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Record Information

Version

5.0

Status

Expected but not Quantified

Creation Date

2021-09-23 17:10:43 UTC

Update Date

2021-09-23 17:10:44 UTC

HMDB ID

HMDB0302358

Secondary Accession Numbers

None

Metabolite Identification

Common Name

Amabiline

Description

Amabiline belongs to alkaloids and derivatives class of compounds. Those are naturally occurring chemical compounds that contain mostly basic nitrogen atoms. This group also includes some related compounds with neutral and even weakly acidic propertiesand is also some synthetic compounds of similar structure are attributed to alkaloids. In addition to carbon, hydrogen and nitrogen, alkaloids may also contain oxygen, sulfur and more rarely other elements such as chlorine, bromine, and phosphorus. Amabiline is soluble (in water) and a very weakly acidic compound (based on its pKa). Amabiline can be found in borage, which makes amabiline a potential biomarker for the consumption of this food product.

Structure

MOL 3D MOL SDF 3D SDF PDB 3D PDB SMILES InChI

HMDB0302358
     RDKit          3D
Amabiline
 45 46  0  0  0  0  0  0  0  0999 V2000
   -2.5221   -1.8655    0.2661 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6673   -0.6890    1.1570 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0347   -0.7607    1.8129 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4897    0.6557    0.5389 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.6734    1.5740    1.6282 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1455    0.8898    0.0044 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3990    1.8000    0.5066 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5796    0.1853   -1.0424 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7098    0.4658   -1.4858 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7887    0.2382   -0.5090 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6630   -0.2040    0.7270 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0311   -0.2837    1.3660 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7474    0.7297    0.6190 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.1612    0.4605    0.5312 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.2705   -0.6994   -0.4587 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9576   -0.7757   -1.1728 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2375    0.4744   -0.7401 C   0  0  1  0  0  0  0  0  0  0  0  0
   -3.5871    1.0034   -0.4458 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.5657    0.2099   -1.7151 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3889    2.3624   -0.7971 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0288   -1.6033   -0.6857 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8703   -2.6599    0.7374 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5021   -2.3715    0.0300 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9060   -0.7854    1.9750 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1160   -1.6338    2.4996 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2604    0.1347    2.4173 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8373   -0.8797    1.0562 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1097    2.3623    1.4426 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8888   -0.2506   -2.3468 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8024    1.4647   -1.9710 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7596   -0.5006    1.2895 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9874   -0.0907    2.4393 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4391   -1.2905    1.1130 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.6124    0.2290    1.5009 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.6447    1.3692    0.1084 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.0912   -0.4489   -1.1624 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.5335   -1.6210    0.1001 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1251   -0.7308   -2.2728 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3954   -1.7015   -0.9593 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4470    1.3221   -1.3965 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5927    0.8833    0.0040 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1939    0.7802   -2.4770 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0558   -0.7757   -1.6326 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5794    0.1371   -2.2002 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1882    2.8900   -0.5611 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  1
  4  6  1  0
  6  7  2  0
  6  8  1  0
  8  9  1  0
  9 10  1  0
 10 11  2  0
 11 12  1  0
 12 13  1  0
 13 14  1  0
 14 15  1  0
 15 16  1  0
 16 17  1  0
  4 18  1  0
 18 19  1  0
 18 20  1  0
 17 10  1  0
 17 13  1  0
  1 21  1  0
  1 22  1  0
  1 23  1  0
  2 24  1  0
  3 25  1  0
  3 26  1  0
  3 27  1  0
  5 28  1  0
  9 29  1  0
  9 30  1  0
 11 31  1  0
 12 32  1  0
 12 33  1  0
 14 34  1  0
 14 35  1  0
 15 36  1  0
 15 37  1  0
 16 38  1  0
 16 39  1  0
 17 40  1  6
 18 41  1  1
 19 42  1  0
 19 43  1  0
 19 44  1  0
 20 45  1  0
M  END


  Mrv0541 02241221122D          

 21 22  0  0  1  0            999 V2000
   10.9047  -12.0474    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   11.6782  -11.7689    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.9323  -12.8689    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   10.1039  -11.8239    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.1835  -12.4152    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.6782  -10.9405    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.7229  -13.0992    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.1623  -13.1577    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.6432  -12.5149    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.3897  -10.5246    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   13.1013  -10.9371    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.8162  -10.5212    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   13.0978  -11.7620    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   13.8129   -9.6962    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.5313  -10.9336    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   14.5231  -10.1036    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   14.5244   -9.2803    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.0944   -9.2837    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.2427  -10.5178    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.5244  -11.7586    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   10.8945  -11.2189    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  3  1  0  0  0  0
  1  4  1  0  0  0  0
  2  5  2  0  0  0  0
  2  6  1  0  0  0  0
  3  7  1  0  0  0  0
  3  8  1  0  0  0  0
  4  9  1  0  0  0  0
  6 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
 11 13  2  0  0  0  0
 12 14  1  6  0  0  0
 12 15  1  0  0  0  0
 12 16  1  1  0  0  0
 14 17  1  0  0  0  0
 14 18  1  0  0  0  0
 15 19  1  0  0  0  0
 15 20  1  6  0  0  0
  5  7  1  0  0  0  0
  8  9  1  0  0  0  0
  1 21  1  6  0  0  0
M  END
> <DATABASE_ID>
HMDB0302358

> <DATABASE_NAME>
hmdb

> <SMILES>
[H][C@@]12CCCN1CC=C2COC(=O)[C@](O)(C(C)C)[C@H](C)O

> <INCHI_IDENTIFIER>
InChI=1S/C15H25NO4/c1-10(2)15(19,11(3)17)14(18)20-9-12-6-8-16-7-4-5-13(12)16/h6,10-11,13,17,19H,4-5,7-9H2,1-3H3/t11-,13-,15-/m0/s1

> <INCHI_KEY>
DRVWTOSBCBKXOR-WHOFXGATSA-N

> <FORMULA>
C15H25NO4

> <MOLECULAR_WEIGHT>
283.3633

> <EXACT_MASS>
283.178358293

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_AVERAGE_POLARIZABILITY>
30.93623197568353

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(7aS)-2,3,5,7a-tetrahydro-1H-pyrrolizin-7-ylmethyl (2S)-2-hydroxy-2-[(1S)-1-hydroxyethyl]-3-methylbutanoate

> <ALOGPS_LOGP>
1.36

> <JCHEM_LOGP>
0.8565826193333326

> <ALOGPS_LOGS>
-0.99

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA>
14.8008992296846

> <JCHEM_PKA_STRONGEST_ACIDIC>
11.347056084806054

> <JCHEM_PKA_STRONGEST_BASIC>
9.357099704932287

> <JCHEM_POLAR_SURFACE_AREA>
70

> <JCHEM_REFRACTIVITY>
76.6246

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.89e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
amabiline

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0302358
     RDKit          3D
Amabiline
 45 46  0  0  0  0  0  0  0  0999 V2000
   -2.5221   -1.8655    0.2661 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6673   -0.6890    1.1570 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0347   -0.7607    1.8129 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4897    0.6557    0.5389 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.6734    1.5740    1.6282 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1455    0.8898    0.0044 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3990    1.8000    0.5066 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5796    0.1853   -1.0424 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7098    0.4658   -1.4858 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7887    0.2382   -0.5090 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6630   -0.2040    0.7270 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0311   -0.2837    1.3660 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7474    0.7297    0.6190 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.1612    0.4605    0.5312 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.2705   -0.6994   -0.4587 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9576   -0.7757   -1.1728 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2375    0.4744   -0.7401 C   0  0  1  0  0  0  0  0  0  0  0  0
   -3.5871    1.0034   -0.4458 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.5657    0.2099   -1.7151 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3889    2.3624   -0.7971 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0288   -1.6033   -0.6857 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8703   -2.6599    0.7374 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5021   -2.3715    0.0300 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9060   -0.7854    1.9750 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1160   -1.6338    2.4996 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2604    0.1347    2.4173 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8373   -0.8797    1.0562 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1097    2.3623    1.4426 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8888   -0.2506   -2.3468 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8024    1.4647   -1.9710 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7596   -0.5006    1.2895 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9874   -0.0907    2.4393 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4391   -1.2905    1.1130 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.6124    0.2290    1.5009 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.6447    1.3692    0.1084 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.0912   -0.4489   -1.1624 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.5335   -1.6210    0.1001 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1251   -0.7308   -2.2728 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3954   -1.7015   -0.9593 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4470    1.3221   -1.3965 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5927    0.8833    0.0040 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1939    0.7802   -2.4770 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0558   -0.7757   -1.6326 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5794    0.1371   -2.2002 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1882    2.8900   -0.5611 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  1
  4  6  1  0
  6  7  2  0
  6  8  1  0
  8  9  1  0
  9 10  1  0
 10 11  2  0
 11 12  1  0
 12 13  1  0
 13 14  1  0
 14 15  1  0
 15 16  1  0
 16 17  1  0
  4 18  1  0
 18 19  1  0
 18 20  1  0
 17 10  1  0
 17 13  1  0
  1 21  1  0
  1 22  1  0
  1 23  1  0
  2 24  1  0
  3 25  1  0
  3 26  1  0
  3 27  1  0
  5 28  1  0
  9 29  1  0
  9 30  1  0
 11 31  1  0
 12 32  1  0
 12 33  1  0
 14 34  1  0
 14 35  1  0
 15 36  1  0
 15 37  1  0
 16 38  1  0
 16 39  1  0
 17 40  1  6
 18 41  1  1
 19 42  1  0
 19 43  1  0
 19 44  1  0
 20 45  1  0
M  END

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      20.355 -22.488   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      21.799 -21.969   0.000  0.00  0.00           C+0
HETATM    3  N   UNK     0      20.407 -24.022   0.000  0.00  0.00           N+0
HETATM    4  C   UNK     0      18.861 -22.071   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      22.743 -23.175   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      21.799 -20.422   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      21.883 -24.452   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      18.970 -24.561   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      18.001 -23.361   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0      23.127 -19.646   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0      24.456 -20.416   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      25.790 -19.640   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0      24.449 -21.956   0.000  0.00  0.00           O+0
HETATM   14  C   UNK     0      25.784 -18.100   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      27.125 -20.409   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0      27.110 -18.860   0.000  0.00  0.00           O+0
HETATM   17  C   UNK     0      27.112 -17.323   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      24.443 -17.330   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      28.453 -19.633   0.000  0.00  0.00           C+0
HETATM   20  O   UNK     0      27.112 -21.949   0.000  0.00  0.00           O+0
HETATM   21  H   UNK     0      20.336 -20.942   0.000  0.00  0.00           H+0
CONECT    1    2    3    4   21                                             
CONECT    2    1    5    6                                                  
CONECT    3    1    7    8                                                  
CONECT    4    1    9                                                       
CONECT    5    2    7                                                       
CONECT    6    2   10                                                       
CONECT    7    3    5                                                       
CONECT    8    3    9                                                       
CONECT    9    4    8                                                       
CONECT   10    6   11                                                       
CONECT   11   10   12   13                                                  
CONECT   12   11   14   15   16                                             
CONECT   13   11                                                            
CONECT   14   12   17   18                                                  
CONECT   15   12   19   20                                                  
CONECT   16   12                                                            
CONECT   17   14                                                            
CONECT   18   14                                                            
CONECT   19   15                                                            
CONECT   20   15                                                            
CONECT   21    1                                                            
MASTER        0    0    0    0    0    0    0    0   21    0   44    0
END

COMPND    HMDB0302358
HETATM    1  C1  UNL     1      -2.522  -1.865   0.266  1.00  0.00           C  
HETATM    2  C2  UNL     1      -2.667  -0.689   1.157  1.00  0.00           C  
HETATM    3  C3  UNL     1      -4.035  -0.761   1.813  1.00  0.00           C  
HETATM    4  C4  UNL     1      -2.490   0.656   0.539  1.00  0.00           C  
HETATM    5  O1  UNL     1      -2.673   1.574   1.628  1.00  0.00           O  
HETATM    6  C5  UNL     1      -1.146   0.890   0.004  1.00  0.00           C  
HETATM    7  O2  UNL     1      -0.399   1.800   0.507  1.00  0.00           O  
HETATM    8  O3  UNL     1      -0.580   0.185  -1.042  1.00  0.00           O  
HETATM    9  C6  UNL     1       0.710   0.466  -1.486  1.00  0.00           C  
HETATM   10  C7  UNL     1       1.789   0.238  -0.509  1.00  0.00           C  
HETATM   11  C8  UNL     1       1.663  -0.204   0.727  1.00  0.00           C  
HETATM   12  C9  UNL     1       3.031  -0.284   1.366  1.00  0.00           C  
HETATM   13  N1  UNL     1       3.747   0.730   0.619  1.00  0.00           N  
HETATM   14  C10 UNL     1       5.161   0.460   0.531  1.00  0.00           C  
HETATM   15  C11 UNL     1       5.270  -0.699  -0.459  1.00  0.00           C  
HETATM   16  C12 UNL     1       3.958  -0.776  -1.173  1.00  0.00           C  
HETATM   17  C13 UNL     1       3.238   0.474  -0.740  1.00  0.00           C  
HETATM   18  C14 UNL     1      -3.587   1.003  -0.446  1.00  0.00           C  
HETATM   19  C15 UNL     1      -3.566   0.210  -1.715  1.00  0.00           C  
HETATM   20  O4  UNL     1      -3.389   2.362  -0.797  1.00  0.00           O  
HETATM   21  H1  UNL     1      -2.029  -1.603  -0.686  1.00  0.00           H  
HETATM   22  H2  UNL     1      -1.870  -2.660   0.737  1.00  0.00           H  
HETATM   23  H3  UNL     1      -3.502  -2.372   0.030  1.00  0.00           H  
HETATM   24  H4  UNL     1      -1.906  -0.785   1.975  1.00  0.00           H  
HETATM   25  H5  UNL     1      -4.116  -1.634   2.500  1.00  0.00           H  
HETATM   26  H6  UNL     1      -4.260   0.135   2.417  1.00  0.00           H  
HETATM   27  H7  UNL     1      -4.837  -0.880   1.056  1.00  0.00           H  
HETATM   28  H8  UNL     1      -2.110   2.362   1.443  1.00  0.00           H  
HETATM   29  H9  UNL     1       0.889  -0.251  -2.347  1.00  0.00           H  
HETATM   30  H10 UNL     1       0.802   1.465  -1.971  1.00  0.00           H  
HETATM   31  H11 UNL     1       0.760  -0.501   1.290  1.00  0.00           H  
HETATM   32  H12 UNL     1       2.987  -0.091   2.439  1.00  0.00           H  
HETATM   33  H13 UNL     1       3.439  -1.290   1.113  1.00  0.00           H  
HETATM   34  H14 UNL     1       5.612   0.229   1.501  1.00  0.00           H  
HETATM   35  H15 UNL     1       5.645   1.369   0.108  1.00  0.00           H  
HETATM   36  H16 UNL     1       6.091  -0.449  -1.162  1.00  0.00           H  
HETATM   37  H17 UNL     1       5.534  -1.621   0.100  1.00  0.00           H  
HETATM   38  H18 UNL     1       4.125  -0.731  -2.273  1.00  0.00           H  
HETATM   39  H19 UNL     1       3.395  -1.702  -0.959  1.00  0.00           H  
HETATM   40  H20 UNL     1       3.447   1.322  -1.396  1.00  0.00           H  
HETATM   41  H21 UNL     1      -4.593   0.883   0.004  1.00  0.00           H  
HETATM   42  H22 UNL     1      -4.194   0.780  -2.477  1.00  0.00           H  
HETATM   43  H23 UNL     1      -4.056  -0.776  -1.633  1.00  0.00           H  
HETATM   44  H24 UNL     1      -2.579   0.137  -2.200  1.00  0.00           H  
HETATM   45  H25 UNL     1      -4.188   2.890  -0.561  1.00  0.00           H  
CONECT    1    2   21   22   23
CONECT    2    3    4   24
CONECT    3   25   26   27
CONECT    4    5    6   18
CONECT    5   28
CONECT    6    7    7    8
CONECT    8    9
CONECT    9   10   29   30
CONECT   10   11   11   17
CONECT   11   12   31
CONECT   12   13   32   33
CONECT   13   14   17
CONECT   14   15   34   35
CONECT   15   16   36   37
CONECT   16   17   38   39
CONECT   17   40
CONECT   18   19   20   41
CONECT   19   42   43   44
CONECT   20   45
END

HMDB0302358
     RDKit          3D
Amabiline
 45 46  0  0  0  0  0  0  0  0999 V2000
   -2.5221   -1.8655    0.2661 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6673   -0.6890    1.1570 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0347   -0.7607    1.8129 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4897    0.6557    0.5389 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.6734    1.5740    1.6282 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1455    0.8898    0.0044 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3990    1.8000    0.5066 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5796    0.1853   -1.0424 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7098    0.4658   -1.4858 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7887    0.2382   -0.5090 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6630   -0.2040    0.7270 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0311   -0.2837    1.3660 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7474    0.7297    0.6190 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.1612    0.4605    0.5312 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.2705   -0.6994   -0.4587 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9576   -0.7757   -1.1728 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2375    0.4744   -0.7401 C   0  0  1  0  0  0  0  0  0  0  0  0
   -3.5871    1.0034   -0.4458 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.5657    0.2099   -1.7151 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3889    2.3624   -0.7971 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0288   -1.6033   -0.6857 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8703   -2.6599    0.7374 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5021   -2.3715    0.0300 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9060   -0.7854    1.9750 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1160   -1.6338    2.4996 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2604    0.1347    2.4173 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8373   -0.8797    1.0562 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1097    2.3623    1.4426 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8888   -0.2506   -2.3468 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8024    1.4647   -1.9710 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7596   -0.5006    1.2895 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9874   -0.0907    2.4393 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4391   -1.2905    1.1130 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.6124    0.2290    1.5009 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.6447    1.3692    0.1084 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.0912   -0.4489   -1.1624 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.5335   -1.6210    0.1001 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1251   -0.7308   -2.2728 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3954   -1.7015   -0.9593 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4470    1.3221   -1.3965 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5927    0.8833    0.0040 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1939    0.7802   -2.4770 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0558   -0.7757   -1.6326 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5794    0.1371   -2.2002 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1882    2.8900   -0.5611 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  1
  4  6  1  0
  6  7  2  0
  6  8  1  0
  8  9  1  0
  9 10  1  0
 10 11  2  0
 11 12  1  0
 12 13  1  0
 13 14  1  0
 14 15  1  0
 15 16  1  0
 16 17  1  0
  4 18  1  0
 18 19  1  0
 18 20  1  0
 17 10  1  0
 17 13  1  0
  1 21  1  0
  1 22  1  0
  1 23  1  0
  2 24  1  0
  3 25  1  0
  3 26  1  0
  3 27  1  0
  5 28  1  0
  9 29  1  0
  9 30  1  0
 11 31  1  0
 12 32  1  0
 12 33  1  0
 14 34  1  0
 14 35  1  0
 15 36  1  0
 15 37  1  0
 16 38  1  0
 16 39  1  0
 17 40  1  6
 18 41  1  1
 19 42  1  0
 19 43  1  0
 19 44  1  0
 20 45  1  0
M  END

View in JSmol View Stereo Labels

Synonyms

Value	Source
Butanoic acid, 2,3-dihydroxy-2-(1-methylethyl)-, (2,3,5,7a-tetrahydro-1H-pyrrolidizin-7-yl)methyl ester	ChEBI
Butanoate, 2,3-dihydroxy-2-(1-methylethyl)-, (2,3,5,7a-tetrahydro-1H-pyrrolidizin-7-yl)methyl ester	Generator

Chemical Formula

C₁₅H₂₅NO₄

Average Molecular Weight

283.3633

Monoisotopic Molecular Weight

283.178358293

IUPAC Name

(7aS)-2,3,5,7a-tetrahydro-1H-pyrrolizin-7-ylmethyl (2S)-2-hydroxy-2-[(1S)-1-hydroxyethyl]-3-methylbutanoate

Traditional Name

amabiline

CAS Registry Number

Not Available

SMILES

[H][C@@]12CCCN1CC=C2COC(=O)[C@](O)(C(C)C)[C@H](C)O

InChI Identifier

InChI=1S/C15H25NO4/c1-10(2)15(19,11(3)17)14(18)20-9-12-6-8-16-7-4-5-13(12)16/h6,10-11,13,17,19H,4-5,7-9H2,1-3H3/t11-,13-,15-/m0/s1

InChI Key

DRVWTOSBCBKXOR-WHOFXGATSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as alkaloids and derivatives. These are naturally occurring chemical compounds that contain mostly basic nitrogen atoms. This group also includes some related compounds with neutral and even weakly acidic properties. Also some synthetic compounds of similar structure are attributed to alkaloids. In addition to carbon, hydrogen and nitrogen, alkaloids may also contain oxygen, sulfur and more rarely other elements such as chlorine, bromine, and phosphorus.

Kingdom

Organic compounds

Super Class

Alkaloids and derivatives

Class

Not Available

Sub Class

Not Available

Direct Parent

Alkaloids and derivatives

Alternative Parents

Substituents

Alkaloid or derivatives
Pyrrolizine
Beta-hydroxy acid
Fatty acid ester
Hydroxy acid
Fatty acyl
N-alkylpyrrolidine
Pyrrolidine
Tertiary alcohol
Pyrroline
1,2-diol
Amino acid or derivatives
Carboxylic acid ester
Tertiary aliphatic amine
Tertiary amine
Secondary alcohol
Carboxylic acid derivative
Azacycle
Monocarboxylic acid or derivatives
Organoheterocyclic compound
Alcohol
Hydrocarbon derivative
Organic oxide
Organic nitrogen compound
Carbonyl group
Organopnictogen compound
Organic oxygen compound
Organonitrogen compound
Organooxygen compound
Amine
Aliphatic heteropolycyclic compound

Molecular Framework

Aliphatic heteropolycyclic compounds

External Descriptors

tertiary alcohol (CHEBI:2617 )
butyrate ester (CHEBI:2617 )
carboxylic ester (CHEBI:2617 )
secondary alcohol (CHEBI:2617 )
pyrrolizines (CHEBI:2617 )
pyrrolizidine alkaloid (CHEBI:2617 )
Pyrrolizidine alkaloids (C10263 )

Ontology

Not Available

Exogenous (HMDB: HMDB0302358)

Food

Herb and spice

Oilseed crop

Borage (FooDB: FOOD00026)

Process

Not Available

Role

Biological role

Hepatotoxic agent (HMDB: HMDB0302358)

Physical Properties

State

Not Available

Experimental Molecular Properties

Property	Value	Reference
Melting Point	Not Available	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	Not Available	Not Available
LogP	Not Available	Not Available

Experimental Chromatographic Properties

Not Available

Predicted Molecular Properties

Property	Value	Source
logP	1.36	ALOGPS
logP	0.86	ChemAxon
logS	-0.99	ALOGPS
pKa (Strongest Acidic)	11.35	ChemAxon
pKa (Strongest Basic)	9.36	ChemAxon
Physiological Charge	1	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	70 Å²	ChemAxon
Rotatable Bond Count	6	ChemAxon
Refractivity	76.62 m³·mol⁻¹	ChemAxon
Polarizability	30.94 Å³	ChemAxon
Number of Rings	2	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Predicted Chromatographic Properties

Predicted Collision Cross Sections

Predictor	Adduct Type	CCS Value (Å²)	Reference
AllCCS	[M+H]+	166.326	32859911
AllCCS	[M+H-H2O]+	163.169	32859911
AllCCS	[M+Na]+	170.089	32859911
AllCCS	[M+NH4]+	169.25	32859911
AllCCS	[M-H]-	170.991	32859911
AllCCS	[M+Na-2H]-	171.376	32859911
AllCCS	[M+HCOO]-	171.921	32859911
DeepCCS	[M-2H]-	200.317	30932474
DeepCCS	[M+Na]+	175.427	30932474

Predicted Retention Times

Underivatized

Chromatographic Method	Retention Time	Reference
Predicted by Siyang on May 30, 2022	9.5037 minutes	33406817
Predicted by Siyang using ReTip algorithm on June 8, 2022	4.05 minutes	32390414
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid	661.5 seconds	40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid	184.1 seconds	40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid	116.5 seconds	40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid	153.2 seconds	40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	48.9 seconds	40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid	269.1 seconds	40023050
BfG_NTS_RP1 =Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) with Water:ACN and 0.1% Formic Acid	293.6 seconds	40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)	287.4 seconds	40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid	623.0 seconds	40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid	135.7 seconds	40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid	739.8 seconds	40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	176.4 seconds	40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	204.5 seconds	40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate	428.1 seconds	40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA	344.5 seconds	40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water	94.7 seconds	40023050

Predicted Kovats Retention Indices

Not Available

Spectra

MS/MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Amabiline 10V, Positive-QTOF	splash10-0089-0890000000-7e49f3a5689877ea8fe3	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Amabiline 20V, Positive-QTOF	splash10-00di-5910000000-dad169d37f1ffcd002e8	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Amabiline 40V, Positive-QTOF	splash10-00dj-9600000000-c8dd97db90e8a3ead586	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Amabiline 10V, Negative-QTOF	splash10-00m0-1790000000-c4f31ef894e2d91a6658	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Amabiline 20V, Negative-QTOF	splash10-07cl-2940000000-5e5fbfd258f381aae5b1	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Amabiline 40V, Negative-QTOF	splash10-01b9-9300000000-d73392bce37dfe6305c5	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Amabiline 10V, Positive-QTOF	splash10-001i-0190000000-6159bb2974b9b0984caa	2021-10-21	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Amabiline 20V, Positive-QTOF	splash10-00di-1920000000-8b27f1e116bffc7fb2aa	2021-10-21	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Amabiline 40V, Positive-QTOF	splash10-00dm-9510000000-2d3bb78068666eb20bae	2021-10-21	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Amabiline 10V, Negative-QTOF	splash10-014l-2910000000-2779e8ac9134af115f2c	2021-10-21	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Amabiline 20V, Negative-QTOF	splash10-014i-2900000000-aa4dafe63caf805139db	2021-10-21	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Amabiline 40V, Negative-QTOF	splash10-001j-9470000000-b7c86e952f087a42e785	2021-10-21	Wishart Lab	View Spectrum

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Not Available

Tissue Locations

Not Available

Pathways

Not Available

Name	SMPDB/PathBank	KEGG

Normal Concentrations

Not Available

Abnormal Concentrations

Not Available

Associated Disorders and Diseases

Disease References

None

Associated OMIM IDs

None

External Links

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

KNApSAcK ID

Chemspider ID

KEGG Compound ID

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

442706

PDB ID

Not Available

ChEBI ID

2617

Food Biomarker Ontology

Not Available

VMH ID

Not Available

MarkerDB ID

Not Available

Good Scents ID

Not Available

References

Synthesis Reference

Not Available

Material Safety Data Sheet (MSDS)

Not Available

General References

Not Available

Showing metabocard for Amabiline (HMDB0302358)

MOL for HMDB0302358 (Amabiline)

3D MOL for HMDB0302358 (Amabiline)

3D SDF for HMDB0302358 (Amabiline)

3D-SDF for HMDB0302358 (Amabiline)

PDB for HMDB0302358 (Amabiline)

3D PDB for HMDB0302358 (Amabiline)

SMILES for HMDB0302358 (Amabiline)

INCHI for HMDB0302358 (Amabiline)

Structure for HMDB0302358 (Amabiline)

3D Structure for HMDB0302358 (Amabiline)

Predicted Collision Cross Sections

Predicted Retention Times

Underivatized

Predicted Kovats Retention Indices

MS/MS Spectra