMeSH
MALONATE ionChEBI
Malonic acid(2-)Generator
Molecular FormulaC3H2O4
Average Mass102.0456
Monoisotopic Mass101.995308552
IUPAC Namepropanedioate
Traditional Namemalonate
CAS Registry NumberNot Available
SMILES
[O-]C(=O)CC([O-])=O
InChI Identifier
InChI=1S/C3H4O4/c4-2(5)1-3(6)7/h1H2,(H,4,5)(H,6,7)/p-2
InChI KeyOFOBLEOULBTSOW-UHFFFAOYSA-L