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Showing NP-Card for Methylmalonic acid (NP0000555)

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Record Information
Version2.0
Created at2005-11-16 15:48:42 UTC
Updated at2020-11-24 22:16:25 UTC
NP-MRD IDNP0000555
Secondary Accession NumbersNone
Natural Product Identification
Common NameMethylmalonic acid
DescriptionMethylmalonic acid is a malonic acid derivative, which is a vital intermediate in the metabolism of fat and protein. In particular, the coenzyme A-linked form of methylmalonic acid, methylmalonyl-CoA, is converted into succinyl-CoA by methylmalonyl-CoA mutase in a reaction that requires vitamin B12 as a cofactor. In this way, methylmalonic acid enters the Krebs cycle and is thus part of one of the anaplerotic reactions. Abnormalities in methylmalonic acid metabolism lead to methylmalonic aciduria. This inborn error of metabolism is attributed to a block in the enzymatic conversion of methylmalonyl CoA to succinyl CoA. Methylmalonic acid is also found to be associated with other inborn errors of metabolism, including cobalamin deficiency, cobalamin malabsorption, malonyl-CoA decarboxylase deficiency, and transcobalamin II deficiency. When present in sufficiently high levels, methylmalonic acid can act as an acidogen and a metabotoxin. An acidogen is an acidic compound that induces acidosis, which has multiple adverse effects on many organ systems. A metabotoxin is an endogenously produced metabolite that causes adverse health effects at chronically high levels. Chronically high levels of methylmalonic acid are associated with at least 5 inborn errors of metabolism, including Malonyl CoA decarboxylase deficiency, Malonic Aciduria, Methylmalonate Semialdehyde Dehydrogenase Deficiency, Methylmalonic Aciduria and Methylmalonic Aciduria Due to Cobalamin-Related Disorders. Methylmalonic acid is an organic acid and abnormally high levels of organic acids in the blood (organic acidemia), urine (organic aciduria), the brain, and other tissues lead to general metabolic acidosis. Acidosis typically occurs when arterial pH falls below 7.35. In infants with acidosis, the initial symptoms include poor feeding, vomiting, loss of appetite, weak muscle tone (hypotonia), and lack of energy (lethargy). These can progress to heart abnormalities, kidney abnormalities, liver damage, seizures, coma, and possibly death. These are also the characteristic symptoms of the untreated IEMs mentioned above. Many affected children with organic acidemias experience intellectual disability or delayed development. In adults, acidosis or acidemia is characterized by headaches, confusion, feeling tired, tremors, sleepiness, and seizures.
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for NP0000555 (Methylmalonic acid)


  Mrv1652305271900212D          

  8  7  0  0  0  0            999 V2000
    2.0625    0.7145    0.0000 C   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    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375    2.1434    0.0000 O   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
    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  0  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  1  0  0  0  0
  3  4  2  0  0  0  0
  3  5  1  0  0  0  0
  2  6  1  0  0  0  0
  6  7  2  0  0  0  0
  6  8  1  0  0  0  0
M  END
Download

3D MOL for NP0000555 (Methylmalonic acid)

HMDB0000202
     RDKit          3D
Methylmalonic acid
 14 13  0  0  0  0  0  0  0  0999 V2000
   -0.0713   -0.4912    1.2791 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1048   -0.3766   -0.2320 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9010    0.8030   -0.5919 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3350    1.7138   -1.2495 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2207    0.9632   -0.2511 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2455   -0.3645   -0.8307 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5790   -1.2719   -1.6650 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1941    0.5808   -0.5449 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1102    0.4838    1.7864 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9342   -1.1118    1.6506 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8573   -1.0216    1.5594 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6628   -1.2733   -0.5937 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9927    0.4363   -0.6617 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4569    0.9300    0.3448 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  0
  3  5  1  0
  2  6  1  0
  6  7  2  0
  6  8  1  0
  1  9  1  0
  1 10  1  0
  1 11  1  0
  2 12  1  0
  5 13  1  0
  8 14  1  0
M  END
Download

3D SDF for NP0000555 (Methylmalonic acid)


  Mrv1652305271900212D          

  8  7  0  0  0  0            999 V2000
    2.0625    0.7145    0.0000 C   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    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375    2.1434    0.0000 O   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
    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  0  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  1  0  0  0  0
  3  4  2  0  0  0  0
  3  5  1  0  0  0  0
  2  6  1  0  0  0  0
  6  7  2  0  0  0  0
  6  8  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0000555

> <DATABASE_NAME>
NP-MRD

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

> <INCHI_IDENTIFIER>
InChI=1S/C4H6O4/c1-2(3(5)6)4(7)8/h2H,1H3,(H,5,6)(H,7,8)

> <INCHI_KEY>
ZIYVHBGGAOATLY-UHFFFAOYSA-N

> <FORMULA>
C4H6O4

> <MOLECULAR_WEIGHT>
118.088

> <EXACT_MASS>
118.02660868

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
14

> <JCHEM_AVERAGE_POLARIZABILITY>
10.057853065917067

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2-methylpropanedioic acid

> <ALOGPS_LOGP>
0.17

> <JCHEM_LOGP>
0.21186901000000008

> <ALOGPS_LOGS>
0.10

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
6.256772105384455

> <JCHEM_PKA_STRONGEST_ACIDIC>
2.4752703991264853

> <JCHEM_POLAR_SURFACE_AREA>
74.6

> <JCHEM_REFRACTIVITY>
23.5623

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.49e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
methylmalonic acid

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for NP0000555 (Methylmalonic acid)

HMDB0000202
     RDKit          3D
Methylmalonic acid
 14 13  0  0  0  0  0  0  0  0999 V2000
   -0.0713   -0.4912    1.2791 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1048   -0.3766   -0.2320 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9010    0.8030   -0.5919 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3350    1.7138   -1.2495 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2207    0.9632   -0.2511 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2455   -0.3645   -0.8307 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5790   -1.2719   -1.6650 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1941    0.5808   -0.5449 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1102    0.4838    1.7864 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9342   -1.1118    1.6506 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8573   -1.0216    1.5594 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6628   -1.2733   -0.5937 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9927    0.4363   -0.6617 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4569    0.9300    0.3448 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  0
  3  5  1  0
  2  6  1  0
  6  7  2  0
  6  8  1  0
  1  9  1  0
  1 10  1  0
  1 11  1  0
  2 12  1  0
  5 13  1  0
  8 14  1  0
M  END
Download

PDB for NP0000555 (Methylmalonic 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       3.850   1.334   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       2.310   1.334   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       1.540   2.667   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0       2.310   4.001   0.000  0.00  0.00           O+0
HETATM    5  O   UNK     0       0.000   2.667   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0       1.540   0.000   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       2.310  -1.334   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    6                                                  
CONECT    3    2    4    5                                                  
CONECT    4    3                                                            
CONECT    5    3                                                            
CONECT    6    2    7    8                                                  
CONECT    7    6                                                            
CONECT    8    6                                                            
MASTER        0    0    0    0    0    0    0    0    8    0   14    0
END
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3D PDB for NP0000555 (Methylmalonic acid)

COMPND    HMDB0000202
HETATM    1  C1  UNL     1      -0.071  -0.491   1.279  1.00  0.00           C  
HETATM    2  C2  UNL     1      -0.105  -0.377  -0.232  1.00  0.00           C  
HETATM    3  C3  UNL     1      -0.901   0.803  -0.592  1.00  0.00           C  
HETATM    4  O1  UNL     1      -0.335   1.714  -1.249  1.00  0.00           O  
HETATM    5  O2  UNL     1      -2.221   0.963  -0.251  1.00  0.00           O  
HETATM    6  C4  UNL     1       1.246  -0.364  -0.831  1.00  0.00           C  
HETATM    7  O3  UNL     1       1.579  -1.272  -1.665  1.00  0.00           O  
HETATM    8  O4  UNL     1       2.194   0.581  -0.545  1.00  0.00           O  
HETATM    9  H1  UNL     1      -0.110   0.484   1.786  1.00  0.00           H  
HETATM   10  H2  UNL     1      -0.934  -1.112   1.651  1.00  0.00           H  
HETATM   11  H3  UNL     1       0.857  -1.022   1.559  1.00  0.00           H  
HETATM   12  H4  UNL     1      -0.663  -1.273  -0.594  1.00  0.00           H  
HETATM   13  H5  UNL     1      -2.993   0.436  -0.662  1.00  0.00           H  
HETATM   14  H6  UNL     1       2.457   0.930   0.345  1.00  0.00           H  
CONECT    1    2    9   10   11
CONECT    2    3    6   12
CONECT    3    4    4    5
CONECT    5   13
CONECT    6    7    7    8
CONECT    8   14
END
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SMILES for NP0000555 (Methylmalonic acid)

CC(C(O)=O)C(O)=O
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INCHI for NP0000555 (Methylmalonic acid)

InChI=1S/C4H6O4/c1-2(3(5)6)4(7)8/h2H,1H3,(H,5,6)(H,7,8)
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View in JSmol
Synonyms
ValueSource
1,1-Ethanedicarboxylic acidChEBI
2-Methylmalonic acidChEBI
alpha-Methylmalonic acidChEBI
Isosuccinic acidChEBI
1,1-EthanedicarboxylateGenerator
2-MethylmalonateGenerator
a-MethylmalonateGenerator
a-Methylmalonic acidGenerator
alpha-MethylmalonateGenerator
Α-methylmalonateGenerator
Α-methylmalonic acidGenerator
IsosuccinateGenerator
MethylmalonateGenerator
Methyl-malonateHMDB
Methyl-malonic acidHMDB
Methyl-propanedioateHMDB
Methyl-propanedioic acidHMDB
MethylpropanedioateHMDB
Methylpropanedioic acidHMDB
Acid, methylmalonicHMDB
Methylmalonic acidKEGG
Chemical FormulaC4H6O4
Average Mass118.0880 Da
Monoisotopic Mass118.02661 Da
IUPAC Name2-methylpropanedioic acid
Traditional Namemethylmalonic acid
CAS Registry Number516-05-2
SMILES
CC(C(O)=O)C(O)=O
InChI Identifier
InChI=1S/C4H6O4/c1-2(3(5)6)4(7)8/h2H,1H3,(H,5,6)(H,7,8)
InChI KeyZIYVHBGGAOATLY-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
Spectrum TypeDescriptionDepositor EmailDepositor OrganizationDepositorDeposition DateView
1D NMR13C NMR Spectrum (1D, 400 MHz, H2O, simulated)varshavi.d26@gmail.comNot AvailableNot Available2021-08-02View Spectrum
Species
Species of Origin
Species NameSourceReference
Anas platyrhynchosFooDB
AnatidaeFooDB
Anser anserFooDB
Arabidopsis thalianaLOTUS Database
Averrhoa carambolaPlant
Bison bisonFooDB
Bos taurusFooDB
Bos taurus X Bison bisonFooDB
Bubalus bubalisFooDB
Cannabis sativaCannabisDB
      Not Available
Capra aegagrus hircusFooDB
CervidaeFooDB
Cervus canadensisFooDB
ColumbaFooDB
ColumbidaeFooDB
Dromaius novaehollandiaeFooDB
Equus caballusFooDB
Gallus gallusFooDB
Homo sapiensLOTUS Database
Lagopus mutaFooDB
LeporidaeFooDB
Lepus timidusFooDB
Melanitta fuscaFooDB
Meleagris gallopavoFooDB
Numida meleagrisFooDB
OdocoileusFooDB
OryctolagusFooDB
Ovis ariesFooDB
PhasianidaeFooDB
Phasianus colchicusFooDB
Pogostemon cablinLOTUS Database
Struthio camelusFooDB
Sus scrofaFooDB
Sus scrofa domesticaFooDB
Triticum aestivumKNApSAcK Database
Vitis viniferaLOTUS Database
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 PointNot AvailableNot Available
Water Solubility679 mg/mLNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
Water Solubility149 g/LALOGPS
logP0.17ALOGPS
logP0.21ChemAxon
logS0.1ALOGPS
pKa (Strongest Acidic)2.48ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count4ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area74.6 ŲChemAxon
Rotatable Bond Count2ChemAxon
Refractivity23.56 m³·mol⁻¹ChemAxon
Polarizability10.06 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDHMDB0000202
DrugBank IDDB04183
Phenol Explorer Compound IDNot Available
FoodDB IDFDB021905
KNApSAcK IDC00052349
Chemspider ID473
KEGG Compound IDC02170
BioCyc IDCPD-546
BiGG IDNot Available
Wikipedia LinkMethylmalonic_acid
METLIN ID3712
PubChem Compound487
PDB IDNot Available
ChEBI ID30860
Good Scents IDNot Available
References
General References
  1. Haurani FI, Hall CA, Rubin R: Megaloblastic anemia as a result of an abnormal transcobalamin II (Cardeza). J Clin Invest. 1979 Nov;64(5):1253-9. [PubMed:500809 ]
  2. Bennett MJ, Ragni MC, Hood I, Hale DE: Comparison of post-mortem urinary and vitreous humour organic acids. Ann Clin Biochem. 1992 Sep;29 ( Pt 5):541-5. [PubMed:1444166 ]
  3. van Asselt DZ, Karlietis MH, Poels PJ, de Jong JG, Wevers RA, Hoefnagels WH: Cerebrospinal fluid methylmalonic acid concentrations in neurological patients with low and normal serum cobalamin concentrations. Acta Neurol Scand. 1998 Jun;97(6):413-6. [PubMed:9669477 ]
  4. Magera MJ, Helgeson JK, Matern D, Rinaldo P: Methylmalonic acid measured in plasma and urine by stable-isotope dilution and electrospray tandem mass spectrometry. Clin Chem. 2000 Nov;46(11):1804-10. [PubMed:11067816 ]
  5. Nakamura E, Rosenberg LE, Tanaka K: Microdetermination of methylmalonic acid and other short chain dicarboxylic acids by gas chromatography: use in prenatal diagnosis of methylmalonic acidemia and in studies of isovaleric acidemia. Clin Chim Acta. 1976 Apr 15;68(2):127-40. [PubMed:1261058 ]
  6. Jakobs C, Sweetman L, Nyhan WL: Hydroxy acid metabolites of branched-chain amino acids in amniotic fluid. Clin Chim Acta. 1984 Jul 16;140(2):157-66. [PubMed:6467607 ]
  7. Coude MM, Charpentier C, Bonnefont JP, Cheron G, Kamoun P: Organic acids in aqueous humour and plasma: post mortem study in infants and diagnosis of enzymopathies. J Inherit Metab Dis. 1991;14(5):668-73. [PubMed:1779612 ]
  8. Aleszczyk J: [Connection between changing the vitamin and immune status and the character of the throat microflora in patients with chronic tonsillitis]. Otolaryngol Pol. 2003;57(2):221-4. [PubMed:12894427 ]
  9. Nagarajan S, Enns GM, Millan MT, Winter S, Sarwal MM: Management of methylmalonic acidaemia by combined liver-kidney transplantation. J Inherit Metab Dis. 2005;28(4):517-24. [PubMed:15902554 ]
  10. Stabler SP, Marcell PD, Podell ER, Allen RH, Lindenbaum J: Assay of methylmalonic acid in the serum of patients with cobalamin deficiency using capillary gas chromatography-mass spectrometry. J Clin Invest. 1986 May;77(5):1606-12. [PubMed:3700655 ]
  11. Leupold D: [Methylmalonic aciduria. Classification, diagnosis and therapy (author's transl)]. Klin Wochenschr. 1977 Jan 15;55(2):57-63. [PubMed:319293 ]
  12. Vrethem M, Mattsson E, Hebelka H, Leerbeck K, Osterberg A, Landtblom AM, Balla B, Nilsson H, Hultgren M, Brattstrom L, Kagedal B: Increased plasma homocysteine levels without signs of vitamin B12 deficiency in patients with multiple sclerosis assessed by blood and cerebrospinal fluid homocysteine and methylmalonic acid. Mult Scler. 2003 Jun;9(3):239-45. [PubMed:12814169 ]
  13. Frenkel EP, Kitchens RL: Applicability of an enzymatic quantitation of methylmalonic, propionic, and acetic acids in normal and megaloblastic states. Blood. 1977 Jan;49(1):125-37. [PubMed:830370 ]