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Showing metabocard for Malonic semialdehyde (HMDB0011111)

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IdentificationTaxonomyOntologyPhysical propertiesSpectraBiological propertiesConcentrationsLinksReferencesenzymes (2) Show 2 proteinsXML
enzymes (2) Show 2 proteins
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
Data?1676999847
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
PropertyValueSource
Water Solubility251 g/LALOGPS
logP-0.69ALOGPS
logP-0.49ChemAxon
logS0.46ALOGPS
pKa (Strongest Acidic)3.76ChemAxon
pKa (Strongest Basic)-7.2ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count3ChemAxon
Hydrogen Donor Count1ChemAxon
Polar Surface Area54.37 ŲChemAxon
Rotatable Bond Count2ChemAxon
Refractivity18.06 m³·mol⁻¹ChemAxon
Polarizability7.27 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
DarkChem[M+H]+115.42331661259
DarkChem[M-H]-110.78431661259
DeepCCS[M+H]+120.53330932474
DeepCCS[M-H]-118.47530932474
DeepCCS[M-2H]-154.24630932474
DeepCCS[M+Na]+128.74530932474
AllCCS[M+H]+123.932859911
AllCCS[M+H-H2O]+119.532859911
AllCCS[M+NH4]+128.032859911
AllCCS[M+Na]+129.232859911
AllCCS[M-H]-123.632859911
AllCCS[M+Na-2H]-128.232859911
AllCCS[M+HCOO]-133.232859911

Predicted Retention Times

Underivatized

Chromatographic MethodRetention TimeReference
Measured using a Waters Acquity ultraperformance liquid chromatography (UPLC) ethylene-bridged hybrid (BEH) C18 column (100 mm × 2.1 mm; 1.7 μmparticle diameter). Predicted by Afia on May 17, 2022. Predicted by Afia on May 17, 2022.1.65 minutes32390414
Predicted by Siyang on May 30, 20228.6118 minutes33406817
Predicted by Siyang using ReTip algorithm on June 8, 20223.01 minutes32390414
AjsUoB = Accucore 150 Amide HILIC with 10mM Ammonium Formate, 0.1% Formic Acid211.5 seconds40023050
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid727.6 seconds40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid347.2 seconds40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid102.8 seconds40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid253.9 seconds40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid72.0 seconds40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid259.4 seconds40023050
BfG_NTS_RP1 =Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) with Water:ACN and 0.1% Formic Acid297.5 seconds40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)271.6 seconds40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid575.0 seconds40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid95.6 seconds40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid780.8 seconds40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid231.1 seconds40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid277.4 seconds40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate690.5 seconds40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA276.3 seconds40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water337.6 seconds40023050

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
Malonic semialdehydeOC(=O)CC=O2043.4Standard polar33892256
Malonic semialdehydeOC(=O)CC=O749.4Standard non polar33892256
Malonic semialdehydeOC(=O)CC=O883.1Semi standard non polar33892256

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
Malonic semialdehyde,1TMS,isomer #1C[Si](C)(C)OC(=O)CC=O987.9Semi standard non polar33892256
Malonic semialdehyde,1TMS,isomer #2C[Si](C)(C)OC=CC(=O)O1110.4Semi standard non polar33892256
Malonic semialdehyde,2TMS,isomer #1C[Si](C)(C)OC=CC(=O)O[Si](C)(C)C1174.2Semi standard non polar33892256
Malonic semialdehyde,2TMS,isomer #1C[Si](C)(C)OC=CC(=O)O[Si](C)(C)C1115.9Standard non polar33892256
Malonic semialdehyde,2TMS,isomer #1C[Si](C)(C)OC=CC(=O)O[Si](C)(C)C1215.2Standard polar33892256
Malonic semialdehyde,1TBDMS,isomer #1CC(C)(C)[Si](C)(C)OC(=O)CC=O1233.0Semi standard non polar33892256
Malonic semialdehyde,1TBDMS,isomer #2CC(C)(C)[Si](C)(C)OC=CC(=O)O1358.1Semi standard non polar33892256
Malonic semialdehyde,2TBDMS,isomer #1CC(C)(C)[Si](C)(C)OC=CC(=O)O[Si](C)(C)C(C)(C)C1609.9Semi standard non polar33892256
Malonic semialdehyde,2TBDMS,isomer #1CC(C)(C)[Si](C)(C)OC=CC(=O)O[Si](C)(C)C(C)(C)C1567.3Standard non polar33892256
Malonic semialdehyde,2TBDMS,isomer #1CC(C)(C)[Si](C)(C)OC=CC(=O)O[Si](C)(C)C(C)(C)C1522.3Standard polar33892256
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