Showing metabocard for Succinic acid semialdehyde (MMDBc0029601)

Record Information
Version1.0
StatusDetected and Quantified
Creation Date2021-11-17 23:33:58 UTC
Update Date2024-04-30 19:38:51 UTC
Metabolite IDMMDBc0029601
Metabolite Identification
Common NameSuccinic acid semialdehyde
DescriptionSuccinic acid semialdehyde is an intermediate in the catabolism of gamma-aminobutyrate (PMID 16435183 ). Succinate semialdehyde dehydrogenase is an enzyme that catalyses the reaction of succinate semialdehyde and NAD+ to form succinate and NADH.
Structure
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for #<Metabolite:0x00007fecac1e7738>


  Mrv1652309042000202D          

  7  6  0  0  0  0            999 V2000
 9999.6386 9999.3862    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9998.9237 9999.7980    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9998.2065 9999.3862    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9998.923710000.6237    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10000.3540 9999.7980    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10001.0676 9999.3862    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10001.7834 9999.7980    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  5  1  0  0  0  0
  2  3  1  0  0  0  0
  2  4  2  0  0  0  0
  5  6  1  0  0  0  0
  6  7  2  0  0  0  0
M  END
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3D MOL for #<Metabolite:0x00007fecac1e7738>

HMDB0001259
     RDKit          3D
Succinic acid semialdehyde
 13 12  0  0  0  0  0  0  0  0999 V2000
    2.4783    0.2961   -1.0226 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.5881   -0.4640   -0.6515 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9807   -0.2974    0.6888 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2923    0.4908    0.5355 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2542   -0.2088   -0.3509 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0514   -1.3216   -0.8731 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4626    0.4417   -0.6068 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2605   -1.2343   -1.2989 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7627   -1.2253    1.2179 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6446    0.3324    1.3452 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7516    0.6653    1.5306 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0262    1.4286    0.0259 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8765    1.0964    0.0314 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  1  0
  5  6  2  0
  5  7  1  0
  2  8  1  0
  3  9  1  0
  3 10  1  0
  4 11  1  0
  4 12  1  0
  7 13  1  0
M  END
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3D SDF for #<Metabolite:0x00007fecac1e7738>


  Mrv1652309042000202D          

  7  6  0  0  0  0            999 V2000
 9999.6386 9999.3862    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9998.9237 9999.7980    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9998.2065 9999.3862    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9998.923710000.6237    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10000.3540 9999.7980    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10001.0676 9999.3862    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10001.7834 9999.7980    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  5  1  0  0  0  0
  2  3  1  0  0  0  0
  2  4  2  0  0  0  0
  5  6  1  0  0  0  0
  6  7  2  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0029601

> <DATABASE_NAME>
MIME

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

> <INCHI_IDENTIFIER>
InChI=1S/C4H6O3/c5-3-1-2-4(6)7/h3H,1-2H2,(H,6,7)

> <INCHI_KEY>
UIUJIQZEACWQSV-UHFFFAOYSA-N

> <FORMULA>
C4H6O3

> <MOLECULAR_WEIGHT>
102.0886

> <EXACT_MASS>
102.031694058

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
13

> <JCHEM_AVERAGE_POLARIZABILITY>
9.263882313671203

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
4-oxobutanoic acid

> <ALOGPS_LOGP>
-0.47

> <JCHEM_LOGP>
-0.5570992196666666

> <ALOGPS_LOGS>
0.28

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
17.53992018087323

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.12725825924451

> <JCHEM_PKA_STRONGEST_BASIC>
-6.956114389966538

> <JCHEM_POLAR_SURFACE_AREA>
54.37

> <JCHEM_REFRACTIVITY>
22.611600000000003

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.94e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
succinic semialdehyde

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for #<Metabolite:0x00007fecac1e7738>

HMDB0001259
     RDKit          3D
Succinic acid semialdehyde
 13 12  0  0  0  0  0  0  0  0999 V2000
    2.4783    0.2961   -1.0226 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.5881   -0.4640   -0.6515 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9807   -0.2974    0.6888 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2923    0.4908    0.5355 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2542   -0.2088   -0.3509 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0514   -1.3216   -0.8731 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4626    0.4417   -0.6068 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2605   -1.2343   -1.2989 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7627   -1.2253    1.2179 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6446    0.3324    1.3452 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7516    0.6653    1.5306 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0262    1.4286    0.0259 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8765    1.0964    0.0314 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  1  0
  5  6  2  0
  5  7  1  0
  2  8  1  0
  3  9  1  0
  3 10  1  0
  4 11  1  0
  4 12  1  0
  7 13  1  0
M  END
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PDB for #<Metabolite:0x00007fecac1e7738>

HEADER    PROTEIN                                 04-SEP-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   04-SEP-20         0                                  
HETATM    1  C   UNK     0    8665.9928665.521   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0    8664.6588666.290   0.000  0.00  0.00           C+0
HETATM    3  O   UNK     0    8663.3198665.521   0.000  0.00  0.00           O+0
HETATM    4  O   UNK     0    8664.6588667.831   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0    8667.3278666.290   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0    8668.6608665.521   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0    8669.9968666.290   0.000  0.00  0.00           O+0
CONECT    1    2    5                                                       
CONECT    2    1    3    4                                                  
CONECT    3    2                                                            
CONECT    4    2                                                            
CONECT    5    1    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6                                                            
MASTER        0    0    0    0    0    0    0    0    7    0   12    0
END
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3D PDB for #<Metabolite:0x00007fecac1e7738>

COMPND    HMDB0001259
HETATM    1  O1  UNL     1       2.478   0.296  -1.023  1.00  0.00           O  
HETATM    2  C1  UNL     1       1.588  -0.464  -0.651  1.00  0.00           C  
HETATM    3  C2  UNL     1       0.981  -0.297   0.689  1.00  0.00           C  
HETATM    4  C3  UNL     1      -0.292   0.491   0.536  1.00  0.00           C  
HETATM    5  C4  UNL     1      -1.254  -0.209  -0.351  1.00  0.00           C  
HETATM    6  O2  UNL     1      -1.051  -1.322  -0.873  1.00  0.00           O  
HETATM    7  O3  UNL     1      -2.463   0.442  -0.607  1.00  0.00           O  
HETATM    8  H1  UNL     1       1.261  -1.234  -1.299  1.00  0.00           H  
HETATM    9  H2  UNL     1       0.763  -1.225   1.218  1.00  0.00           H  
HETATM   10  H3  UNL     1       1.645   0.332   1.345  1.00  0.00           H  
HETATM   11  H4  UNL     1      -0.752   0.665   1.531  1.00  0.00           H  
HETATM   12  H5  UNL     1      -0.026   1.429   0.026  1.00  0.00           H  
HETATM   13  H6  UNL     1      -2.877   1.096   0.031  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3    8
CONECT    3    4    9   10
CONECT    4    5   11   12
CONECT    5    6    6    7
CONECT    7   13
END
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SMILES for #<Metabolite:0x00007fecac1e7738>

OC(=O)CCC=O
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INCHI for #<Metabolite:0x00007fecac1e7738>

InChI=1S/C4H6O3/c5-3-1-2-4(6)7/h3H,1-2H2,(H,6,7)
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Synonyms
ValueSource
3-Formylpropanoic acidChEBI
3-Formylpropionic acidChEBI
4-OxobutanoateChEBI
beta-Formylpropionic acidChEBI
Semialdehyde succiniqueChEBI
Succinaldehydic acidChEBI
Succinate semialdehydeChEBI
Succinic semialdehydeKegg
3-FormylpropanoateGenerator
3-FormylpropionateGenerator
4-Oxobutanoic acidGenerator
b-FormylpropionateGenerator
b-Formylpropionic acidGenerator
beta-FormylpropionateGenerator
Β-formylpropionateGenerator
Β-formylpropionic acidGenerator
SuccinaldehydateGenerator
2-Formylpropionic acid ethyl esterHMDB
ButryaldehydateHMDB
Butryaldehydic acidHMDB
gamma-OxybutyrateHMDB
gamma-Oxybutyric acidHMDB
Succinic semialdehyde, calcium saltHMDB
Succinic acid semialdehydeChEBI
Molecular FormulaC4H6O3
Average Mass102.0886
Monoisotopic Mass102.031694058
IUPAC Name4-oxobutanoic acid
Traditional Namesuccinic semialdehyde
CAS Registry Number692-29-5
SMILES
OC(=O)CCC=O
InChI Identifier
InChI=1S/C4H6O3/c5-3-1-2-4(6)7/h3H,1-2H2,(H,6,7)
InChI KeyUIUJIQZEACWQSV-UHFFFAOYSA-N