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Showing metabocard for Malonic semialdehyde (HMDB0011111)

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IdentificationTaxonomyOntologyPhysical propertiesSpectraBiological propertiesConcentrationsLinksReferencesenzymes (2) Show 2 proteinsXML
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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2008-10-16 22:29:05 UTC
Update Date2023-02-21 17:17:27 UTC
HMDB IDHMDB0011111
Secondary Accession Numbers
  • HMDB0011666
  • HMDB11111
  • HMDB11666
Metabolite Identification
Common NameMalonic semialdehyde
DescriptionMalonic semialdehyde belongs to the class of organic compounds known as 1,3-dicarbonyl compounds. These are carbonyl compounds with the generic formula O=C(R)C(H)C(R')=O, where R and R' can be any group. Malonic semialdehyde is an extremely weak basic (essentially neutral) compound (based on its pKa). Malonic semialdehyde exists in all living organisms, ranging from bacteria to humans. malonic semialdehyde and L-glutamic acid can be biosynthesized from β-alanine and oxoglutaric acid through its interaction with the enzyme 4-aminobutyrate aminotransferase, mitochondrial. In humans, malonic semialdehyde is involved in beta-alanine metabolism.
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0011111 (Malonic semialdehyde)

  Mrv0541 02241201192D          

  6  5  0  0  0  0            999 V2000
   -0.1207   -0.3448    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5965    0.0690    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8344    0.0690    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3102   -0.3448    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5965    0.8930    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5482   -0.3448    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  3  1  0  0  0  0
  2  4  1  0  0  0  0
  2  5  2  0  0  0  0
  3  6  2  0  0  0  0
M  END
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3D MOL for HMDB0011111 (Malonic semialdehyde)

HMDB0011111
     RDKit          3D
Malonic semialdehyde
 10  9  0  0  0  0  0  0  0  0999 V2000
   -2.1683   -0.1945    0.8424 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4782    0.3519   -0.0152 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2888   -0.3690   -0.4992 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8156   -0.1505    0.4830 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8267   -0.8329    1.5142 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7986    0.7837    0.2492 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7915    1.3305   -0.3597 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0888   -0.0531   -1.4804 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4826   -1.4729   -0.5428 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6796    0.6068   -0.1916 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  3  4  1  0
  4  5  2  0
  4  6  1  0
  2  7  1  0
  3  8  1  0
  3  9  1  0
  6 10  1  0
M  END
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3D SDF for HMDB0011111 (Malonic semialdehyde)

  Mrv0541 02241201192D          

  6  5  0  0  0  0            999 V2000
   -0.1207   -0.3448    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5965    0.0690    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8344    0.0690    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3102   -0.3448    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5965    0.8930    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5482   -0.3448    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  3  1  0  0  0  0
  2  4  1  0  0  0  0
  2  5  2  0  0  0  0
  3  6  2  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0011111

> <DATABASE_NAME>
hmdb

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

> <INCHI_IDENTIFIER>
InChI=1S/C3H4O3/c4-2-1-3(5)6/h2H,1H2,(H,5,6)

> <INCHI_KEY>
OAKURXIZZOAYBC-UHFFFAOYSA-N

> <FORMULA>
C3H4O3

> <MOLECULAR_WEIGHT>
88.0621

> <EXACT_MASS>
88.016043994

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_AVERAGE_POLARIZABILITY>
7.274262978216537

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
3-oxopropanoic acid

> <ALOGPS_LOGP>
-0.69

> <JCHEM_LOGP>
-0.48973352066666664

> <ALOGPS_LOGS>
0.46

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
14.702401134335275

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.7620503977209387

> <JCHEM_PKA_STRONGEST_BASIC>
-7.174413486324497

> <JCHEM_POLAR_SURFACE_AREA>
54.37

> <JCHEM_REFRACTIVITY>
18.062400000000004

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.51e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
3-oxopropanoic acid

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for HMDB0011111 (Malonic semialdehyde)

HMDB0011111
     RDKit          3D
Malonic semialdehyde
 10  9  0  0  0  0  0  0  0  0999 V2000
   -2.1683   -0.1945    0.8424 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4782    0.3519   -0.0152 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2888   -0.3690   -0.4992 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8156   -0.1505    0.4830 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8267   -0.8329    1.5142 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7986    0.7837    0.2492 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7915    1.3305   -0.3597 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0888   -0.0531   -1.4804 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4826   -1.4729   -0.5428 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6796    0.6068   -0.1916 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  3  4  1  0
  4  5  2  0
  4  6  1  0
  2  7  1  0
  3  8  1  0
  3  9  1  0
  6 10  1  0
M  END
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PDB for HMDB0011111 (Malonic semialdehyde)

HEADER    PROTEIN                                 24-FEB-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-FEB-12         0                                  
HETATM    1  C   UNK     0      -0.225  -0.644   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       1.113   0.129   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -1.558   0.129   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0       2.446  -0.644   0.000  0.00  0.00           O+0
HETATM    5  O   UNK     0       1.113   1.667   0.000  0.00  0.00           O+0
HETATM    6  O   UNK     0      -2.890  -0.644   0.000  0.00  0.00           O+0
CONECT    1    2    3                                                       
CONECT    2    1    4    5                                                  
CONECT    3    1    6                                                       
CONECT    4    2                                                            
CONECT    5    2                                                            
CONECT    6    3                                                            
MASTER        0    0    0    0    0    0    0    0    6    0   10    0
END
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3D PDB for HMDB0011111 (Malonic semialdehyde)

COMPND    HMDB0011111
HETATM    1  O1  UNL     1      -2.168  -0.195   0.842  1.00  0.00           O  
HETATM    2  C1  UNL     1      -1.478   0.352  -0.015  1.00  0.00           C  
HETATM    3  C2  UNL     1      -0.289  -0.369  -0.499  1.00  0.00           C  
HETATM    4  C3  UNL     1       0.816  -0.151   0.483  1.00  0.00           C  
HETATM    5  O2  UNL     1       0.827  -0.833   1.514  1.00  0.00           O  
HETATM    6  O3  UNL     1       1.799   0.784   0.249  1.00  0.00           O  
HETATM    7  H1  UNL     1      -1.792   1.330  -0.360  1.00  0.00           H  
HETATM    8  H2  UNL     1       0.089  -0.053  -1.480  1.00  0.00           H  
HETATM    9  H3  UNL     1      -0.483  -1.473  -0.543  1.00  0.00           H  
HETATM   10  H4  UNL     1       2.680   0.607  -0.192  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3    7
CONECT    3    4    8    9
CONECT    4    5    5    6
CONECT    6   10
END
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SMILES for HMDB0011111 (Malonic semialdehyde)

OC(=O)CC=O
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INCHI for HMDB0011111 (Malonic semialdehyde)

InChI=1S/C3H4O3/c4-2-1-3(5)6/h2H,1H2,(H,5,6)
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View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
ValueSource
Malonate semialdehydeKegg
Malonic acid semialdehydeGenerator
Formylacetic acidChEBI
FormylacetateGenerator
3-OxopropanoateHMDB
3-Oxopropanoic acidHMDB
3-Oxopropionic acidHMDB
Formyl acetateHMDB
Formyl acetic acidHMDB
Malonaldehydic acidHMDB
Malonic semialdehyde sodium saltMeSH, HMDB
Chemical FormulaC3H4O3
Average Molecular Weight88.0621
Monoisotopic Molecular Weight88.016043994
IUPAC Name3-oxopropanoic acid
Traditional Name3-oxopropanoic acid
CAS Registry Number926-61-4
SMILES
OC(=O)CC=O
InChI Identifier
InChI=1S/C3H4O3/c4-2-1-3(5)6/h2H,1H2,(H,5,6)
InChI KeyOAKURXIZZOAYBC-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as 1,3-dicarbonyl compounds. These are carbonyl compounds with the generic formula O=C(R)C(H)C(R')=O, where R and R' can be any group.
KingdomOrganic compounds
Super ClassOrganic oxygen compounds
ClassOrganooxygen compounds
Sub ClassCarbonyl compounds
Direct Parent1,3-dicarbonyl compounds
Alternative Parents
Substituents
  • 1,3-dicarbonyl compound
  • Alpha-hydrogen aldehyde
  • Monocarboxylic acid or derivatives
  • Carboxylic acid
  • Carboxylic acid derivative
  • Organic oxide
  • Hydrocarbon derivative
  • Short-chain aldehyde
  • Aldehyde
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Ontology
Physiological effectNot Available
Disposition
Route of exposureSource
Process
Naturally occurring process
RoleNot Available
Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
Predicted Chromatographic Properties
Spectra
Biological Properties
Cellular LocationsNot Available
Biospecimen LocationsNot Available
Tissue LocationsNot Available
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB027893
KNApSAcK IDNot Available
Chemspider ID845
KEGG Compound IDC00222
BioCyc IDMALONATE-S-ALD
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound868
PDB IDNot Available
ChEBI ID17960
Food Biomarker OntologyNot Available
VMH IDMSA
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General References
  1. Scholem RD, Brown GK: Metabolism of malonic semialdehyde in man. Biochem J. 1983 Oct 15;216(1):81-5. [PubMed:6418146 ]

Enzymes

Enzyme Details
1. Methylmalonate-semialdehyde dehydrogenase [acylating], mitochondrial
General function:
Involved in oxidoreductase activity
Specific function:
Plays a role in valine and pyrimidine metabolism. Binds fatty acyl-CoA.
Gene Name:
ALDH6A1
Uniprot ID:
Q02252
Molecular weight:
57839.31
Reactions
Malonic semialdehyde + Coenzyme A + NAD(P)(+) → Acetyl-CoA + CO(2) + NAD(P)Hdetails
Malonic semialdehyde + Coenzyme A + NAD → Acetyl-CoA + Carbon dioxide + NADH + Hydrogen Iondetails
Malonic semialdehyde + Coenzyme A + NADP → Acetyl-CoA + Carbon dioxide + NADPH + Hydrogen Iondetails
Malonic semialdehyde + Coenzyme A + NADP → Malonyl-CoA + NADPH + Hydrogen Iondetails
Enzyme Details
2. 4-aminobutyrate aminotransferase, mitochondrial
General function:
Involved in 4-aminobutyrate transaminase activity
Specific function:
Catalyzes the conversion of gamma-aminobutyrate and L-beta-aminoisobutyrate to succinate semialdehyde and methylmalonate semialdehyde, respectively. Can also convert delta-aminovalerate and beta-alanine.
Gene Name:
ABAT
Uniprot ID:
P80404
Molecular weight:
56438.405
Reactions
beta-Alanine + Oxoglutaric acid → Malonic semialdehyde + Glutamic aciddetails