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Showing metabocard for Vigabatrin (HMDB0015212)

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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2012-09-06 15:16:51 UTC
Update Date2023-02-21 17:18:27 UTC
HMDB IDHMDB0015212
Secondary Accession Numbers
  • HMDB15212
Metabolite Identification
Common NameVigabatrin
DescriptionVigabatrin is only found in individuals that have used or taken this drug. It is an analogue of gamma-aminobutyric acid. It is an irreversible inhibitor of 4-aminobutyrate transaminase, the enzyme responsible for the catabolism of gamma-aminobutyric acid. (From Martindale The Extra Pharmacopoeia, 31st ed)It is believed that vigabatrin increases brain concentrations of gamma-aminobutyric acid (GABA), an inhibitory neurotransmitter in the CNS, by irreversibly inhibiting enzymes that catabolize GABA (gamma-aminobutyric acid transaminase GABA-T) or block the reuptake of GABA into glia and nerve endings. Vigabatrin may also work by suppressing repetitive neuronal firing through inhibition of voltage-sensitive sodium channels.
Structure
Data?1676999907
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0015212 (Vigabatrin)

1080
  Mrv0541 02231215132D          

  9  8  0  0  1  0            999 V2000
    2.0930    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8075    1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.6655    0.4125    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.2365    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9509    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5220    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9509   -0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8075    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2365   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  8  1  0  0  0  0
  2  8  2  0  0  0  0
  3  5  1  0  0  0  0
  4  5  1  0  0  0  0
  4  6  1  0  0  0  0
  5  7  1  0  0  0  0
  6  8  1  0  0  0  0
  7  9  2  0  0  0  0
M  END
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3D MOL for HMDB0015212 (Vigabatrin)

HMDB0015212
     RDKit          3D
Vigabatrin
 20 19  0  0  0  0  0  0  0  0999 V2000
   -2.5345    0.4502   -0.8830 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5350   -0.2179   -0.3474 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6291    0.4879    0.5975 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4288    0.9017    1.7518 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.4463   -0.4251    1.1176 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3147   -0.9842    0.0277 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9923    0.1085   -0.7173 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3394    0.7419   -1.5638 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.3201    0.4544   -0.5115 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6796    1.4864   -0.6313 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1980   -0.0523   -1.5712 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3827   -1.2667   -0.5983 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2193    1.3949    0.1086 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8398    0.0575    2.2004 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7289    1.2733    2.4511 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0535   -1.2843    1.6122 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0945    0.1515    1.8023 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7206   -1.6305   -0.6533 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1022   -1.5945    0.5139 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8991   -0.0528    0.1625 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  3
  2  3  1  0
  3  4  1  0
  3  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  2  0
  7  9  1  0
  1 10  1  0
  1 11  1  0
  2 12  1  0
  3 13  1  0
  4 14  1  0
  4 15  1  0
  5 16  1  0
  5 17  1  0
  6 18  1  0
  6 19  1  0
  9 20  1  0
M  END
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3D SDF for HMDB0015212 (Vigabatrin)

1080
  Mrv0541 02231215132D          

  9  8  0  0  1  0            999 V2000
    2.0930    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8075    1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.6655    0.4125    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.2365    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9509    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5220    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9509   -0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8075    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2365   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  8  1  0  0  0  0
  2  8  2  0  0  0  0
  3  5  1  0  0  0  0
  4  5  1  0  0  0  0
  4  6  1  0  0  0  0
  5  7  1  0  0  0  0
  6  8  1  0  0  0  0
  7  9  2  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0015212

> <DATABASE_NAME>
hmdb

> <SMILES>
NC(CCC(O)=O)C=C

> <INCHI_IDENTIFIER>
InChI=1S/C6H11NO2/c1-2-5(7)3-4-6(8)9/h2,5H,1,3-4,7H2,(H,8,9)

> <INCHI_KEY>
PJDFLNIOAUIZSL-UHFFFAOYSA-N

> <FORMULA>
C6H11NO2

> <MOLECULAR_WEIGHT>
129.157

> <EXACT_MASS>
129.078978601

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_AVERAGE_POLARIZABILITY>
13.635304328033918

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
4-aminohex-5-enoic acid

> <ALOGPS_LOGP>
-2.56

> <JCHEM_LOGP>
-2.0949147846992218

> <ALOGPS_LOGS>
-0.13

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.6081127693185415

> <JCHEM_PKA_STRONGEST_BASIC>
9.905622436434145

> <JCHEM_POLAR_SURFACE_AREA>
63.31999999999999

> <JCHEM_REFRACTIVITY>
34.2907

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
9.66e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
vigabatrin

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for HMDB0015212 (Vigabatrin)

HMDB0015212
     RDKit          3D
Vigabatrin
 20 19  0  0  0  0  0  0  0  0999 V2000
   -2.5345    0.4502   -0.8830 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5350   -0.2179   -0.3474 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6291    0.4879    0.5975 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4288    0.9017    1.7518 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.4463   -0.4251    1.1176 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3147   -0.9842    0.0277 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9923    0.1085   -0.7173 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3394    0.7419   -1.5638 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.3201    0.4544   -0.5115 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6796    1.4864   -0.6313 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1980   -0.0523   -1.5712 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3827   -1.2667   -0.5983 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2193    1.3949    0.1086 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8398    0.0575    2.2004 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7289    1.2733    2.4511 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0535   -1.2843    1.6122 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0945    0.1515    1.8023 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7206   -1.6305   -0.6533 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1022   -1.5945    0.5139 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8991   -0.0528    0.1625 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  3
  2  3  1  0
  3  4  1  0
  3  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  2  0
  7  9  1  0
  1 10  1  0
  1 11  1  0
  2 12  1  0
  3 13  1  0
  4 14  1  0
  4 15  1  0
  5 16  1  0
  5 17  1  0
  6 18  1  0
  6 19  1  0
  9 20  1  0
M  END
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PDB for HMDB0015212 (Vigabatrin)

HEADER    PROTEIN                                 23-FEB-12   NONE
TITLE     NULL                                                        
COMPND    MOLECULE: 1080                                              
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   23-FEB-12         0                                  
HETATM    1  O   UNK     0       3.907   0.000   0.000  0.00  0.00           O+0
HETATM    2  O   UNK     0       5.241   2.310   0.000  0.00  0.00           O+0
HETATM    3  N   UNK     0      10.576   0.770   0.000  0.00  0.00           N+0
HETATM    4  C   UNK     0       7.908   0.770   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       9.242   0.000   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       6.574   0.000   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       9.242  -1.540   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       5.241   0.770   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       7.908  -2.310   0.000  0.00  0.00           C+0
CONECT    1    8                                                            
CONECT    2    8                                                            
CONECT    3    5                                                            
CONECT    4    5    6                                                       
CONECT    5    3    4    7                                                  
CONECT    6    4    8                                                       
CONECT    7    5    9                                                       
CONECT    8    1    2    6                                                  
CONECT    9    7                                                            
MASTER        0    0    0    0    0    0    0    0    9    0   16    0
END
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3D PDB for HMDB0015212 (Vigabatrin)

COMPND    HMDB0015212
HETATM    1  C1  UNL     1      -2.535   0.450  -0.883  1.00  0.00           C  
HETATM    2  C2  UNL     1      -1.535  -0.218  -0.347  1.00  0.00           C  
HETATM    3  C3  UNL     1      -0.629   0.488   0.598  1.00  0.00           C  
HETATM    4  N1  UNL     1      -1.429   0.902   1.752  1.00  0.00           N  
HETATM    5  C4  UNL     1       0.446  -0.425   1.118  1.00  0.00           C  
HETATM    6  C5  UNL     1       1.315  -0.984   0.028  1.00  0.00           C  
HETATM    7  C6  UNL     1       1.992   0.109  -0.717  1.00  0.00           C  
HETATM    8  O1  UNL     1       1.339   0.742  -1.564  1.00  0.00           O  
HETATM    9  O2  UNL     1       3.320   0.454  -0.512  1.00  0.00           O  
HETATM   10  H1  UNL     1      -2.680   1.486  -0.631  1.00  0.00           H  
HETATM   11  H2  UNL     1      -3.198  -0.052  -1.571  1.00  0.00           H  
HETATM   12  H3  UNL     1      -1.383  -1.267  -0.598  1.00  0.00           H  
HETATM   13  H4  UNL     1      -0.219   1.395   0.109  1.00  0.00           H  
HETATM   14  H5  UNL     1      -1.840   0.058   2.200  1.00  0.00           H  
HETATM   15  H6  UNL     1      -0.729   1.273   2.451  1.00  0.00           H  
HETATM   16  H7  UNL     1      -0.053  -1.284   1.612  1.00  0.00           H  
HETATM   17  H8  UNL     1       1.094   0.152   1.802  1.00  0.00           H  
HETATM   18  H9  UNL     1       0.721  -1.631  -0.653  1.00  0.00           H  
HETATM   19  H10 UNL     1       2.102  -1.595   0.514  1.00  0.00           H  
HETATM   20  H11 UNL     1       3.899  -0.053   0.163  1.00  0.00           H  
CONECT    1    2    2   10   11
CONECT    2    3   12
CONECT    3    4    5   13
CONECT    4   14   15
CONECT    5    6   16   17
CONECT    6    7   18   19
CONECT    7    8    8    9
CONECT    9   20
END
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SMILES for HMDB0015212 (Vigabatrin)

NC(CCC(O)=O)C=C
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INCHI for HMDB0015212 (Vigabatrin)

InChI=1S/C6H11NO2/c1-2-5(7)3-4-6(8)9/h2,5H,1,3-4,7H2,(H,8,9)
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View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
Chemical FormulaC6H11NO2
Average Molecular Weight129.157
Monoisotopic Molecular Weight129.078978601
IUPAC Name4-aminohex-5-enoic acid
Traditional Namevigabatrin
CAS Registry Number60643-86-9
SMILES
NC(CCC(O)=O)C=C
InChI Identifier
InChI=1S/C6H11NO2/c1-2-5(7)3-4-6(8)9/h2,5H,1,3-4,7H2,(H,8,9)
InChI KeyPJDFLNIOAUIZSL-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as gamma amino acids and derivatives. These are amino acids having a (-NH2) group attached to the gamma carbon atom.
KingdomOrganic compounds
Super ClassOrganic acids and derivatives
ClassCarboxylic acids and derivatives
Sub ClassAmino acids, peptides, and analogues
Direct ParentGamma amino acids and derivatives
Alternative Parents
Substituents
  • Gamma amino acid or derivatives
  • Medium-chain fatty acid
  • Amino fatty acid
  • Unsaturated fatty acid
  • Fatty acyl
  • Fatty acid
  • Amino acid
  • Carboxylic acid
  • Monocarboxylic acid or derivatives
  • Amine
  • Hydrocarbon derivative
  • Primary amine
  • Organooxygen compound
  • Organonitrogen compound
  • Organic oxide
  • Primary aliphatic amine
  • Organopnictogen compound
  • Organic oxygen compound
  • Carbonyl group
  • Organic nitrogen compound
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Ontology
Physiological effectNot Available
Disposition
Biological locationSource
ProcessNot Available
RoleNot Available
Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water Solubility96.6 g/LNot Available
LogP0.1Not Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
Predicted Chromatographic Properties
Spectra
Biological Properties
Cellular Locations
  • Cytoplasm
  • Extracellular
  • Membrane
Biospecimen Locations
  • Blood
  • Urine
Tissue LocationsNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodExpected but not QuantifiedNot QuantifiedNot AvailableNot AvailableTaking drug identified by DrugBank entry DB01080 details
UrineExpected but not QuantifiedNot QuantifiedNot AvailableNot AvailableTaking drug identified by DrugBank entry DB01080 details
Abnormal Concentrations
Not Available
Predicted Concentrations
BiospecimenValueOriginal ageOriginal sexOriginal conditionComments
Blood0.000 uMAdult (>18 years old)BothNormalPredicted based on drug qualities
Blood0.000 umol/mmol creatinineAdult (>18 years old)BothNormalPredicted based on drug qualities
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDDB01080
Phenol Explorer Compound IDNot Available
FooDB IDNot Available
KNApSAcK IDNot Available
Chemspider ID5463
KEGG Compound IDC07500
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkVigabatrin
METLIN IDNot Available
PubChem Compound5665
PDB IDNot Available
ChEBI ID63638
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 References
  1. Lindberger M, Luhr O, Johannessen SI, Larsson S, Tomson T: Serum concentrations and effects of gabapentin and vigabatrin: observations from a dose titration study. Ther Drug Monit. 2003 Aug;25(4):457-62. [PubMed:12883229 ]
  2. Gram L, Larsson OM, Johnsen A, Schousboe A: Experimental studies of the influence of vigabatrin on the GABA system. Br J Clin Pharmacol. 1989;27 Suppl 1:13S-17S. [PubMed:2757904 ]
  3. Browne TR: Pharmacokinetics of antiepileptic drugs. Neurology. 1998 Nov;51(5 Suppl 4):S2-7. [PubMed:9818917 ]
  4. Zwanzger P, Baghai TC, Schuele C, Strohle A, Padberg F, Kathmann N, Schwarz M, Moller HJ, Rupprecht R: Vigabatrin decreases cholecystokinin-tetrapeptide (CCK-4) induced panic in healthy volunteers. Neuropsychopharmacology. 2001 Nov;25(5):699-703. [PubMed:11682253 ]
  5. Hawker DD, Silverman RB: Synthesis and evaluation of novel heteroaromatic substrates of GABA aminotransferase. Bioorg Med Chem. 2012 Oct 1;20(19):5763-73. doi: 10.1016/j.bmc.2012.08.009. Epub 2012 Aug 16. [PubMed:22944334 ]
  6. Tulloch JK, Carr RR, Ensom MH: A systematic review of the pharmacokinetics of antiepileptic drugs in neonates with refractory seizures. J Pediatr Pharmacol Ther. 2012 Jan;17(1):31-44. doi: 10.5863/1551-6776-17.1.31. [PubMed:23118657 ]
  7. Clayton LM, Stern WM, Newman WD, Sander JW, Acheson J, Sisodiya SM: Evolution of visual field loss over ten years in individuals taking vigabatrin. Epilepsy Res. 2013 Aug;105(3):262-71. doi: 10.1016/j.eplepsyres.2013.02.014. Epub 2013 Mar 28. [PubMed:23541931 ]

Enzymes

Enzyme Details
1. 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
References
  1. Weber OM, Verhagen A, Duc CO, Meier D, Leenders KL, Boesiger P: Effects of vigabatrin intake on brain GABA activity as monitored by spectrally edited magnetic resonance spectroscopy and positron emission tomography. Magn Reson Imaging. 1999 Apr;17(3):417-25. [PubMed:10195585 ]
  2. Valdizan EM, Garcia AP, Armijo JA: Effects of increasing doses of vigabatrin on platelet gamma-aminobutyric acid-transaminase and brain gamma-aminobutyric acid in rats. Eur J Pharmacol. 1999 Mar 19;369(2):169-73. [PubMed:10206175 ]
  3. Arndt CF, Derambure P, Defoort-Dhellemmes S, Hache JC: Outer retinal dysfunction in patients treated with vigabatrin. Neurology. 1999 Apr 12;52(6):1201-5. [PubMed:10214744 ]
  4. Molina PE, Ahmed N, Ajmal M, Dewey S, Volkow N, Fowler J, Abumrad N: Co-administration of gamma-vinyl GABA and cocaine: preclinical assessment of safety. Life Sci. 1999;65(11):1175-82. [PubMed:10503933 ]
  5. French JA: Vigabatrin. Epilepsia. 1999;40 Suppl 5:S11-6. [PubMed:10530689 ]
  6. Chen X, Ji ZL, Chen YZ: TTD: Therapeutic Target Database. Nucleic Acids Res. 2002 Jan 1;30(1):412-5. [PubMed:11752352 ]
Enzyme Details
2. Gamma-aminobutyric acid type B receptor subunit 1
General function:
Involved in G-protein coupled receptor activity
Specific function:
Isoform 1E function may be to regulate the availability of functional GABA-B-R1A/GABA-B-R2 heterodimers by competing for GABA-B-R2 dimerization. This could explain the observation that certain small molecule ligands exhibit differential affinity for central versus peripheral sites
Gene Name:
GABBR1
Uniprot ID:
Q9UBS5
Molecular weight:
108319.4
References
  1. Tyacke RJ, Lingford-Hughes A, Reed LJ, Nutt DJ: GABAB receptors in addiction and its treatment. Adv Pharmacol. 2010;58:373-96. doi: 10.1016/S1054-3589(10)58014-1. [PubMed:20655489 ]