Showing NP-Card for Malonic acid (NP0001303)

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Record Information
Version2.0
Created at2005-11-16 15:48:42 UTC
Updated at2025-02-11 15:41:40 UTC
NP-MRD IDNP0001303
Secondary Accession NumbersNone
Natural Product 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
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for NP0001303 (Malonic acid)

  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 NP0001303 (Malonic acid)

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 NP0001303 (Malonic acid)

  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>
NP0001303

> <DATABASE_NAME>
NP-MRD

> <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 NP0001303 (Malonic acid)

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 NP0001303 (Malonic acid)

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 NP0001303 (Malonic acid)

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 NP0001303 (Malonic acid)

OC(=O)CC(O)=O
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INCHI for NP0001303 (Malonic acid)

InChI=1S/C3H4O4/c4-2(5)1-3(6)7/h1H2,(H,4,5)(H,6,7)
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View in JSmol
Synonyms
Chemical FormulaC3H4O4
Average Mass104.0615 Da
Monoisotopic Mass104.01096 Da
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
Experimental Spectra
Spectrum TypeDescriptionDepositor EmailDepositor OrganizationDepositorDeposition DateView
1D NMR1H NMR Spectrum (1D, 700 MHz, H2O, simulated)Ahselim2022-02-14View Spectrum
1D NMR1H NMR Spectrum (1D, 500 MHz, H2O, simulated)Varshavi.d262021-10-29View 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
Spectrum TypeDescriptionDepositor EmailDepositor OrganizationDepositorDeposition DateView
1D NMR1H NMR Spectrum (1D, 500 MHz, H2O, simulated)varshavi.d26@gmail.comNot AvailableNot Available2021-08-08View Spectrum
1D NMR13C NMR Spectrum (1D, 400 MHz, H2O, simulated)v.dorna83@yahoo.comNot AvailableNot Available2021-08-07View Spectrum
Species
Species of Origin
Species Where Detected
Species NameSourceReference
Homo sapiens (Serum)KNApSAcK Database
Homo sapiens (Urine)KNApSAcK Database
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
  • 1,3-dicarbonyl compound
  • 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 Point135 °CNot Available
Boiling Point264.00 °C. @ 760.00 mm HgThe Good Scents Company Information System
Water Solubility763 mg/mLNot Available
LogP-0.81Hansch CH, Leo A and Hoekman DH. "Exploring QSAR: Hydrophobic, Electronic, and Steric Constraints. Volume 1" ACS Publications (1995).
Predicted Properties
PropertyValueSource
Water Solubility197 g/LALOGPS
logP-0.6ALOGPS
logP-0.33ChemAxon
logS0.28ALOGPS
pKa (Strongest Acidic)2.43ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count4ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area74.6 ŲChemAxon
Rotatable Bond Count2ChemAxon
Refractivity18.99 m³·mol⁻¹ChemAxon
Polarizability8.13 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDHMDB0000691
DrugBank IDDB02175
Phenol Explorer Compound IDNot Available
FoodDB IDFDB008117
KNApSAcK IDC00001193
Chemspider ID844
KEGG Compound IDC04025
BioCyc IDMALONATE
BiGG IDNot Available
Wikipedia LinkMalonic_acid
METLIN ID3237
PubChem Compound867
PDB IDNot Available
ChEBI ID30794
Good Scents IDrw1030881
References
General References
  1. Yano S, Sweetman L, Thorburn DR, Mofidi S, Williams JC: A new case of malonyl coenzyme A decarboxylase deficiency presenting with cardiomyopathy. Eur J Pediatr. 1997 May;156(5):382-3. [PubMed:9177981 ]
  2. Belgorodsky B, Fadeev L, Ittah V, Benyamini H, Zelner S, Huppert D, Kotlyar AB, Gozin M: Formation and characterization of stable human serum albumin-tris-malonic acid [C60]fullerene complex. Bioconjug Chem. 2005 Sep-Oct;16(5):1058-62. [PubMed:16173780 ]
  3. Buyukgebiz B, Jakobs C, Scholte HR, Huijmans JG, Kleijer WJ: Fatal neonatal malonic aciduria. J Inherit Metab Dis. 1998 Feb;21(1):76-7. [PubMed:9501274 ]
  4. Haan EA, Scholem RD, Croll HB, Brown GK: Malonyl coenzyme A decarboxylase deficiency. Clinical and biochemical findings in a second child with a more severe enzyme defect. Eur J Pediatr. 1986 Apr;144(6):567-70. [PubMed:3709568 ]
  5. Pollitt RJ, Fowler B, Sardharwalla IB, Edwards MA, Gray RG: Increased excretion of propan-1,3-diol and 3-hydroxypropionic acid apparently caused by abnormal bacterial metabolism in the gut. Clin Chim Acta. 1987 Nov 16;169(2-3):151-7. [PubMed:3427776 ]
  6. Honda A, Yamashita K, Ikegami T, Hara T, Miyazaki T, Hirayama T, Numazawa M, Matsuzaki Y: Highly sensitive quantification of serum malonate, a possible marker for de novo lipogenesis, by LC-ESI-MS/MS. J Lipid Res. 2009 Oct;50(10):2124-30. doi: 10.1194/jlr.D800054-JLR200. Epub 2009 Apr 29. [PubMed:19403942 ]
  7. Mitra T, Sailakshmi G, Gnanamani A, Mandal AB: Preparation and characterization of malonic acid cross-linked chitosan and collagen 3D scaffolds: an approach on non-covalent interactions. J Mater Sci Mater Med. 2012 May;23(5):1309-21. doi: 10.1007/s10856-012-4586-6. Epub 2012 Feb 26. [PubMed:22367159 ]