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Showing metabocard for 3-(Aminomethyl)-5-methylhexanoic acid (HMDB0245784)

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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2021-09-10 22:50:13 UTC
Update Date2021-09-26 22:54:28 UTC
HMDB IDHMDB0245784
Secondary Accession NumbersNone
Metabolite Identification
Common Name3-(Aminomethyl)-5-methylhexanoic acid
Description3-(Aminomethyl)-5-methylhexanoic acid, also known as 3-isobutyl gaba or pregabalin, 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. Based on a literature review a significant number of articles have been published on 3-(Aminomethyl)-5-methylhexanoic acid. This compound has been identified in human blood as reported by (PMID: 31557052 ). 3-(aminomethyl)-5-methylhexanoic acid is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically 3-(Aminomethyl)-5-methylhexanoic acid is part of the human exposome. The exposome can be defined as the collection of all the exposures of an individual in a lifetime and how those exposures relate to health. An individual's exposure begins before birth and includes insults from environmental and occupational sources.
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0245784 (3-(Aminomethyl)-5-methylhexanoic acid)

  Mrv0541 02241205492D          

 11 10  0  0  0  0            999 V2000
    1.7605    1.8414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4750    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4750    0.6039    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1895    1.8414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9039    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9039    0.6039    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6184    0.1914    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.6184    1.8414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3329    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.0474    1.8414    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.3329    0.6039    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  2  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  5  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
  9 11  2  0  0  0  0
M  END
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3D MOL for HMDB0245784 (3-(Aminomethyl)-5-methylhexanoic acid)

HMDB0245784
     RDKit          3D
3-(Aminomethyl)-5-methylhexanoic acid
 28 27  0  0  0  0  0  0  0  0999 V2000
   -2.3318    0.8109   -0.1021 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6693   -0.4533    0.2476 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3973   -1.6239   -0.4425 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2247   -0.6289   -0.0686 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7284    0.3122    0.5546 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5611    1.7686    0.2126 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7117    2.0497   -1.2002 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.1506   -0.0405    0.2117 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5155   -1.3611    0.7176 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7821   -2.0325    1.4522 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.7782   -1.8795    0.3344 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9164    1.3096   -0.9811 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5244    1.4916    0.7714 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3940    0.5448   -0.4199 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7755   -0.6448    1.3463 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8159   -1.9589   -1.3349 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4142   -1.3165   -0.7595 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5253   -2.4709    0.2566 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0209   -1.6699    0.2299 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1057   -0.6646   -1.1943 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6087    0.2413    1.6708 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2987    2.2650    0.6641 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4593    2.2756    0.6940 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1024    2.8634   -1.4283 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3504    1.2320   -1.7305 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7928    0.7675    0.6613 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2877    0.0388   -0.8981 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.5434   -1.2260    0.5350 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  2  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  5  8  1  0
  8  9  1  0
  9 10  2  0
  9 11  1  0
  1 12  1  0
  1 13  1  0
  1 14  1  0
  2 15  1  0
  3 16  1  0
  3 17  1  0
  3 18  1  0
  4 19  1  0
  4 20  1  0
  5 21  1  0
  6 22  1  0
  6 23  1  0
  7 24  1  0
  7 25  1  0
  8 26  1  0
  8 27  1  0
 11 28  1  0
M  END
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3D SDF for HMDB0245784 (3-(Aminomethyl)-5-methylhexanoic acid)

  Mrv0541 02241205492D          

 11 10  0  0  0  0            999 V2000
    1.7605    1.8414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4750    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4750    0.6039    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1895    1.8414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9039    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9039    0.6039    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6184    0.1914    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.6184    1.8414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3329    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.0474    1.8414    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.3329    0.6039    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  2  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  5  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
  9 11  2  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0245784

> <DATABASE_NAME>
hmdb

> <SMILES>
CC(C)CC(CN)CC(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C8H17NO2/c1-6(2)3-7(5-9)4-8(10)11/h6-7H,3-5,9H2,1-2H3,(H,10,11)

> <INCHI_KEY>
AYXYPKUFHZROOJ-UHFFFAOYSA-N

> <FORMULA>
C8H17NO2

> <MOLECULAR_WEIGHT>
159.2261

> <EXACT_MASS>
159.125928793

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_AVERAGE_POLARIZABILITY>
18.007386565347897

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
3-(aminomethyl)-5-methylhexanoic acid

> <ALOGPS_LOGP>
-1.35

> <JCHEM_LOGP>
-1.3455846782464078

> <ALOGPS_LOGS>
-1.15

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.800920428196899

> <JCHEM_PKA_STRONGEST_BASIC>
10.229664216443084

> <JCHEM_POLAR_SURFACE_AREA>
63.32

> <JCHEM_REFRACTIVITY>
43.68000000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.13e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
3-(aminomethyl)-5-methylhexanoic acid

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for HMDB0245784 (3-(Aminomethyl)-5-methylhexanoic acid)

HMDB0245784
     RDKit          3D
3-(Aminomethyl)-5-methylhexanoic acid
 28 27  0  0  0  0  0  0  0  0999 V2000
   -2.3318    0.8109   -0.1021 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6693   -0.4533    0.2476 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3973   -1.6239   -0.4425 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2247   -0.6289   -0.0686 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7284    0.3122    0.5546 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5611    1.7686    0.2126 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7117    2.0497   -1.2002 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.1506   -0.0405    0.2117 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5155   -1.3611    0.7176 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7821   -2.0325    1.4522 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.7782   -1.8795    0.3344 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9164    1.3096   -0.9811 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5244    1.4916    0.7714 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3940    0.5448   -0.4199 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7755   -0.6448    1.3463 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8159   -1.9589   -1.3349 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4142   -1.3165   -0.7595 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5253   -2.4709    0.2566 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0209   -1.6699    0.2299 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1057   -0.6646   -1.1943 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6087    0.2413    1.6708 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2987    2.2650    0.6641 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4593    2.2756    0.6940 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1024    2.8634   -1.4283 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3504    1.2320   -1.7305 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7928    0.7675    0.6613 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2877    0.0388   -0.8981 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.5434   -1.2260    0.5350 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  2  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  5  8  1  0
  8  9  1  0
  9 10  2  0
  9 11  1  0
  1 12  1  0
  1 13  1  0
  1 14  1  0
  2 15  1  0
  3 16  1  0
  3 17  1  0
  3 18  1  0
  4 19  1  0
  4 20  1  0
  5 21  1  0
  6 22  1  0
  6 23  1  0
  7 24  1  0
  7 25  1  0
  8 26  1  0
  8 27  1  0
 11 28  1  0
M  END
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PDB for HMDB0245784 (3-(Aminomethyl)-5-methylhexanoic acid)

HEADER    PROTEIN                                 24-FEB-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-FEB-12         0                                  
HETATM    1  C   UNK     0       3.286   3.437   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       4.620   2.667   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       4.620   1.127   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       5.954   3.437   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       7.287   2.667   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       7.287   1.127   0.000  0.00  0.00           C+0
HETATM    7  N   UNK     0       8.621   0.357   0.000  0.00  0.00           N+0
HETATM    8  C   UNK     0       8.621   3.437   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       9.955   2.667   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0      11.288   3.437   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0       9.955   1.127   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    4                                                  
CONECT    3    2                                                            
CONECT    4    2    5                                                       
CONECT    5    4    6    8                                                  
CONECT    6    5    7                                                       
CONECT    7    6                                                            
CONECT    8    5    9                                                       
CONECT    9    8   10   11                                                  
CONECT   10    9                                                            
CONECT   11    9                                                            
MASTER        0    0    0    0    0    0    0    0   11    0   20    0
END
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3D PDB for HMDB0245784 (3-(Aminomethyl)-5-methylhexanoic acid)

COMPND    HMDB0245784
HETATM    1  C1  UNL     1      -2.332   0.811  -0.102  1.00  0.00           C  
HETATM    2  C2  UNL     1      -1.669  -0.453   0.248  1.00  0.00           C  
HETATM    3  C3  UNL     1      -2.397  -1.624  -0.442  1.00  0.00           C  
HETATM    4  C4  UNL     1      -0.225  -0.629  -0.069  1.00  0.00           C  
HETATM    5  C5  UNL     1       0.728   0.312   0.555  1.00  0.00           C  
HETATM    6  C6  UNL     1       0.561   1.769   0.213  1.00  0.00           C  
HETATM    7  N1  UNL     1       0.712   2.050  -1.200  1.00  0.00           N  
HETATM    8  C7  UNL     1       2.151  -0.040   0.212  1.00  0.00           C  
HETATM    9  C8  UNL     1       2.515  -1.361   0.718  1.00  0.00           C  
HETATM   10  O1  UNL     1       1.782  -2.032   1.452  1.00  0.00           O  
HETATM   11  O2  UNL     1       3.778  -1.879   0.334  1.00  0.00           O  
HETATM   12  H1  UNL     1      -1.916   1.310  -0.981  1.00  0.00           H  
HETATM   13  H2  UNL     1      -2.524   1.492   0.771  1.00  0.00           H  
HETATM   14  H3  UNL     1      -3.394   0.545  -0.420  1.00  0.00           H  
HETATM   15  H4  UNL     1      -1.775  -0.645   1.346  1.00  0.00           H  
HETATM   16  H5  UNL     1      -1.816  -1.959  -1.335  1.00  0.00           H  
HETATM   17  H6  UNL     1      -3.414  -1.316  -0.759  1.00  0.00           H  
HETATM   18  H7  UNL     1      -2.525  -2.471   0.257  1.00  0.00           H  
HETATM   19  H8  UNL     1       0.021  -1.670   0.230  1.00  0.00           H  
HETATM   20  H9  UNL     1      -0.106  -0.665  -1.194  1.00  0.00           H  
HETATM   21  H10 UNL     1       0.609   0.241   1.671  1.00  0.00           H  
HETATM   22  H11 UNL     1      -0.299   2.265   0.664  1.00  0.00           H  
HETATM   23  H12 UNL     1       1.459   2.276   0.694  1.00  0.00           H  
HETATM   24  H13 UNL     1       0.102   2.863  -1.428  1.00  0.00           H  
HETATM   25  H14 UNL     1       0.350   1.232  -1.731  1.00  0.00           H  
HETATM   26  H15 UNL     1       2.793   0.767   0.661  1.00  0.00           H  
HETATM   27  H16 UNL     1       2.288   0.039  -0.898  1.00  0.00           H  
HETATM   28  H17 UNL     1       4.543  -1.226   0.535  1.00  0.00           H  
CONECT    1    2   12   13   14
CONECT    2    3    4   15
CONECT    3   16   17   18
CONECT    4    5   19   20
CONECT    5    6    8   21
CONECT    6    7   22   23
CONECT    7   24   25
CONECT    8    9   26   27
CONECT    9   10   10   11
CONECT   11   28
END
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SMILES for HMDB0245784 (3-(Aminomethyl)-5-methylhexanoic acid)

CC(C)CC(CN)CC(O)=O
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INCHI for HMDB0245784 (3-(Aminomethyl)-5-methylhexanoic acid)

InChI=1S/C8H17NO2/c1-6(2)3-7(5-9)4-8(10)11/h6-7H,3-5,9H2,1-2H3,(H,10,11)
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View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
ValueSource
3-(Aminomethyl)-5-methylhexanoateGenerator
PregabalinHMDB
LyricaHMDB
3-Isobutyl gabaHMDB
3 Isobutyl gabaHMDB
(S)-3-(Aminomethyl)-5-methylhexanoic acidHMDB
GABA, 3-isobutylHMDB
(R-)-3-Isobutyl gabaHMDB
(S+)-3-isobutyl gabaHMDB
Chemical FormulaC8H17NO2
Average Molecular Weight159.2261
Monoisotopic Molecular Weight159.125928793
IUPAC Name3-(aminomethyl)-5-methylhexanoic acid
Traditional Name3-(aminomethyl)-5-methylhexanoic acid
CAS Registry NumberNot Available
SMILES
CC(C)CC(CN)CC(O)=O
InChI Identifier
InChI=1S/C8H17NO2/c1-6(2)3-7(5-9)4-8(10)11/h6-7H,3-5,9H2,1-2H3,(H,10,11)
InChI KeyAYXYPKUFHZROOJ-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
  • Branched fatty acid
  • Fatty acyl
  • Fatty acid
  • Amino acid
  • Carboxylic acid
  • Monocarboxylic acid or derivatives
  • Amine
  • Primary amine
  • Organooxygen compound
  • Organonitrogen compound
  • Hydrocarbon derivative
  • Primary aliphatic amine
  • Organic oxide
  • Organopnictogen compound
  • Carbonyl group
  • Organic oxygen compound
  • Organic nitrogen compound
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External DescriptorsNot Available
Ontology
Physiological effectNot Available
Disposition
Biological locationSource
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
Predicted Chromatographic Properties
Spectra
Biological Properties
Cellular LocationsNot Available
Biospecimen Locations
  • Blood
Tissue LocationsNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodDetected but not QuantifiedNot QuantifiedNot SpecifiedNot SpecifiedNormal details
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDNot Available
KNApSAcK IDNot Available
Chemspider ID3902475
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound4715169
PDB IDNot Available
ChEBI IDNot Available
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. Barupal DK, Fiehn O: Generating the Blood Exposome Database Using a Comprehensive Text Mining and Database Fusion Approach. Environ Health Perspect. 2019 Sep;127(9):97008. doi: 10.1289/EHP4713. Epub 2019 Sep 26. [PubMed:31557052 ]