Showing metabocard for gamma-Hydroxybutyrate (MMDBc0030344)

Record Information
Version1.0
StatusDetected and Quantified
Creation Date2021-11-18 00:04:25 UTC
Update Date2024-10-09 19:19:49 UTC
Metabolite IDMMDBc0030344
Metabolite Identification
Common Namegamma-Hydroxybutyrate
DescriptionGamma-hydroxybutyrate (GHB) is also known as 4-hydroxybutanoic acid. It is a carboxylic acid with an attached alcohol (hydroxyl) group. GHB can be produced as a result of fermentation, and so is found in small quantities in some beers and wines. (Wikipedia , PMID 15939164 ) In E. coli, 4-hydroxybutanoate can be produced from the reduction of succinate semialdehyde by the enzyme 4-hydroxybutanoate dehydrogenase. (EcoCyc, PMID: 19372223 )
Structure
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for #<Metabolite:0x00007f9253ed5b88>


  Mrv1652307072019582D          

  7  6  0  0  0  0            999 V2000
   -0.3578   -0.6186    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0727   -0.2068    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7876   -0.6186    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0727    0.6186    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3563   -0.2068    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0719   -0.6186    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7876   -0.2068    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  1  0  0  0  0
M  END
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3D MOL for #<Metabolite:0x00007f9253ed5b88>

HMDB0000710
     RDKit          3D
4-Hydroxybutyric acid
 15 14  0  0  0  0  0  0  0  0999 V2000
   -2.1528   -0.1631    1.1215 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9111    0.2158   -0.0595 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9931    0.3371   -0.9162 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5016    0.5004   -0.4295 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2840   -0.7629   -0.0936 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7659   -0.5838   -0.4160 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3476    0.4350    0.3065 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1608    1.2490   -1.3394 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3752    0.7302   -1.4861 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1134    1.3710    0.1749 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0841   -1.5641   -0.7822 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1608   -1.0367    0.9684 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2378   -1.5758   -0.2467 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8207   -0.3323   -1.5075 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6751    1.1801   -0.2779 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  2  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  3  8  1  0
  4  9  1  0
  4 10  1  0
  5 11  1  0
  5 12  1  0
  6 13  1  0
  6 14  1  0
  7 15  1  0
M  END
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3D SDF for #<Metabolite:0x00007f9253ed5b88>


  Mrv1652307072019582D          

  7  6  0  0  0  0            999 V2000
   -0.3578   -0.6186    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0727   -0.2068    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7876   -0.6186    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0727    0.6186    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3563   -0.2068    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0719   -0.6186    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7876   -0.2068    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  1  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0030344

> <DATABASE_NAME>
MIME

> <SMILES>
OCCCC(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C4H8O3/c5-3-1-2-4(6)7/h5H,1-3H2,(H,6,7)

> <INCHI_KEY>
SJZRECIVHVDYJC-UHFFFAOYSA-N

> <FORMULA>
C4H8O3

> <MOLECULAR_WEIGHT>
104.1045

> <EXACT_MASS>
104.047344122

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
15

> <JCHEM_AVERAGE_POLARIZABILITY>
10.166134903961725

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
4-hydroxybutanoic acid

> <ALOGPS_LOGP>
-0.63

> <JCHEM_LOGP>
-0.5149198190000002

> <ALOGPS_LOGS>
0.68

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
15.98255965448772

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.440873954984472

> <JCHEM_PKA_STRONGEST_BASIC>
-2.3817124873466886

> <JCHEM_POLAR_SURFACE_AREA>
57.53

> <JCHEM_REFRACTIVITY>
23.800299999999996

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
4.94e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
gamma hydroxybutyric acid

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for #<Metabolite:0x00007f9253ed5b88>

HMDB0000710
     RDKit          3D
4-Hydroxybutyric acid
 15 14  0  0  0  0  0  0  0  0999 V2000
   -2.1528   -0.1631    1.1215 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9111    0.2158   -0.0595 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9931    0.3371   -0.9162 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5016    0.5004   -0.4295 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2840   -0.7629   -0.0936 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7659   -0.5838   -0.4160 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3476    0.4350    0.3065 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1608    1.2490   -1.3394 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3752    0.7302   -1.4861 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1134    1.3710    0.1749 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0841   -1.5641   -0.7822 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1608   -1.0367    0.9684 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2378   -1.5758   -0.2467 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8207   -0.3323   -1.5075 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6751    1.1801   -0.2779 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  2  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  3  8  1  0
  4  9  1  0
  4 10  1  0
  5 11  1  0
  5 12  1  0
  6 13  1  0
  6 14  1  0
  7 15  1  0
M  END
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PDB for #<Metabolite:0x00007f9253ed5b88>

HEADER    PROTEIN                                 07-JUL-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   07-JUL-20         0                                  
HETATM    1  C   UNK     0      -0.668  -1.155   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -2.002  -0.386   0.000  0.00  0.00           C+0
HETATM    3  O   UNK     0      -3.337  -1.155   0.000  0.00  0.00           O+0
HETATM    4  O   UNK     0      -2.002   1.155   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0       0.665  -0.386   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       2.001  -1.155   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       3.337  -0.386   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:0x00007f9253ed5b88>

COMPND    HMDB0000710
HETATM    1  O1  UNL     1      -2.153  -0.163   1.121  1.00  0.00           O  
HETATM    2  C1  UNL     1      -1.911   0.216  -0.060  1.00  0.00           C  
HETATM    3  O2  UNL     1      -2.993   0.337  -0.916  1.00  0.00           O  
HETATM    4  C2  UNL     1      -0.502   0.500  -0.430  1.00  0.00           C  
HETATM    5  C3  UNL     1       0.284  -0.763  -0.094  1.00  0.00           C  
HETATM    6  C4  UNL     1       1.766  -0.584  -0.416  1.00  0.00           C  
HETATM    7  O3  UNL     1       2.348   0.435   0.307  1.00  0.00           O  
HETATM    8  H1  UNL     1      -3.161   1.249  -1.339  1.00  0.00           H  
HETATM    9  H2  UNL     1      -0.375   0.730  -1.486  1.00  0.00           H  
HETATM   10  H3  UNL     1      -0.113   1.371   0.175  1.00  0.00           H  
HETATM   11  H4  UNL     1      -0.084  -1.564  -0.782  1.00  0.00           H  
HETATM   12  H5  UNL     1       0.161  -1.037   0.968  1.00  0.00           H  
HETATM   13  H6  UNL     1       2.238  -1.576  -0.247  1.00  0.00           H  
HETATM   14  H7  UNL     1       1.821  -0.332  -1.508  1.00  0.00           H  
HETATM   15  H8  UNL     1       2.675   1.180  -0.278  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3    4
CONECT    3    8
CONECT    4    5    9   10
CONECT    5    6   11   12
CONECT    6    7   13   14
CONECT    7   15
END
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SMILES for #<Metabolite:0x00007f9253ed5b88>

OCCCC(O)=O
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INCHI for #<Metabolite:0x00007f9253ed5b88>

InChI=1S/C4H8O3/c5-3-1-2-4(6)7/h5H,1-3H2,(H,6,7)
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Synonyms
ValueSource
3-Carboxypropoxy acidChEBI
4-Hydroxy-butyric acidChEBI
4-Hydroxyalkanoic acidChEBI
4-HydroxybutanoateChEBI
4-Hydroxybutanoic acidChEBI
4-Hydroxycarboxylic acidChEBI
Gamma Hydroxybutyric acidChEBI
gamma-Hydroxybutyric acidChEBI
GHBChEBI
Oxy-N-butyric acidChEBI
XyremChEBI
4-Hydroxy-butyrateGenerator
4-HydroxyalkanoateGenerator
4-HydroxycarboxylateGenerator
g HydroxybutyrateGenerator
g Hydroxybutyric acidGenerator
gamma HydroxybutyrateGenerator
Γ hydroxybutyrateGenerator
Γ hydroxybutyric acidGenerator
g-HydroxybutyrateGenerator
g-Hydroxybutyric acidGenerator
gamma-HydroxybutyrateGenerator
Γ-hydroxybutyrateGenerator
Γ-hydroxybutyric acidGenerator
Oxy-N-butyrateGenerator
4-HydroxybutyrateGenerator
4-Hydroxy-butanoateHMDB
4-Hydroxy-butanoic acidHMDB
4-Hydroxybutyrate sodiumHMDB
4-Hydroxybutyric acid monosodium saltHMDB
gamma-Hydroxy butyrateHMDB
gamma-Hydroxy sodium butyrateHMDB
gamma-Hydroxybutyrate sodiumHMDB
Hydroxybutyric acidHMDB
Molecular FormulaC4H8O3
Average Mass104.1045
Monoisotopic Mass104.047344122
IUPAC Name4-hydroxybutanoic acid
Traditional Namegamma hydroxybutyric acid
CAS Registry Number591-81-1
SMILES
OCCCC(O)=O
InChI Identifier
InChI=1S/C4H8O3/c5-3-1-2-4(6)7/h5H,1-3H2,(H,6,7)
InChI KeySJZRECIVHVDYJC-UHFFFAOYSA-N