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Showing NP-Card for Dimethylmalonic acid (NP0001272)

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Record Information
Version2.0
Created at2006-05-22 14:17:31 UTC
Updated at2021-10-07 20:40:34 UTC
NP-MRD IDNP0001272
Secondary Accession NumbersNone
Natural Product Identification
Common NameDimethylmalonic acid
DescriptionDimethylmalonic acid is a dicarboxylic acid that is malonic acid in which both methylene hydrogens have been replaced by methyl groups. It has a role as a fatty acid synthesis inhibitor. Dimethylmalonic acid, also known as 2,2-dimethylmalonate or propanedioate, belongs to the class of organic compounds known as dicarboxylic acids and derivatives. These are organic compounds containing exactly two carboxylic acid groups. Dimethylmalonic acid is a very hydrophobic molecule, practically insoluble in water, and relatively neutral.
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for NP0001272 (Dimethylmalonic acid)


  Mrv1652305271900102D          

  9  8  0  0  0  0            999 V2000
   14.8255  -10.8812    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.5400  -10.4687    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.2545  -10.8812    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   15.5400   -9.6437    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   14.1110  -10.4687    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.3966  -10.8812    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   14.8255  -11.7062    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.8255  -10.0562    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.1110   -9.6437    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  2  4  2  0  0  0  0
  1  5  1  0  0  0  0
  5  6  2  0  0  0  0
  1  7  1  0  0  0  0
  1  8  1  0  0  0  0
  5  9  1  0  0  0  0
M  END
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3D MOL for NP0001272 (Dimethylmalonic acid)

HMDB0002001
     RDKit          3D
Dimethylmalonic acid
 17 16  0  0  0  0  0  0  0  0999 V2000
    0.1648    1.0906   -0.9005 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0220   -0.1090    0.0021 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1528   -1.4122   -0.7395 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0470   -0.0483    1.0349 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7161    0.0257    2.2290 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.3778   -0.0747    0.6582 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3702   -0.0852    0.5923 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1937   -1.0167    0.4027 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8234    0.9687    1.3987 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1996    0.9110   -1.9319 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1953    1.4839   -0.8935 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4763    1.9090   -0.4851 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0065   -2.2232    0.0054 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1622   -1.4850   -1.2136 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6560   -1.4848   -1.4834 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7349    0.3618   -0.1647 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8031    1.1885    1.4890 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  2  4  1  0
  4  5  2  0
  4  6  1  0
  2  7  1  0
  7  8  2  0
  7  9  1  0
  1 10  1  0
  1 11  1  0
  1 12  1  0
  3 13  1  0
  3 14  1  0
  3 15  1  0
  6 16  1  0
  9 17  1  0
M  END
Download

3D SDF for NP0001272 (Dimethylmalonic acid)


  Mrv1652305271900102D          

  9  8  0  0  0  0            999 V2000
   14.8255  -10.8812    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.5400  -10.4687    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.2545  -10.8812    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   15.5400   -9.6437    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   14.1110  -10.4687    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.3966  -10.8812    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   14.8255  -11.7062    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.8255  -10.0562    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.1110   -9.6437    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  2  4  2  0  0  0  0
  1  5  1  0  0  0  0
  5  6  2  0  0  0  0
  1  7  1  0  0  0  0
  1  8  1  0  0  0  0
  5  9  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0001272

> <DATABASE_NAME>
NP-MRD

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

> <INCHI_IDENTIFIER>
InChI=1S/C5H8O4/c1-5(2,3(6)7)4(8)9/h1-2H3,(H,6,7)(H,8,9)

> <INCHI_KEY>
OREAFAJWWJHCOT-UHFFFAOYSA-N

> <FORMULA>
C5H8O4

> <MOLECULAR_WEIGHT>
132.1146

> <EXACT_MASS>
132.042258744

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
17

> <JCHEM_AVERAGE_POLARIZABILITY>
11.864207570757447

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
dimethylpropanedioic acid

> <ALOGPS_LOGP>
0.22

> <JCHEM_LOGP>
0.7678833120000002

> <ALOGPS_LOGS>
0.09

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
6.502721330205223

> <JCHEM_PKA_STRONGEST_ACIDIC>
2.4934249814742135

> <JCHEM_POLAR_SURFACE_AREA>
74.6

> <JCHEM_REFRACTIVITY>
28.063299999999998

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.61e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
dimethylmalonic acid

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for NP0001272 (Dimethylmalonic acid)

HMDB0002001
     RDKit          3D
Dimethylmalonic acid
 17 16  0  0  0  0  0  0  0  0999 V2000
    0.1648    1.0906   -0.9005 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0220   -0.1090    0.0021 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1528   -1.4122   -0.7395 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0470   -0.0483    1.0349 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7161    0.0257    2.2290 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.3778   -0.0747    0.6582 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3702   -0.0852    0.5923 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1937   -1.0167    0.4027 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8234    0.9687    1.3987 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1996    0.9110   -1.9319 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1953    1.4839   -0.8935 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4763    1.9090   -0.4851 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0065   -2.2232    0.0054 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1622   -1.4850   -1.2136 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6560   -1.4848   -1.4834 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7349    0.3618   -0.1647 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8031    1.1885    1.4890 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  2  4  1  0
  4  5  2  0
  4  6  1  0
  2  7  1  0
  7  8  2  0
  7  9  1  0
  1 10  1  0
  1 11  1  0
  1 12  1  0
  3 13  1  0
  3 14  1  0
  3 15  1  0
  6 16  1  0
  9 17  1  0
M  END
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PDB for NP0001272 (Dimethylmalonic acid)

HEADER    PROTEIN                                 27-MAY-19   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   27-MAY-19         0                                  
HETATM    1  C   UNK     0      27.674 -20.312   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      29.008 -19.542   0.000  0.00  0.00           C+0
HETATM    3  O   UNK     0      30.342 -20.312   0.000  0.00  0.00           O+0
HETATM    4  O   UNK     0      29.008 -18.002   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0      26.341 -19.542   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0      25.007 -20.312   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0      27.674 -21.852   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      27.674 -18.772   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0      26.341 -18.002   0.000  0.00  0.00           O+0
CONECT    1    2    5    7    8                                             
CONECT    2    1    3    4                                                  
CONECT    3    2                                                            
CONECT    4    2                                                            
CONECT    5    1    6    9                                                  
CONECT    6    5                                                            
CONECT    7    1                                                            
CONECT    8    1                                                            
CONECT    9    5                                                            
MASTER        0    0    0    0    0    0    0    0    9    0   16    0
END
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3D PDB for NP0001272 (Dimethylmalonic acid)

COMPND    HMDB0002001
HETATM    1  C1  UNL     1       0.165   1.091  -0.900  1.00  0.00           C  
HETATM    2  C2  UNL     1      -0.022  -0.109   0.002  1.00  0.00           C  
HETATM    3  C3  UNL     1       0.153  -1.412  -0.740  1.00  0.00           C  
HETATM    4  C4  UNL     1       1.047  -0.048   1.035  1.00  0.00           C  
HETATM    5  O1  UNL     1       0.716   0.026   2.229  1.00  0.00           O  
HETATM    6  O2  UNL     1       2.378  -0.075   0.658  1.00  0.00           O  
HETATM    7  C5  UNL     1      -1.370  -0.085   0.592  1.00  0.00           C  
HETATM    8  O3  UNL     1      -2.194  -1.017   0.403  1.00  0.00           O  
HETATM    9  O4  UNL     1      -1.823   0.969   1.399  1.00  0.00           O  
HETATM   10  H1  UNL     1      -0.200   0.911  -1.932  1.00  0.00           H  
HETATM   11  H2  UNL     1       1.195   1.484  -0.893  1.00  0.00           H  
HETATM   12  H3  UNL     1      -0.476   1.909  -0.485  1.00  0.00           H  
HETATM   13  H4  UNL     1      -0.006  -2.223   0.005  1.00  0.00           H  
HETATM   14  H5  UNL     1       1.162  -1.485  -1.214  1.00  0.00           H  
HETATM   15  H6  UNL     1      -0.656  -1.485  -1.483  1.00  0.00           H  
HETATM   16  H7  UNL     1       2.735   0.362  -0.165  1.00  0.00           H  
HETATM   17  H8  UNL     1      -2.803   1.189   1.489  1.00  0.00           H  
CONECT    1    2   10   11   12
CONECT    2    3    4    7
CONECT    3   13   14   15
CONECT    4    5    5    6
CONECT    6   16
CONECT    7    8    8    9
CONECT    9   17
END
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SMILES for NP0001272 (Dimethylmalonic acid)

CC(C)(C(O)=O)C(O)=O
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INCHI for NP0001272 (Dimethylmalonic acid)

InChI=1S/C5H8O4/c1-5(2,3(6)7)4(8)9/h1-2H3,(H,6,7)(H,8,9)
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View in JSmol
Synonyms
ValueSource
2,2-Dimethylmalonic acidChEBI
2,2-DimethylmalonateGenerator
DimethylmalonateGenerator
2,2-PropanedicarboxylateHMDB
2,2-Propanedicarboxylic acidHMDB
PropanedioateHMDB
Propanedioic acidHMDB
Propanedioic acid dimethylHMDB
Hydrogen 2,2-dimethylmalonateHMDB
Dimethyl-malonateHMDB
Chemical FormulaC5H8O4
Average Mass132.1146 Da
Monoisotopic Mass132.04226 Da
IUPAC Namedimethylpropanedioic acid
Traditional Namedimethylmalonic acid
CAS Registry Number595-46-0
SMILES
CC(C)(C(O)=O)C(O)=O
InChI Identifier
InChI=1S/C5H8O4/c1-5(2,3(6)7)4(8)9/h1-2H3,(H,6,7)(H,8,9)
InChI KeyOREAFAJWWJHCOT-UHFFFAOYSA-N
Experimental Spectra
Spectrum TypeDescriptionDepositor EmailDepositor OrganizationDepositorDeposition DateView
1D NMR1H NMR Spectrum (1D, 500 MHz, H2O, experimental)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
2D NMR[1H, 13C]-HSQC NMR Spectrum (2D, 600 MHz, H2O, experimental)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
Predicted Spectra
Not Available
Chemical Shift Submissions
Not Available
Species
Species of Origin
Species NameSourceReference
Ananas comosusLOTUS Database
Anas platyrhynchosFooDB
AnatidaeFooDB
Anser anserFooDB
Bison bisonFooDB
Bos taurusFooDB
Bos taurus X Bison bisonFooDB
Bubalus bubalisFooDB
Capra aegagrus hircusFooDB
CervidaeFooDB
Cervus canadensisFooDB
Citrus sinensisKNApSAcK Database
Citrus X sinensis (L.) Osbeck (pro. sp.)Plant
ColumbaFooDB
ColumbidaeFooDB
Dromaius novaehollandiaeFooDB
Equus caballusFooDB
Gallus gallusFooDB
Lagopus mutaFooDB
LeporidaeFooDB
Lepus timidusFooDB
Melanitta fuscaFooDB
Meleagris gallopavoFooDB
Numida meleagrisFooDB
OdocoileusFooDB
OryctolagusFooDB
Ovis ariesFooDB
PhasianidaeFooDB
Phasianus colchicusFooDB
Struthio camelusFooDB
Sus scrofaFooDB
Sus scrofa domesticaFooDB
Chemical Taxonomy
Description Belongs to the class of organic compounds known as dicarboxylic acids and derivatives. These are organic compounds containing exactly two carboxylic acid groups.
KingdomOrganic compounds
Super ClassOrganic acids and derivatives
ClassCarboxylic acids and derivatives
Sub ClassDicarboxylic acids and derivatives
Direct ParentDicarboxylic acids and derivatives
Alternative Parents
Substituents
  • Dicarboxylic acid or derivatives
  • Carboxylic acid
  • Organic oxygen compound
  • Organic oxide
  • Hydrocarbon derivative
  • Organooxygen compound
  • Carbonyl group
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Physical Properties
StateSolid
Experimental Properties
PropertyValueReference
Melting Point192 °CNot Available
Boiling PointNot AvailableNot Available
Water Solubility90 mg/mL at 13 °CNot Available
LogP0.39Hansch CH, Leo A and Hoekman DH. "Exploring QSAR: Hydrophobic, Electronic, and Steric Constraints. Volume 1" ACS Publications (1995).
Predicted Properties
PropertyValueSource
Water Solubility161 g/LALOGPS
logP0.22ALOGPS
logP0.77ChemAxon
logS0.09ALOGPS
pKa (Strongest Acidic)2.49ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count4ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area74.6 ŲChemAxon
Rotatable Bond Count2ChemAxon
Refractivity28.06 m³·mol⁻¹ChemAxon
Polarizability11.86 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDHMDB0002001
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDFDB022787
KNApSAcK IDC00053114
Chemspider ID11195
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN ID6425
PubChem Compound11686
PDB IDNot Available
ChEBI ID111517
Good Scents IDNot Available
References
General References
  1. Kniemeyer O, Probian C, Rossello-Mora R, Harder J: Anaerobic mineralization of quaternary carbon atoms: isolation of denitrifying bacteria on dimethylmalonate. Appl Environ Microbiol. 1999 Aug;65(8):3319-24. doi: 10.1128/AEM.65.8.3319-3324.1999. [PubMed:10427013 ]
  2. Izydore RA, Hall IH: Hypolipidemic activity of aliphatic dicarboxylic acids in rodents. Acta Pharm Nord. 1991;3(3):141-6. [PubMed:1793508 ]
  3. Yamazaki N, Demizu Y, Sato Y, Doi M, Kurihara M: Helical foldamer containing a combination of cyclopentane-1,2-diamine and 2,2-dimethylmalonic acid. J Org Chem. 2013 Oct 4;78(19):9991-4. doi: 10.1021/jo401505b. Epub 2013 Sep 17. [PubMed:23957650 ]