Showing metabocard for (S)-Methylmalonic acid semialdehyde (MMDBc0029689)

Record Information
Version1.0
StatusDetected and Quantified
Creation Date2021-11-17 23:37:39 UTC
Update Date2024-04-30 19:40:42 UTC
Metabolite IDMMDBc0029689
Metabolite Identification
Common Name(S)-Methylmalonic acid semialdehyde
DescriptionMethylmalonic semialdehyde is a metabolite in valine catabolism, inositol metabolism and propanoate metabolism. Methylmalonate-semialdehyde dehydrogenase (MMSDH) catalyses the NAD+ and coenzyme A-dependent conversion of methylmalonate semialdehyde to propionyl-CoA in the distal region of the L-valine catabolic pathway. Direct enzymatic assay of MMSDH is difficult since the substrate, methylmalonate semialdehyde, is both commercially unavailable and notoriously unstable as a b-keto acid. (PMID: 10947204 )
Structure
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for #<Metabolite:0x00007f92319d8710>


  Mrv1652306222023472D          

  8  7  0  0  1  0            999 V2000
    2.0625    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    0.7145    0.0000 C   0  0  1  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    2.1434    0.0000 O   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
    1.6500    1.4289    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  3  1  1  6  0  0  0
  3  2  1  0  0  0  0
  4  3  1  0  0  0  0
  5  2  2  0  0  0  0
  6  4  2  0  0  0  0
  7  4  1  0  0  0  0
  3  8  1  1  0  0  0
M  END
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3D MOL for #<Metabolite:0x00007f92319d8710>

HMDB0002217
     RDKit          3D
(S)-Methylmalonic acid semialdehyde
 13 12  0  0  0  0  0  0  0  0999 V2000
    1.4143    0.1129    0.4467 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0585    0.3244    0.6514 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.5277    1.2924   -0.3872 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2562    2.1152   -0.8055 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8378   -0.9212    0.4897 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5075   -1.3197    1.4686 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8046   -1.6009   -0.7227 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.5913   -0.3013   -0.5528 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8087   -0.4875    1.2710 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8933    1.1194    0.4733 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2104    0.7841    1.6464 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5556    1.2517   -0.7550 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4619   -2.3696   -0.8383 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  1
  3 12  1  0
  7 13  1  0
M  END
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3D SDF for #<Metabolite:0x00007f92319d8710>


  Mrv1652306222023472D          

  8  7  0  0  1  0            999 V2000
    2.0625    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    0.7145    0.0000 C   0  0  1  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    2.1434    0.0000 O   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
    1.6500    1.4289    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  3  1  1  6  0  0  0
  3  2  1  0  0  0  0
  4  3  1  0  0  0  0
  5  2  2  0  0  0  0
  6  4  2  0  0  0  0
  7  4  1  0  0  0  0
  3  8  1  1  0  0  0
M  END
> <DATABASE_ID>
MMDBc0029689

> <DATABASE_NAME>
MIME

> <SMILES>
[H][C@](C)(C=O)C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C4H6O3/c1-3(2-5)4(6)7/h2-3H,1H3,(H,6,7)/t3-/m0/s1

> <INCHI_KEY>
VOKUMXABRRXHAR-VKHMYHEASA-N

> <FORMULA>
C4H6O3

> <MOLECULAR_WEIGHT>
102.0886

> <EXACT_MASS>
102.031694058

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
13

> <JCHEM_AVERAGE_POLARIZABILITY>
9.16242691245968

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2S)-2-methyl-3-oxopropanoic acid

> <ALOGPS_LOGP>
-0.00

> <JCHEM_LOGP>
0.05325275766666666

> <ALOGPS_LOGS>
0.42

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
17.47521673394892

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.9838439710362112

> <JCHEM_PKA_STRONGEST_BASIC>
-7.233962384073207

> <JCHEM_POLAR_SURFACE_AREA>
54.37

> <JCHEM_REFRACTIVITY>
22.636900000000004

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.66e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(S)-methylmalonaldehydic acid

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for #<Metabolite:0x00007f92319d8710>

HMDB0002217
     RDKit          3D
(S)-Methylmalonic acid semialdehyde
 13 12  0  0  0  0  0  0  0  0999 V2000
    1.4143    0.1129    0.4467 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0585    0.3244    0.6514 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.5277    1.2924   -0.3872 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2562    2.1152   -0.8055 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8378   -0.9212    0.4897 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5075   -1.3197    1.4686 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8046   -1.6009   -0.7227 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.5913   -0.3013   -0.5528 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8087   -0.4875    1.2710 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8933    1.1194    0.4733 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2104    0.7841    1.6464 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5556    1.2517   -0.7550 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4619   -2.3696   -0.8383 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  1
  3 12  1  0
  7 13  1  0
M  END
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PDB for #<Metabolite:0x00007f92319d8710>

HEADER    PROTEIN                                 22-JUN-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   22-JUN-20         0                                  
HETATM    1  C   UNK     0       3.850   1.334   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       1.540   2.667   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       2.310   1.334   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       1.540   0.000   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0       2.310   4.001   0.000  0.00  0.00           O+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+0
HETATM    8  H   UNK     0       3.080   2.667   0.000  0.00  0.00           H+0
CONECT    1    3                                                            
CONECT    2    3    5                                                       
CONECT    3    1    2    4    8                                             
CONECT    4    3    6    7                                                  
CONECT    5    2                                                            
CONECT    6    4                                                            
CONECT    7    4                                                            
CONECT    8    3                                                            
MASTER        0    0    0    0    0    0    0    0    8    0   14    0
END
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3D PDB for #<Metabolite:0x00007f92319d8710>

COMPND    HMDB0002217
HETATM    1  C1  UNL     1       1.414   0.113   0.447  1.00  0.00           C  
HETATM    2  C2  UNL     1      -0.058   0.324   0.651  1.00  0.00           C  
HETATM    3  C3  UNL     1      -0.528   1.292  -0.387  1.00  0.00           C  
HETATM    4  O1  UNL     1       0.256   2.115  -0.806  1.00  0.00           O  
HETATM    5  C4  UNL     1      -0.838  -0.921   0.490  1.00  0.00           C  
HETATM    6  O2  UNL     1      -1.507  -1.320   1.469  1.00  0.00           O  
HETATM    7  O3  UNL     1      -0.805  -1.601  -0.723  1.00  0.00           O  
HETATM    8  H1  UNL     1       1.591  -0.301  -0.553  1.00  0.00           H  
HETATM    9  H2  UNL     1       1.809  -0.488   1.271  1.00  0.00           H  
HETATM   10  H3  UNL     1       1.893   1.119   0.473  1.00  0.00           H  
HETATM   11  H4  UNL     1      -0.210   0.784   1.646  1.00  0.00           H  
HETATM   12  H5  UNL     1      -1.556   1.252  -0.755  1.00  0.00           H  
HETATM   13  H6  UNL     1      -1.462  -2.370  -0.838  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
CONECT    7   13
END
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SMILES for #<Metabolite:0x00007f92319d8710>

[H][C@](C)(C=O)C(O)=O
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INCHI for #<Metabolite:0x00007f92319d8710>

InChI=1S/C4H6O3/c1-3(2-5)4(6)7/h2-3H,1H3,(H,6,7)/t3-/m0/s1
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Synonyms
ValueSource
(S)-Methylmalonate semialdehydeChEBI
(2S)-2-Methyl-3-oxopropanoateHMDB
(2S)-2-Methyl-3-oxopropanoic acidHMDB
Molecular FormulaC4H6O3
Average Mass102.0886
Monoisotopic Mass102.031694058
IUPAC Name(2S)-2-methyl-3-oxopropanoic acid
Traditional Name(S)-methylmalonaldehydic acid
CAS Registry Number99043-16-0
SMILES
[H][C@](C)(C=O)C(O)=O
InChI Identifier
InChI=1S/C4H6O3/c1-3(2-5)4(6)7/h2-3H,1H3,(H,6,7)/t3-/m0/s1
InChI KeyVOKUMXABRRXHAR-VKHMYHEASA-N