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Showing metabocard for (S)-methylmalonate-semialdehyde (HMDB0304000)

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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2021-09-24 06:19:01 UTC
Update Date2021-09-24 06:19:02 UTC
HMDB IDHMDB0304000
Secondary Accession NumbersNone
Metabolite Identification
Common Name(S)-methylmalonate-semialdehyde
Description(s)-methylmalonate-semialdehyde is a member of the class of compounds known as 1,3-dicarbonyl compounds. 1,3-dicarbonyl compounds are carbonyl compounds with the generic formula O=C(R)C(H)C(R')=O, where R and R' can be any group (s)-methylmalonate-semialdehyde is soluble (in water) and a weakly acidic compound (based on its pKa). (s)-methylmalonate-semialdehyde can be found in a number of food items such as oil-seed camellia, jostaberry, yellow pond-lily, and pasta, which makes (s)-methylmalonate-semialdehyde a potential biomarker for the consumption of these food products.
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0304000 ((S)-methylmalonate-semialdehyde)


  Mrv1533005141512242D          

  7  6  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
    0.8250    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  5  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
  2  5  1  0  0  0  0
  5  6  2  0  0  0  0
  5  7  1  0  0  0  0
M  CHG  1   7  -1
M  END
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3D MOL for HMDB0304000 ((S)-methylmalonate-semialdehyde)

HMDB0304000
     RDKit          3D
(S)-methylmalonate-semialdehyde
 12 11  0  0  0  0  0  0  0  0999 V2000
   -1.2316   -0.0186   -0.4152 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0601   -0.0660    0.3820 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8515   -1.2782    0.1120 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8566   -1.3195   -0.5779 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7927    1.1844    0.1233 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8570    1.2681   -0.5096 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.2463    2.3602    0.6290 O   0  0  0  0  0  1  0  0  0  0  0  0
   -1.8197    0.8385    0.0162 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8295   -0.9290   -0.2873 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0549    0.2525   -1.4818 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2550   -0.0788    1.4544 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5266   -2.2136    0.5549 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
  2  5  1  0
  5  6  2  0
  5  7  1  0
  1  8  1  0
  1  9  1  0
  1 10  1  0
  2 11  1  0
  3 12  1  0
M  CHG  1   7  -1
M  END
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3D SDF for HMDB0304000 ((S)-methylmalonate-semialdehyde)


  Mrv1533005141512242D          

  7  6  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
    0.8250    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  5  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
  2  5  1  0  0  0  0
  5  6  2  0  0  0  0
  5  7  1  0  0  0  0
M  CHG  1   7  -1
M  END
> <DATABASE_ID>
HMDB0304000

> <DATABASE_NAME>
hmdb

> <SMILES>
CC(C=O)C([O-])=O

> <INCHI_IDENTIFIER>
InChI=1S/C4H6O3/c1-3(2-5)4(6)7/h2-3H,1H3,(H,6,7)/p-1

> <INCHI_KEY>
VOKUMXABRRXHAR-UHFFFAOYSA-M

> <FORMULA>
C4H5O3

> <MOLECULAR_WEIGHT>
101.082

> <EXACT_MASS>
101.024417601

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
12

> <JCHEM_AVERAGE_POLARIZABILITY>
8.768953686141568

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
-1

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2-methyl-3-oxopropanoate

> <ALOGPS_LOGP>
-0.21

> <JCHEM_LOGP>
0.05325275766666666

> <ALOGPS_LOGS>
0.41

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
17.475216733948912

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.9838439710362112

> <JCHEM_PKA_STRONGEST_BASIC>
-7.233962384073207

> <JCHEM_POLAR_SURFACE_AREA>
57.2

> <JCHEM_REFRACTIVITY>
33.474000000000004

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
3.03e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
2-methyl-3-oxopropanoate

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for HMDB0304000 ((S)-methylmalonate-semialdehyde)

HMDB0304000
     RDKit          3D
(S)-methylmalonate-semialdehyde
 12 11  0  0  0  0  0  0  0  0999 V2000
   -1.2316   -0.0186   -0.4152 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0601   -0.0660    0.3820 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8515   -1.2782    0.1120 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8566   -1.3195   -0.5779 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7927    1.1844    0.1233 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8570    1.2681   -0.5096 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.2463    2.3602    0.6290 O   0  0  0  0  0  1  0  0  0  0  0  0
   -1.8197    0.8385    0.0162 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8295   -0.9290   -0.2873 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0549    0.2525   -1.4818 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2550   -0.0788    1.4544 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5266   -2.2136    0.5549 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
  2  5  1  0
  5  6  2  0
  5  7  1  0
  1  8  1  0
  1  9  1  0
  1 10  1  0
  2 11  1  0
  3 12  1  0
M  CHG  1   7  -1
M  END
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PDB for HMDB0304000 ((S)-methylmalonate-semialdehyde)

HEADER    PROTEIN                                 14-MAY-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   14-MAY-15         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  C   UNK     0       1.540   0.000   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0       2.310  -1.334   0.000  0.00  0.00           O+0
HETATM    7  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O-1
CONECT    1    2                                                            
CONECT    2    1    3    5                                                  
CONECT    3    2    4                                                       
CONECT    4    3                                                            
CONECT    5    2    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 HMDB0304000 ((S)-methylmalonate-semialdehyde)

COMPND    HMDB0304000
HETATM    1  C1  UNL     1      -1.232  -0.019  -0.415  1.00  0.00           C  
HETATM    2  C2  UNL     1       0.060  -0.066   0.382  1.00  0.00           C  
HETATM    3  C3  UNL     1       0.852  -1.278   0.112  1.00  0.00           C  
HETATM    4  O1  UNL     1       1.857  -1.320  -0.578  1.00  0.00           O  
HETATM    5  C4  UNL     1       0.793   1.184   0.123  1.00  0.00           C  
HETATM    6  O2  UNL     1       1.857   1.268  -0.510  1.00  0.00           O  
HETATM    7  O3  UNL     1       0.246   2.360   0.629  1.00  0.00           O1-
HETATM    8  H1  UNL     1      -1.820   0.838   0.016  1.00  0.00           H  
HETATM    9  H2  UNL     1      -1.829  -0.929  -0.287  1.00  0.00           H  
HETATM   10  H3  UNL     1      -1.055   0.253  -1.482  1.00  0.00           H  
HETATM   11  H4  UNL     1      -0.255  -0.079   1.454  1.00  0.00           H  
HETATM   12  H5  UNL     1       0.527  -2.214   0.555  1.00  0.00           H  
CONECT    1    2    8    9   10
CONECT    2    3    5   11
CONECT    3    4    4   12
CONECT    5    6    6    7
END
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SMILES for HMDB0304000 ((S)-methylmalonate-semialdehyde)

CC(C=O)C([O-])=O
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INCHI for HMDB0304000 ((S)-methylmalonate-semialdehyde)

InChI=1S/C4H6O3/c1-3(2-5)4(6)7/h2-3H,1H3,(H,6,7)/p-1
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View in JSmolView Stereo Labels
Synonyms
ValueSource
2-Methyl-3-oxopropanoic acidGenerator
(S)-Methylmalonic acid-semialdehydeGenerator
Chemical FormulaC4H5O3
Average Molecular Weight101.082
Monoisotopic Molecular Weight101.024417601
IUPAC Name2-methyl-3-oxopropanoate
Traditional Name2-methyl-3-oxopropanoate
CAS Registry NumberNot Available
SMILES
CC(C=O)C([O-])=O
InChI Identifier
InChI=1S/C4H6O3/c1-3(2-5)4(6)7/h2-3H,1H3,(H,6,7)/p-1
InChI KeyVOKUMXABRRXHAR-UHFFFAOYSA-M
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
  • Monocarboxylic acid or derivatives
  • Carboxylic acid
  • Carboxylic acid derivative
  • Organic oxide
  • Hydrocarbon derivative
  • Short-chain aldehyde
  • Aldehyde
  • Organic anion
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Ontology
Physiological effectNot Available
Disposition
Source
ProcessNot Available
RoleNot Available
Physical Properties
StateNot Available
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
logP-0.21ALOGPS
logP0.053ChemAxon
logS0.41ALOGPS
pKa (Strongest Acidic)3.98ChemAxon
pKa (Strongest Basic)-7.2ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count3ChemAxon
Hydrogen Donor Count0ChemAxon
Polar Surface Area57.2 ŲChemAxon
Rotatable Bond Count2ChemAxon
Refractivity33.47 m³·mol⁻¹ChemAxon
Polarizability8.77 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
AllCCS[M+H]+126.4332859911
AllCCS[M+H-H2O]+122.08432859911
AllCCS[M+Na]+131.65532859911
AllCCS[M+NH4]+130.48532859911
AllCCS[M-H]-120.4432859911
AllCCS[M+Na-2H]-124.27332859911
AllCCS[M+HCOO]-128.49732859911
DeepCCS[M+H]+128.87830932474
DeepCCS[M-H]-126.08130932474
DeepCCS[M-2H]-162.9630932474
DeepCCS[M+Na]+137.48630932474

Predicted Kovats Retention Indices

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
(S)-methylmalonate-semialdehyde,1TMS,isomer #1CC(=CO[Si](C)(C)C)C(=O)[O-]994.5Semi standard non polar33892256
(S)-methylmalonate-semialdehyde,1TMS,isomer #1CC(=CO[Si](C)(C)C)C(=O)[O-]935.3Standard non polar33892256
(S)-methylmalonate-semialdehyde,1TMS,isomer #1CC(=CO[Si](C)(C)C)C(=O)[O-]1332.3Standard polar33892256
(S)-methylmalonate-semialdehyde,1TBDMS,isomer #1CC(=CO[Si](C)(C)C(C)(C)C)C(=O)[O-]1232.3Semi standard non polar33892256
(S)-methylmalonate-semialdehyde,1TBDMS,isomer #1CC(=CO[Si](C)(C)C(C)(C)C)C(=O)[O-]1153.9Standard non polar33892256
(S)-methylmalonate-semialdehyde,1TBDMS,isomer #1CC(=CO[Si](C)(C)C(C)(C)C)C(=O)[O-]1503.8Standard polar33892256
Spectra

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - (S)-methylmalonate-semialdehyde 10V, Negative-QTOFsplash10-0udi-3900000000-388be580d4c99ece37de2019-02-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - (S)-methylmalonate-semialdehyde 20V, Negative-QTOFsplash10-0pi0-9200000000-90011370ad0d623a1dc52019-02-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - (S)-methylmalonate-semialdehyde 40V, Negative-QTOFsplash10-0a4i-9000000000-4225df38130f7992fcc82019-02-23Wishart LabView Spectrum
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 IDFDB030171
KNApSAcK IDNot Available
Chemspider ID10669754
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound21917715
PDB IDNot Available
ChEBI ID57700
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General ReferencesNot Available