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Record Information

Version

5.0

Status

Expected but not Quantified

Creation Date

2021-09-23 03:00:26 UTC

Update Date

2021-09-23 03:00:26 UTC

HMDB ID

HMDB0301846

Secondary Accession Numbers

None

Metabolite Identification

Common Name

Lycopsamine

Description

Lycopsamine, also known as indicine or 9-viridiflorylretronecine, 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. Lycopsamine is soluble (in water) and a very weakly acidic compound (based on its pKa). Lycopsamine can be found in borage, which makes lycopsamine a potential biomarker for the consumption of this food product.

Structure

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

HMDB0301846
     RDKit          3D
Lycopsamine
 46 47  0  0  0  0  0  0  0  0999 V2000
   -5.0033   -0.0375    0.4727 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5818    0.1938    0.8658 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4522    1.6926    1.1795 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5633   -0.1100   -0.1785 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.8292    0.7085   -1.2830 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2275    0.1919    0.3993 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7784   -0.4170    1.3931 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4372    1.1733   -0.1624 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8231    1.4627    0.3700 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7910    0.3436    0.3292 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7193   -0.8860   -0.1111 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9898   -1.6387    0.0781 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8095   -0.7550    0.8464 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.1289   -0.5910    0.2725 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3802    0.8761    0.1225 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9825    1.4528   -0.0019 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.5314    1.4021   -1.3022 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.1870    0.5260    0.8773 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.5216   -1.5305   -0.6379 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.6983   -2.0128   -1.4057 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2676   -2.4179    0.4068 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6834    0.7802    0.8590 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4427   -0.9668    0.9393 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1504   -0.0110   -0.6259 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2893   -0.3722    1.7855 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6122    1.8919    2.2493 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2103    2.2738    0.6144 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4520    2.0686    0.9031 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5171    1.6356   -1.1408 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7551    1.8000    1.4463 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2750    2.3550   -0.1533 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8556   -1.3333   -0.5689 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4577   -1.8662   -0.9130 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8590   -2.5774    0.6384 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.1514   -1.0488   -0.7436 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.9105   -1.0847    0.8825 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.9993    1.0811   -0.7671 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.8676    1.2400    1.0642 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9102    2.4673    0.4277 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.0177    2.0682   -1.8502 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1643    0.9031    1.9056 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6286   -1.6477   -1.3226 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5629   -2.3273   -0.8232 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3619   -2.9420   -1.9587 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9553   -1.3055   -2.2473 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3396   -2.7091    0.4644 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  6
  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
 16 18  1  0
  4 19  1  0
 19 20  1  0
 19 21  1  0
 18 10  1  0
 18 13  1  0
  1 22  1  0
  1 23  1  0
  1 24  1  0
  2 25  1  0
  3 26  1  0
  3 27  1  0
  3 28  1  0
  5 29  1  0
  9 30  1  0
  9 31  1  0
 11 32  1  0
 12 33  1  0
 12 34  1  0
 14 35  1  0
 14 36  1  0
 15 37  1  0
 15 38  1  0
 16 39  1  1
 17 40  1  0
 18 41  1  1
 19 42  1  6
 20 43  1  0
 20 44  1  0
 20 45  1  0
 21 46  1  0
M  END


  Mrv0541 02241212572D          

 24 25  0  0  0  0            999 V2000
   -4.6054    1.3465    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -5.0903    0.6790    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6054    0.0116    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0361    1.3465    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8207    1.0915    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -3.8207    0.2665    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0361    0.0116    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5512    0.6790    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7812    2.1311    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9742    2.3026    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7193    3.0872    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9123    3.2587    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.2713    3.7003    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6574    4.0434    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.3603    2.6457    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1496    4.2149    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2094    4.6565    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1672    2.4741    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6152    1.8610    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4467    2.8172    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6574    4.8684    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8207    1.9165    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4023    1.5600    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0179    2.0609    0.0000 H   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
  3  6  1  0  0  0  0
  4  5  1  0  0  0  0
  4  8  2  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  5  6  1  0  0  0  0
  4  9  1  0  0  0  0
  9 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  0  0  0  0
 12 15  1  1  0  0  0
 14 16  1  6  0  0  0
 14 17  1  0  0  0  0
 12 18  1  6  0  0  0
 15 19  1  0  0  0  0
 15 20  1  0  0  0  0
 14 21  1  1  0  0  0
  5 22  1  6  0  0  0
  1 23  1  1  0  0  0
  1 24  1  6  0  0  0
M  END
> <DATABASE_ID>
HMDB0301846

> <DATABASE_NAME>
hmdb

> <SMILES>
[H][C@@](C)(O)[C@@](O)(C(C)C)C(=O)OCC1=CCN2CC[C@@]([H])(O)[C@@]12[H]

> <INCHI_IDENTIFIER>
InChI=1S/C15H25NO5/c1-9(2)15(20,10(3)17)14(19)21-8-11-4-6-16-7-5-12(18)13(11)16/h4,9-10,12-13,17-18,20H,5-8H2,1-3H3/t10-,12+,13+,15-/m0/s1

> <INCHI_KEY>
SFVVQRJOGUKCEG-ZGFBFQLVSA-N

> <FORMULA>
C15H25NO5

> <MOLECULAR_WEIGHT>
299.3627

> <EXACT_MASS>
299.173272915

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_AVERAGE_POLARIZABILITY>
31.74697694699978

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
[(1R,7aR)-1-hydroxy-2,3,5,7a-tetrahydro-1H-pyrrolizin-7-yl]methyl (2S)-2-hydroxy-2-[(1S)-1-hydroxyethyl]-3-methylbutanoate

> <ALOGPS_LOGP>
0.41

> <JCHEM_LOGP>
-0.291114993666667

> <ALOGPS_LOGS>
-0.77

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA>
14.31270179754289

> <JCHEM_PKA_STRONGEST_ACIDIC>
11.342357304233317

> <JCHEM_PKA_STRONGEST_BASIC>
7.816512056494238

> <JCHEM_POLAR_SURFACE_AREA>
90.23

> <JCHEM_REFRACTIVITY>
77.9425

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
5.08e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
lycopsamine

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0301846
     RDKit          3D
Lycopsamine
 46 47  0  0  0  0  0  0  0  0999 V2000
   -5.0033   -0.0375    0.4727 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5818    0.1938    0.8658 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4522    1.6926    1.1795 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5633   -0.1100   -0.1785 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.8292    0.7085   -1.2830 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2275    0.1919    0.3993 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7784   -0.4170    1.3931 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4372    1.1733   -0.1624 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8231    1.4627    0.3700 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7910    0.3436    0.3292 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7193   -0.8860   -0.1111 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9898   -1.6387    0.0781 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8095   -0.7550    0.8464 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.1289   -0.5910    0.2725 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3802    0.8761    0.1225 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9825    1.4528   -0.0019 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.5314    1.4021   -1.3022 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.1870    0.5260    0.8773 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.5216   -1.5305   -0.6379 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.6983   -2.0128   -1.4057 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2676   -2.4179    0.4068 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6834    0.7802    0.8590 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4427   -0.9668    0.9393 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1504   -0.0110   -0.6259 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2893   -0.3722    1.7855 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6122    1.8919    2.2493 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2103    2.2738    0.6144 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4520    2.0686    0.9031 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5171    1.6356   -1.1408 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7551    1.8000    1.4463 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2750    2.3550   -0.1533 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8556   -1.3333   -0.5689 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4577   -1.8662   -0.9130 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8590   -2.5774    0.6384 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.1514   -1.0488   -0.7436 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.9105   -1.0847    0.8825 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.9993    1.0811   -0.7671 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.8676    1.2400    1.0642 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9102    2.4673    0.4277 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.0177    2.0682   -1.8502 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1643    0.9031    1.9056 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6286   -1.6477   -1.3226 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5629   -2.3273   -0.8232 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3619   -2.9420   -1.9587 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9553   -1.3055   -2.2473 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3396   -2.7091    0.4644 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  6
  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
 16 18  1  0
  4 19  1  0
 19 20  1  0
 19 21  1  0
 18 10  1  0
 18 13  1  0
  1 22  1  0
  1 23  1  0
  1 24  1  0
  2 25  1  0
  3 26  1  0
  3 27  1  0
  3 28  1  0
  5 29  1  0
  9 30  1  0
  9 31  1  0
 11 32  1  0
 12 33  1  0
 12 34  1  0
 14 35  1  0
 14 36  1  0
 15 37  1  0
 15 38  1  0
 16 39  1  1
 17 40  1  0
 18 41  1  1
 19 42  1  6
 20 43  1  0
 20 44  1  0
 20 45  1  0
 21 46  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      -8.597   2.513   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -9.502   1.267   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -8.597   0.022   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -5.667   2.513   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -7.132   2.037   0.000  0.00  0.00           C+0
HETATM    6  N   UNK     0      -7.132   0.497   0.000  0.00  0.00           N+0
HETATM    7  C   UNK     0      -5.667   0.022   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -4.762   1.267   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -5.192   3.978   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0      -3.685   4.298   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0      -3.209   5.763   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      -1.703   6.083   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0      -4.240   6.907   0.000  0.00  0.00           O+0
HETATM   14  C   UNK     0      -1.227   7.548   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      -0.673   4.939   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0       0.279   7.868   0.000  0.00  0.00           O+0
HETATM   17  C   UNK     0      -2.258   8.692   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0      -2.179   4.618   0.000  0.00  0.00           O+0
HETATM   19  C   UNK     0      -1.148   3.474   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       0.834   5.259   0.000  0.00  0.00           C+0
HETATM   21  H   UNK     0      -1.227   9.088   0.000  0.00  0.00           H+0
HETATM   22  H   UNK     0      -7.132   3.577   0.000  0.00  0.00           H+0
HETATM   23  O   UNK     0     -10.084   2.912   0.000  0.00  0.00           O+0
HETATM   24  H   UNK     0      -9.367   3.847   0.000  0.00  0.00           H+0
CONECT    1    2    5   23   24                                             
CONECT    2    1    3                                                       
CONECT    3    2    6                                                       
CONECT    4    5    8    9                                                  
CONECT    5    1    4    6   22                                             
CONECT    6    3    7    5                                                  
CONECT    7    6    8                                                       
CONECT    8    4    7                                                       
CONECT    9    4   10                                                       
CONECT   10    9   11                                                       
CONECT   11   10   12   13                                                  
CONECT   12   11   14   15   18                                             
CONECT   13   11                                                            
CONECT   14   12   16   17   21                                             
CONECT   15   12   19   20                                                  
CONECT   16   14                                                            
CONECT   17   14                                                            
CONECT   18   12                                                            
CONECT   19   15                                                            
CONECT   20   15                                                            
CONECT   21   14                                                            
CONECT   22    5                                                            
CONECT   23    1                                                            
CONECT   24    1                                                            
MASTER        0    0    0    0    0    0    0    0   24    0   50    0
END

COMPND    HMDB0301846
HETATM    1  C1  UNL     1      -5.003  -0.037   0.473  1.00  0.00           C  
HETATM    2  C2  UNL     1      -3.582   0.194   0.866  1.00  0.00           C  
HETATM    3  C3  UNL     1      -3.452   1.693   1.179  1.00  0.00           C  
HETATM    4  C4  UNL     1      -2.563  -0.110  -0.178  1.00  0.00           C  
HETATM    5  O1  UNL     1      -2.829   0.708  -1.283  1.00  0.00           O  
HETATM    6  C5  UNL     1      -1.227   0.192   0.399  1.00  0.00           C  
HETATM    7  O2  UNL     1      -0.778  -0.417   1.393  1.00  0.00           O  
HETATM    8  O3  UNL     1      -0.437   1.173  -0.162  1.00  0.00           O  
HETATM    9  C6  UNL     1       0.823   1.463   0.370  1.00  0.00           C  
HETATM   10  C7  UNL     1       1.791   0.344   0.329  1.00  0.00           C  
HETATM   11  C8  UNL     1       1.719  -0.886  -0.111  1.00  0.00           C  
HETATM   12  C9  UNL     1       2.990  -1.639   0.078  1.00  0.00           C  
HETATM   13  N1  UNL     1       3.809  -0.755   0.846  1.00  0.00           N  
HETATM   14  C10 UNL     1       5.129  -0.591   0.273  1.00  0.00           C  
HETATM   15  C11 UNL     1       5.380   0.876   0.122  1.00  0.00           C  
HETATM   16  C12 UNL     1       3.983   1.453  -0.002  1.00  0.00           C  
HETATM   17  O4  UNL     1       3.531   1.402  -1.302  1.00  0.00           O  
HETATM   18  C13 UNL     1       3.187   0.526   0.877  1.00  0.00           C  
HETATM   19  C14 UNL     1      -2.522  -1.531  -0.638  1.00  0.00           C  
HETATM   20  C15 UNL     1      -3.698  -2.013  -1.406  1.00  0.00           C  
HETATM   21  O5  UNL     1      -2.268  -2.418   0.407  1.00  0.00           O  
HETATM   22  H1  UNL     1      -5.683   0.780   0.859  1.00  0.00           H  
HETATM   23  H2  UNL     1      -5.443  -0.967   0.939  1.00  0.00           H  
HETATM   24  H3  UNL     1      -5.150  -0.011  -0.626  1.00  0.00           H  
HETATM   25  H4  UNL     1      -3.289  -0.372   1.786  1.00  0.00           H  
HETATM   26  H5  UNL     1      -3.612   1.892   2.249  1.00  0.00           H  
HETATM   27  H6  UNL     1      -4.210   2.274   0.614  1.00  0.00           H  
HETATM   28  H7  UNL     1      -2.452   2.069   0.903  1.00  0.00           H  
HETATM   29  H8  UNL     1      -2.517   1.636  -1.141  1.00  0.00           H  
HETATM   30  H9  UNL     1       0.755   1.800   1.446  1.00  0.00           H  
HETATM   31  H10 UNL     1       1.275   2.355  -0.153  1.00  0.00           H  
HETATM   32  H11 UNL     1       0.856  -1.333  -0.569  1.00  0.00           H  
HETATM   33  H12 UNL     1       3.458  -1.866  -0.913  1.00  0.00           H  
HETATM   34  H13 UNL     1       2.859  -2.577   0.638  1.00  0.00           H  
HETATM   35  H14 UNL     1       5.151  -1.049  -0.744  1.00  0.00           H  
HETATM   36  H15 UNL     1       5.911  -1.085   0.882  1.00  0.00           H  
HETATM   37  H16 UNL     1       5.999   1.081  -0.767  1.00  0.00           H  
HETATM   38  H17 UNL     1       5.868   1.240   1.064  1.00  0.00           H  
HETATM   39  H18 UNL     1       3.910   2.467   0.428  1.00  0.00           H  
HETATM   40  H19 UNL     1       4.018   2.068  -1.850  1.00  0.00           H  
HETATM   41  H20 UNL     1       3.164   0.903   1.906  1.00  0.00           H  
HETATM   42  H21 UNL     1      -1.629  -1.648  -1.323  1.00  0.00           H  
HETATM   43  H22 UNL     1      -4.563  -2.327  -0.823  1.00  0.00           H  
HETATM   44  H23 UNL     1      -3.362  -2.942  -1.959  1.00  0.00           H  
HETATM   45  H24 UNL     1      -3.955  -1.305  -2.247  1.00  0.00           H  
HETATM   46  H25 UNL     1      -1.340  -2.709   0.464  1.00  0.00           H  
CONECT    1    2   22   23   24
CONECT    2    3    4   25
CONECT    3   26   27   28
CONECT    4    5    6   19
CONECT    5   29
CONECT    6    7    7    8
CONECT    8    9
CONECT    9   10   30   31
CONECT   10   11   11   18
CONECT   11   12   32
CONECT   12   13   33   34
CONECT   13   14   18
CONECT   14   15   35   36
CONECT   15   16   37   38
CONECT   16   17   18   39
CONECT   17   40
CONECT   18   41
CONECT   19   20   21   42
CONECT   20   43   44   45
CONECT   21   46
END

HMDB0301846
     RDKit          3D
Lycopsamine
 46 47  0  0  0  0  0  0  0  0999 V2000
   -5.0033   -0.0375    0.4727 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5818    0.1938    0.8658 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4522    1.6926    1.1795 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5633   -0.1100   -0.1785 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.8292    0.7085   -1.2830 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2275    0.1919    0.3993 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7784   -0.4170    1.3931 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4372    1.1733   -0.1624 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8231    1.4627    0.3700 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7910    0.3436    0.3292 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7193   -0.8860   -0.1111 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9898   -1.6387    0.0781 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8095   -0.7550    0.8464 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.1289   -0.5910    0.2725 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3802    0.8761    0.1225 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9825    1.4528   -0.0019 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.5314    1.4021   -1.3022 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.1870    0.5260    0.8773 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.5216   -1.5305   -0.6379 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.6983   -2.0128   -1.4057 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2676   -2.4179    0.4068 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6834    0.7802    0.8590 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4427   -0.9668    0.9393 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1504   -0.0110   -0.6259 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2893   -0.3722    1.7855 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6122    1.8919    2.2493 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2103    2.2738    0.6144 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4520    2.0686    0.9031 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5171    1.6356   -1.1408 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7551    1.8000    1.4463 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2750    2.3550   -0.1533 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8556   -1.3333   -0.5689 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4577   -1.8662   -0.9130 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8590   -2.5774    0.6384 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.1514   -1.0488   -0.7436 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.9105   -1.0847    0.8825 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.9993    1.0811   -0.7671 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.8676    1.2400    1.0642 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9102    2.4673    0.4277 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.0177    2.0682   -1.8502 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1643    0.9031    1.9056 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6286   -1.6477   -1.3226 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5629   -2.3273   -0.8232 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3619   -2.9420   -1.9587 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9553   -1.3055   -2.2473 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3396   -2.7091    0.4644 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  6
  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
 16 18  1  0
  4 19  1  0
 19 20  1  0
 19 21  1  0
 18 10  1  0
 18 13  1  0
  1 22  1  0
  1 23  1  0
  1 24  1  0
  2 25  1  0
  3 26  1  0
  3 27  1  0
  3 28  1  0
  5 29  1  0
  9 30  1  0
  9 31  1  0
 11 32  1  0
 12 33  1  0
 12 34  1  0
 14 35  1  0
 14 36  1  0
 15 37  1  0
 15 38  1  0
 16 39  1  1
 17 40  1  0
 18 41  1  1
 19 42  1  6
 20 43  1  0
 20 44  1  0
 20 45  1  0
 21 46  1  0
M  END

View in JSmol View Stereo Labels

Synonyms

Value	Source
9-Viridiflorylretronecine	Kegg
Echinatine	MeSH
Indicine	MeSH
Indicine, (1R-(1alpha,7(2S,3R),7abeta))-isomer	MeSH
Indicine, (1R-(1alpha,7(2S,3S),7abeta))-isomer	MeSH
Indicine, (1S-(1alpha,7(2R,3R),7aalpha))-isomer	MeSH
Indicine, (1S-(1alpha,7(2R,3S),7aalpha))-isomer	MeSH
Rinderine	MeSH

Chemical Formula

C₁₅H₂₅NO₅

Average Molecular Weight

299.3627

Monoisotopic Molecular Weight

299.173272915

IUPAC Name

[(1R,7aR)-1-hydroxy-2,3,5,7a-tetrahydro-1H-pyrrolizin-7-yl]methyl (2S)-2-hydroxy-2-[(1S)-1-hydroxyethyl]-3-methylbutanoate

Traditional Name

lycopsamine

CAS Registry Number

Not Available

SMILES

[H][C@@](C)(O)[C@@](O)(C(C)C)C(=O)OCC1=CCN2CC[C@@]([H])(O)[C@@]12[H]

InChI Identifier

InChI=1S/C15H25NO5/c1-9(2)15(20,10(3)17)14(19)21-8-11-4-6-16-7-5-12(18)13(11)16/h4,9-10,12-13,17-18,20H,5-8H2,1-3H3/t10-,12+,13+,15-/m0/s1

InChI Key

SFVVQRJOGUKCEG-ZGFBFQLVSA-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
N-alkylpyrrolidine
Fatty acyl
Tertiary alcohol
Pyrroline
Pyrrolidine
Amino acid or derivatives
Tertiary aliphatic amine
Tertiary amine
Secondary alcohol
Carboxylic acid ester
Azacycle
Organoheterocyclic compound
Carboxylic acid derivative
Monocarboxylic acid or derivatives
Hydrocarbon derivative
Organonitrogen compound
Alcohol
Organic oxygen compound
Organooxygen compound
Organopnictogen compound
Carbonyl group
Organic nitrogen compound
Organic oxide
Amine
Aliphatic heteropolycyclic compound

Molecular Framework

Aliphatic heteropolycyclic compounds

External Descriptors

pyrrolizines (CHEBI:6598 )
Pyrrolizidine alkaloids (C10347 )

Ontology

Not Available

Borage (FooDB: FOOD00026)

Process

Not Available

Role

Biological role

hepatotoxic agent (HMDB: HMDB0301846)

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	0.41	ALOGPS
logP	-0.29	ChemAxon
logS	-0.77	ALOGPS
pKa (Strongest Acidic)	11.34	ChemAxon
pKa (Strongest Basic)	7.82	ChemAxon
Physiological Charge	1	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	90.23 Å²	ChemAxon
Rotatable Bond Count	6	ChemAxon
Refractivity	77.94 m³·mol⁻¹	ChemAxon
Polarizability	31.75 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]+	169.713	32859911
AllCCS	[M+H-H2O]+	166.701	32859911
AllCCS	[M+Na]+	173.299	32859911
AllCCS	[M+NH4]+	172.499	32859911
AllCCS	[M-H]-	173.39	32859911
AllCCS	[M+Na-2H]-	173.731	32859911
AllCCS	[M+HCOO]-	174.229	32859911
DeepCCS	[M-2H]-	199.051	30932474
DeepCCS	[M+Na]+	174.045	30932474

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 - Lycopsamine 10V, Positive-QTOF	splash10-0f89-0894000000-0ca28f402d6c3271b3a2	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Lycopsamine 20V, Positive-QTOF	splash10-00dv-5930000000-4468609a3d1860632eef	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Lycopsamine 40V, Positive-QTOF	splash10-007a-7900000000-5a507c75289e1cb511d8	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Lycopsamine 10V, Negative-QTOF	splash10-00kb-1690000000-463ea0b40b7c8f9f7914	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Lycopsamine 20V, Negative-QTOF	splash10-02aa-1960000000-f1389da2df24657ebf1e	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Lycopsamine 40V, Negative-QTOF	splash10-00xs-9500000000-374e4d150e4fd3eaa16f	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Lycopsamine 10V, Positive-QTOF	splash10-03e9-0090000000-7e32b64b6fff4e23d127	2021-10-21	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Lycopsamine 20V, Positive-QTOF	splash10-000i-0911000000-42d820f83de3bb59ab7e	2021-10-21	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Lycopsamine 40V, Positive-QTOF	splash10-11b9-8900000000-f5dfbc011dfd41683fb5	2021-10-21	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Lycopsamine 10V, Negative-QTOF	splash10-014i-0910000000-44d7b0c1861aa61defd1	2021-10-21	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Lycopsamine 20V, Negative-QTOF	splash10-014r-0910000000-f078e4dfb2c55e1d95fc	2021-10-21	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Lycopsamine 40V, Negative-QTOF	splash10-0077-4900000000-89c2f24d6fe8ef8c54bf	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

107938

PDB ID

Not Available

ChEBI ID

Not Available

Food Biomarker Ontology

Not Available

VMH ID

Not Available

MarkerDB ID

Not Available

Good Scents ID

rw1080021

References

Synthesis Reference

Not Available

Material Safety Data Sheet (MSDS)

Not Available

General References

Not Available

Showing metabocard for Lycopsamine (HMDB0301846)

MOL for HMDB0301846 (Lycopsamine)

3D MOL for HMDB0301846 (Lycopsamine)

3D SDF for HMDB0301846 (Lycopsamine)

3D-SDF for HMDB0301846 (Lycopsamine)

PDB for HMDB0301846 (Lycopsamine)

3D PDB for HMDB0301846 (Lycopsamine)

SMILES for HMDB0301846 (Lycopsamine)

INCHI for HMDB0301846 (Lycopsamine)

Structure for HMDB0301846 (Lycopsamine)

3D Structure for HMDB0301846 (Lycopsamine)

Predicted Collision Cross Sections

Predicted Kovats Retention Indices

MS/MS Spectra