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Record Information

Version

5.0

Status

Expected but not Quantified

Creation Date

2012-09-12 01:54:41 UTC

Update Date

2022-03-07 02:56:34 UTC

HMDB ID

HMDB0040383

Secondary Accession Numbers

HMDB40383

Metabolite Identification

Common Name

(±)-Pandamarine

Description

(±)-Pandamarine belongs to the class of organic compounds known as azaspirodecane derivatives. These are organic compounds containing a spirodecane moiety with at least one nitrogen atom. Based on a literature review very few articles have been published on (±)-Pandamarine.

Structure

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

HMDB0040383
     RDKit          3D
(±)-Pandamarine
 48 50  0  0  0  0  0  0  0  0999 V2000
    6.5205   -0.4483    0.2876 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.4142    0.0437   -0.5824 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1045   -0.0551   -0.3136 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3096    0.5196   -1.3620 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9823    0.5925   -1.4150 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1865    0.0434   -0.3102 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2820    1.0957    0.3506 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4748    0.5043    1.4625 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3791   -0.5588    1.2225 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8744   -1.0729    2.5081 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1157   -2.5383    2.3291 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8912   -2.6754    1.0185 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5444   -1.3531    0.6618 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4387   -0.3280    0.3051 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0640    0.9889    0.4092 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2169    1.5128   -0.7771 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8253    2.8623   -1.1052 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6874    0.5900   -1.7715 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6944    0.8169   -3.0092 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1986   -0.5417   -1.0704 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.2383    0.9995   -2.3351 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.5458    0.7133   -1.8684 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.6672    0.9534   -2.3960 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.6375   -1.5587    0.1927 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.2892   -0.2815    1.3630 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.4627    0.0711    0.0819 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7638   -0.5109    0.5798 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5402    1.0592   -2.2828 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5243   -0.7305   -0.7506 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7695   -0.4509    0.4673 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3231    1.6207   -0.4168 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9831    1.8546    0.7556 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0866    1.3074    1.9782 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2351    0.1879    2.2505 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0022   -0.9395    3.2105 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7018   -0.5006    2.9225 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6265   -3.0453    3.1437 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1037   -3.0135    2.2403 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2280   -2.9791    0.1937 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6881   -3.4158    1.1956 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2114   -1.5058   -0.2130 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0728   -0.9463    1.5252 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3550    1.4491    1.3651 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5244    2.7102   -1.9275 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3563    3.2742   -0.2452 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0055    3.5498   -1.3865 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7520   -1.3402   -1.5954 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9855    1.4699   -3.2176 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  0
  3  4  1  0
  4  5  2  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  9 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  1  0
 13 14  1  0
 14 15  1  0
 15 16  2  0
 16 17  1  0
 16 18  1  0
 18 19  2  0
 18 20  1  0
  4 21  1  0
 21 22  1  0
 22 23  2  0
 22  2  1  0
 14  9  1  0
 20 14  1  0
  1 24  1  0
  1 25  1  0
  1 26  1  0
  3 27  1  0
  5 28  1  0
  6 29  1  0
  6 30  1  0
  7 31  1  0
  7 32  1  0
  8 33  1  0
  8 34  1  0
 10 35  1  0
 10 36  1  0
 11 37  1  0
 11 38  1  0
 12 39  1  0
 12 40  1  0
 13 41  1  0
 13 42  1  0
 15 43  1  0
 17 44  1  0
 17 45  1  0
 17 46  1  0
 20 47  1  0
 21 48  1  0
M  END


  Mrv0541 09121201542D          

 23 25  0  0  0  0            999 V2000
    3.7234    0.0004    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9136    0.0004    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4286   -0.6474    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6188   -0.4854    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4568   -1.2945    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8904   -1.8617    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0813   -1.6184    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0813   -0.8094    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8091   -0.4041    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.5664    0.4041    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1612    0.7281    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2425    1.6184    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0516    1.8617    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6188    1.3759    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6188    0.4854    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3472    0.2422    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5898   -0.5661    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7234    0.8094    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9136    0.8900    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4278    1.5378    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.6188    0.3235    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.4286    0.6474    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6711    1.4564    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  2  0  0  0  0
  2 22  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  4  9  1  0  0  0  0
  4 21  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  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
 12 13  1  0  0  0  0
 13 14  2  0  0  0  0
 14 15  1  0  0  0  0
 14 20  1  0  0  0  0
 15 16  2  0  0  0  0
 16 17  1  0  0  0  0
 16 19  1  0  0  0  0
 18 19  2  0  0  0  0
 19 20  1  0  0  0  0
 21 22  1  0  0  0  0
 22 23  2  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0040383

> <DATABASE_NAME>
hmdb

> <SMILES>
CC1=C\C(NC1=O)=C/CCCN1CCCCC11NC(=O)C(C)=C1

> <INCHI_IDENTIFIER>
InChI=1S/C18H25N3O2/c1-13-11-15(19-16(13)22)7-3-5-9-21-10-6-4-8-18(21)12-14(2)17(23)20-18/h7,11-12H,3-6,8-10H2,1-2H3,(H,19,22)(H,20,23)/b15-7+

> <INCHI_KEY>
YMXRBZVJOJYAFJ-VIZOYTHASA-N

> <FORMULA>
C18H25N3O2

> <MOLECULAR_WEIGHT>
315.41

> <EXACT_MASS>
315.194677059

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_AVERAGE_POLARIZABILITY>
35.49713974535278

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
3-methyl-6-{4-[(2E)-4-methyl-5-oxo-2,5-dihydro-1H-pyrrol-2-ylidene]butyl}-1,6-diazaspiro[4.5]dec-3-en-2-one

> <ALOGPS_LOGP>
2.11

> <JCHEM_LOGP>
1.717715108333333

> <ALOGPS_LOGS>
-2.89

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA>
11.709293097704826

> <JCHEM_PKA_STRONGEST_ACIDIC>
11.140893128401755

> <JCHEM_PKA_STRONGEST_BASIC>
7.301381289367128

> <JCHEM_POLAR_SURFACE_AREA>
61.440000000000005

> <JCHEM_REFRACTIVITY>
93.53089999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
4.06e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
3-methyl-6-{4-[(2E)-4-methyl-5-oxo-1H-pyrrol-2-ylidene]butyl}-1,6-diazaspiro[4.5]dec-3-en-2-one

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0040383
     RDKit          3D
(±)-Pandamarine
 48 50  0  0  0  0  0  0  0  0999 V2000
    6.5205   -0.4483    0.2876 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.4142    0.0437   -0.5824 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1045   -0.0551   -0.3136 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3096    0.5196   -1.3620 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9823    0.5925   -1.4150 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1865    0.0434   -0.3102 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2820    1.0957    0.3506 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4748    0.5043    1.4625 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3791   -0.5588    1.2225 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8744   -1.0729    2.5081 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1157   -2.5383    2.3291 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8912   -2.6754    1.0185 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5444   -1.3531    0.6618 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4387   -0.3280    0.3051 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0640    0.9889    0.4092 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2169    1.5128   -0.7771 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8253    2.8623   -1.1052 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6874    0.5900   -1.7715 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6944    0.8169   -3.0092 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1986   -0.5417   -1.0704 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.2383    0.9995   -2.3351 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.5458    0.7133   -1.8684 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.6672    0.9534   -2.3960 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.6375   -1.5587    0.1927 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.2892   -0.2815    1.3630 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.4627    0.0711    0.0819 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7638   -0.5109    0.5798 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5402    1.0592   -2.2828 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5243   -0.7305   -0.7506 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7695   -0.4509    0.4673 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3231    1.6207   -0.4168 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9831    1.8546    0.7556 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0866    1.3074    1.9782 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2351    0.1879    2.2505 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0022   -0.9395    3.2105 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7018   -0.5006    2.9225 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6265   -3.0453    3.1437 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1037   -3.0135    2.2403 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2280   -2.9791    0.1937 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6881   -3.4158    1.1956 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2114   -1.5058   -0.2130 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0728   -0.9463    1.5252 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3550    1.4491    1.3651 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5244    2.7102   -1.9275 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3563    3.2742   -0.2452 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0055    3.5498   -1.3865 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7520   -1.3402   -1.5954 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9855    1.4699   -3.2176 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  0
  3  4  1  0
  4  5  2  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  9 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  1  0
 13 14  1  0
 14 15  1  0
 15 16  2  0
 16 17  1  0
 16 18  1  0
 18 19  2  0
 18 20  1  0
  4 21  1  0
 21 22  1  0
 22 23  2  0
 22  2  1  0
 14  9  1  0
 20 14  1  0
  1 24  1  0
  1 25  1  0
  1 26  1  0
  3 27  1  0
  5 28  1  0
  6 29  1  0
  6 30  1  0
  7 31  1  0
  7 32  1  0
  8 33  1  0
  8 34  1  0
 10 35  1  0
 10 36  1  0
 11 37  1  0
 11 38  1  0
 12 39  1  0
 12 40  1  0
 13 41  1  0
 13 42  1  0
 15 43  1  0
 17 44  1  0
 17 45  1  0
 17 46  1  0
 20 47  1  0
 21 48  1  0
M  END

HEADER    PROTEIN                                 12-SEP-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   12-SEP-12         0                                  
HETATM    1  C   UNK     0       6.950   0.001   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       5.439   0.001   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       4.533  -1.208   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       3.022  -0.906   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       2.719  -2.416   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       1.662  -3.475   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       0.152  -3.021   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       0.152  -1.511   0.000  0.00  0.00           C+0
HETATM    9  N   UNK     0       1.510  -0.754   0.000  0.00  0.00           N+0
HETATM   10  C   UNK     0       1.057   0.754   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      -0.301   1.359   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      -0.453   3.021   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      -1.963   3.475   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      -3.022   2.568   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      -3.022   0.906   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      -4.381   0.452   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      -4.834  -1.057   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0      -6.950   1.511   0.000  0.00  0.00           O+0
HETATM   19  C   UNK     0      -5.439   1.661   0.000  0.00  0.00           C+0
HETATM   20  N   UNK     0      -4.532   2.871   0.000  0.00  0.00           N+0
HETATM   21  N   UNK     0       3.022   0.604   0.000  0.00  0.00           N+0
HETATM   22  C   UNK     0       4.533   1.208   0.000  0.00  0.00           C+0
HETATM   23  O   UNK     0       4.986   2.719   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3   22                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5    9   21                                             
CONECT    5    4    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7    9                                                       
CONECT    9    4    8   10                                                  
CONECT   10    9   11                                                       
CONECT   11   10   12                                                       
CONECT   12   11   13                                                       
CONECT   13   12   14                                                       
CONECT   14   13   15   20                                                  
CONECT   15   14   16                                                       
CONECT   16   15   17   19                                                  
CONECT   17   16                                                            
CONECT   18   19                                                            
CONECT   19   16   18   20                                                  
CONECT   20   14   19                                                       
CONECT   21    4   22                                                       
CONECT   22    2   21   23                                                  
CONECT   23   22                                                            
MASTER        0    0    0    0    0    0    0    0   23    0   50    0
END

COMPND    HMDB0040383
HETATM    1  C1  UNL     1       6.521  -0.448   0.288  1.00  0.00           C  
HETATM    2  C2  UNL     1       5.414   0.044  -0.582  1.00  0.00           C  
HETATM    3  C3  UNL     1       4.105  -0.055  -0.314  1.00  0.00           C  
HETATM    4  C4  UNL     1       3.310   0.520  -1.362  1.00  0.00           C  
HETATM    5  C5  UNL     1       1.982   0.592  -1.415  1.00  0.00           C  
HETATM    6  C6  UNL     1       1.186   0.043  -0.310  1.00  0.00           C  
HETATM    7  C7  UNL     1       0.282   1.096   0.351  1.00  0.00           C  
HETATM    8  C8  UNL     1      -0.475   0.504   1.462  1.00  0.00           C  
HETATM    9  N1  UNL     1      -1.379  -0.559   1.222  1.00  0.00           N  
HETATM   10  C9  UNL     1      -1.874  -1.073   2.508  1.00  0.00           C  
HETATM   11  C10 UNL     1      -2.116  -2.538   2.329  1.00  0.00           C  
HETATM   12  C11 UNL     1      -2.891  -2.675   1.019  1.00  0.00           C  
HETATM   13  C12 UNL     1      -3.544  -1.353   0.662  1.00  0.00           C  
HETATM   14  C13 UNL     1      -2.439  -0.328   0.305  1.00  0.00           C  
HETATM   15  C14 UNL     1      -3.064   0.989   0.409  1.00  0.00           C  
HETATM   16  C15 UNL     1      -3.217   1.513  -0.777  1.00  0.00           C  
HETATM   17  C16 UNL     1      -3.825   2.862  -1.105  1.00  0.00           C  
HETATM   18  C17 UNL     1      -2.687   0.590  -1.772  1.00  0.00           C  
HETATM   19  O1  UNL     1      -2.694   0.817  -3.009  1.00  0.00           O  
HETATM   20  N2  UNL     1      -2.199  -0.542  -1.070  1.00  0.00           N  
HETATM   21  N3  UNL     1       4.238   0.999  -2.335  1.00  0.00           N  
HETATM   22  C18 UNL     1       5.546   0.713  -1.868  1.00  0.00           C  
HETATM   23  O2  UNL     1       6.667   0.953  -2.396  1.00  0.00           O  
HETATM   24  H1  UNL     1       6.637  -1.559   0.193  1.00  0.00           H  
HETATM   25  H2  UNL     1       6.289  -0.282   1.363  1.00  0.00           H  
HETATM   26  H3  UNL     1       7.463   0.071   0.082  1.00  0.00           H  
HETATM   27  H4  UNL     1       3.764  -0.511   0.580  1.00  0.00           H  
HETATM   28  H5  UNL     1       1.540   1.059  -2.283  1.00  0.00           H  
HETATM   29  H6  UNL     1       0.524  -0.730  -0.751  1.00  0.00           H  
HETATM   30  H7  UNL     1       1.770  -0.451   0.467  1.00  0.00           H  
HETATM   31  H8  UNL     1      -0.323   1.621  -0.417  1.00  0.00           H  
HETATM   32  H9  UNL     1       0.983   1.855   0.756  1.00  0.00           H  
HETATM   33  H10 UNL     1      -1.087   1.307   1.978  1.00  0.00           H  
HETATM   34  H11 UNL     1       0.235   0.188   2.250  1.00  0.00           H  
HETATM   35  H12 UNL     1      -1.002  -0.940   3.210  1.00  0.00           H  
HETATM   36  H13 UNL     1      -2.702  -0.501   2.922  1.00  0.00           H  
HETATM   37  H14 UNL     1      -2.626  -3.045   3.144  1.00  0.00           H  
HETATM   38  H15 UNL     1      -1.104  -3.014   2.240  1.00  0.00           H  
HETATM   39  H16 UNL     1      -2.228  -2.979   0.194  1.00  0.00           H  
HETATM   40  H17 UNL     1      -3.688  -3.416   1.196  1.00  0.00           H  
HETATM   41  H18 UNL     1      -4.211  -1.506  -0.213  1.00  0.00           H  
HETATM   42  H19 UNL     1      -4.073  -0.946   1.525  1.00  0.00           H  
HETATM   43  H20 UNL     1      -3.355   1.449   1.365  1.00  0.00           H  
HETATM   44  H21 UNL     1      -4.524   2.710  -1.928  1.00  0.00           H  
HETATM   45  H22 UNL     1      -4.356   3.274  -0.245  1.00  0.00           H  
HETATM   46  H23 UNL     1      -3.005   3.550  -1.387  1.00  0.00           H  
HETATM   47  H24 UNL     1      -1.752  -1.340  -1.595  1.00  0.00           H  
HETATM   48  H25 UNL     1       3.986   1.470  -3.218  1.00  0.00           H  
CONECT    1    2   24   25   26
CONECT    2    3    3   22
CONECT    3    4   27
CONECT    4    5    5   21
CONECT    5    6   28
CONECT    6    7   29   30
CONECT    7    8   31   32
CONECT    8    9   33   34
CONECT    9   10   14
CONECT   10   11   35   36
CONECT   11   12   37   38
CONECT   12   13   39   40
CONECT   13   14   41   42
CONECT   14   15   20
CONECT   15   16   16   43
CONECT   16   17   18
CONECT   17   44   45   46
CONECT   18   19   19   20
CONECT   20   47
CONECT   21   22   48
CONECT   22   23   23
END

HMDB0040383
     RDKit          3D
(±)-Pandamarine
 48 50  0  0  0  0  0  0  0  0999 V2000
    6.5205   -0.4483    0.2876 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.4142    0.0437   -0.5824 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1045   -0.0551   -0.3136 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3096    0.5196   -1.3620 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9823    0.5925   -1.4150 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1865    0.0434   -0.3102 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2820    1.0957    0.3506 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4748    0.5043    1.4625 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3791   -0.5588    1.2225 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8744   -1.0729    2.5081 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1157   -2.5383    2.3291 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8912   -2.6754    1.0185 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5444   -1.3531    0.6618 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4387   -0.3280    0.3051 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0640    0.9889    0.4092 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2169    1.5128   -0.7771 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8253    2.8623   -1.1052 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6874    0.5900   -1.7715 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6944    0.8169   -3.0092 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1986   -0.5417   -1.0704 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.2383    0.9995   -2.3351 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.5458    0.7133   -1.8684 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.6672    0.9534   -2.3960 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.6375   -1.5587    0.1927 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.2892   -0.2815    1.3630 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.4627    0.0711    0.0819 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7638   -0.5109    0.5798 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5402    1.0592   -2.2828 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5243   -0.7305   -0.7506 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7695   -0.4509    0.4673 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3231    1.6207   -0.4168 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9831    1.8546    0.7556 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0866    1.3074    1.9782 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2351    0.1879    2.2505 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0022   -0.9395    3.2105 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7018   -0.5006    2.9225 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6265   -3.0453    3.1437 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1037   -3.0135    2.2403 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2280   -2.9791    0.1937 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6881   -3.4158    1.1956 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2114   -1.5058   -0.2130 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0728   -0.9463    1.5252 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3550    1.4491    1.3651 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5244    2.7102   -1.9275 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3563    3.2742   -0.2452 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0055    3.5498   -1.3865 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7520   -1.3402   -1.5954 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9855    1.4699   -3.2176 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  0
  3  4  1  0
  4  5  2  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  9 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  1  0
 13 14  1  0
 14 15  1  0
 15 16  2  0
 16 17  1  0
 16 18  1  0
 18 19  2  0
 18 20  1  0
  4 21  1  0
 21 22  1  0
 22 23  2  0
 22  2  1  0
 14  9  1  0
 20 14  1  0
  1 24  1  0
  1 25  1  0
  1 26  1  0
  3 27  1  0
  5 28  1  0
  6 29  1  0
  6 30  1  0
  7 31  1  0
  7 32  1  0
  8 33  1  0
  8 34  1  0
 10 35  1  0
 10 36  1  0
 11 37  1  0
 11 38  1  0
 12 39  1  0
 12 40  1  0
 13 41  1  0
 13 42  1  0
 15 43  1  0
 17 44  1  0
 17 45  1  0
 17 46  1  0
 20 47  1  0
 21 48  1  0
M  END

View in JSmol View Stereo Labels

Synonyms

Not Available

Chemical Formula

C₁₈H₂₅N₃O₂

Average Molecular Weight

315.41

Monoisotopic Molecular Weight

315.194677059

IUPAC Name

3-methyl-6-{4-[(2E)-4-methyl-5-oxo-2,5-dihydro-1H-pyrrol-2-ylidene]butyl}-1,6-diazaspiro[4.5]dec-3-en-2-one

Traditional Name

3-methyl-6-{4-[(2E)-4-methyl-5-oxo-1H-pyrrol-2-ylidene]butyl}-1,6-diazaspiro[4.5]dec-3-en-2-one

CAS Registry Number

145940-69-8

SMILES

CC1=C\C(NC1=O)=C/CCCN1CCCCC11NC(=O)C(C)=C1

InChI Identifier

InChI=1S/C18H25N3O2/c1-13-11-15(19-16(13)22)7-3-5-9-21-10-6-4-8-18(21)12-14(2)17(23)20-18/h7,11-12H,3-6,8-10H2,1-2H3,(H,19,22)(H,20,23)/b15-7+

InChI Key

YMXRBZVJOJYAFJ-VIZOYTHASA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as azaspirodecane derivatives. These are organic compounds containing a spirodecane moiety with at least one nitrogen atom.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Azaspirodecane derivatives

Sub Class

Not Available

Direct Parent

Azaspirodecane derivatives

Alternative Parents

Substituents

Azaspirodecane
Piperidine
Pyrroline
Carboxamide group
Lactam
Secondary carboxylic acid amide
Carboxylic acid derivative
Azacycle
Organic oxide
Organooxygen compound
Organonitrogen compound
Organopnictogen compound
Organic oxygen compound
Carbonyl group
Hydrocarbon derivative
Organic nitrogen compound
Aliphatic heteropolycyclic compound

Molecular Framework

Aliphatic heteropolycyclic compounds

External Descriptors

Not Available

Ontology

Physiological effect

Not Available

Disposition

Biological location

Cellular substructure

Extracellular (HMDB: HMDB0040383)
Cytoplasm (HMDB: HMDB0040383)

Process

Not Available

Role

Not Available

Physical Properties

State

Solid

Experimental Molecular Properties

Property	Value	Reference
Melting Point	210 - 211 °C	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
Water Solubility	0.41 g/L	ALOGPS
logP	2.11	ALOGPS
logP	1.72	ChemAxon
logS	-2.9	ALOGPS
pKa (Strongest Acidic)	11.14	ChemAxon
pKa (Strongest Basic)	7.3	ChemAxon
Physiological Charge	1	ChemAxon
Hydrogen Acceptor Count	3	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	61.44 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	93.53 m³·mol⁻¹	ChemAxon
Polarizability	35.5 Å³	ChemAxon
Number of Rings	3	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
DeepCCS	[M-2H]-	212.656	30932474
DeepCCS	[M+Na]+	188.221	30932474
AllCCS	[M+H]+	177.6	32859911
AllCCS	[M+H-H2O]+	174.4	32859911
AllCCS	[M+NH4]+	180.5	32859911
AllCCS	[M+Na]+	181.4	32859911
AllCCS	[M-H]-	180.3	32859911
AllCCS	[M+Na-2H]-	180.5	32859911
AllCCS	[M+HCOO]-	180.9	32859911

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
(??)-Pandamarine	CC1=C\C(NC1=O)=C/CCCN1CCCCC11NC(=O)C(C)=C1	4172.5	Standard polar	33892256
(??)-Pandamarine	CC1=C\C(NC1=O)=C/CCCN1CCCCC11NC(=O)C(C)=C1	2872.2	Standard non polar	33892256
(??)-Pandamarine	CC1=C\C(NC1=O)=C/CCCN1CCCCC11NC(=O)C(C)=C1	3075.8	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
(±)-Pandamarine,1TMS,isomer #1	CC1=CC2(CCCCN2CCC/C=C2\C=C(C)C(=O)N2[Si](C)(C)C)NC1=O	3062.6	Semi standard non polar	33892256
(±)-Pandamarine,1TMS,isomer #1	CC1=CC2(CCCCN2CCC/C=C2\C=C(C)C(=O)N2[Si](C)(C)C)NC1=O	2929.6	Standard non polar	33892256
(±)-Pandamarine,1TMS,isomer #2	CC1=C/C(=C\CCCN2CCCCC23C=C(C)C(=O)N3[Si](C)(C)C)NC1=O	3045.4	Semi standard non polar	33892256
(±)-Pandamarine,1TMS,isomer #2	CC1=C/C(=C\CCCN2CCCCC23C=C(C)C(=O)N3[Si](C)(C)C)NC1=O	2970.8	Standard non polar	33892256
(±)-Pandamarine,2TMS,isomer #1	CC1=C/C(=C\CCCN2CCCCC23C=C(C)C(=O)N3[Si](C)(C)C)N([Si](C)(C)C)C1=O	2961.6	Semi standard non polar	33892256
(±)-Pandamarine,2TMS,isomer #1	CC1=C/C(=C\CCCN2CCCCC23C=C(C)C(=O)N3[Si](C)(C)C)N([Si](C)(C)C)C1=O	2946.8	Standard non polar	33892256
(±)-Pandamarine,1TBDMS,isomer #1	CC1=CC2(CCCCN2CCC/C=C2\C=C(C)C(=O)N2[Si](C)(C)C(C)(C)C)NC1=O	3271.7	Semi standard non polar	33892256
(±)-Pandamarine,1TBDMS,isomer #1	CC1=CC2(CCCCN2CCC/C=C2\C=C(C)C(=O)N2[Si](C)(C)C(C)(C)C)NC1=O	3146.7	Standard non polar	33892256
(±)-Pandamarine,1TBDMS,isomer #2	CC1=C/C(=C\CCCN2CCCCC23C=C(C)C(=O)N3[Si](C)(C)C(C)(C)C)NC1=O	3214.6	Semi standard non polar	33892256
(±)-Pandamarine,1TBDMS,isomer #2	CC1=C/C(=C\CCCN2CCCCC23C=C(C)C(=O)N3[Si](C)(C)C(C)(C)C)NC1=O	3187.2	Standard non polar	33892256
(±)-Pandamarine,2TBDMS,isomer #1	CC1=C/C(=C\CCCN2CCCCC23C=C(C)C(=O)N3[Si](C)(C)C(C)(C)C)N([Si](C)(C)C(C)(C)C)C1=O	3350.2	Semi standard non polar	33892256
(±)-Pandamarine,2TBDMS,isomer #1	CC1=C/C(=C\CCCN2CCCCC23C=C(C)C(=O)N3[Si](C)(C)C(C)(C)C)N([Si](C)(C)C(C)(C)C)C1=O	3318.0	Standard non polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted GC-MS	Predicted GC-MS Spectrum - (±)-Pandamarine GC-MS (Non-derivatized) - 70eV, Positive	splash10-002r-3930000000-70eb31365e221e49ae90	2017-09-01	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - (±)-Pandamarine GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - (±)-Pandamarine GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum

MS/MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (±)-Pandamarine 10V, Positive-QTOF	splash10-014i-0119000000-9169ac83febe23d37b67	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (±)-Pandamarine 20V, Positive-QTOF	splash10-014i-2983000000-d47fa08ec0d95db88f4c	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (±)-Pandamarine 40V, Positive-QTOF	splash10-0gb9-7910000000-9b2d842281795b463374	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (±)-Pandamarine 10V, Negative-QTOF	splash10-03di-0009000000-f81686ab387181484df7	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (±)-Pandamarine 20V, Negative-QTOF	splash10-014i-0912000000-d23c48b581124f48115e	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (±)-Pandamarine 40V, Negative-QTOF	splash10-00ke-2900000000-4a2a43649f2ec141b670	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (±)-Pandamarine 10V, Negative-QTOF	splash10-03di-0019000000-537c7b06b13a6f91bd91	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (±)-Pandamarine 20V, Negative-QTOF	splash10-03di-1349000000-4ca82c43df52883e78bc	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (±)-Pandamarine 40V, Negative-QTOF	splash10-0296-2940000000-86c72783b7f9dd30374f	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (±)-Pandamarine 10V, Positive-QTOF	splash10-014i-0009000000-03ba20dd3906006491b9	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (±)-Pandamarine 20V, Positive-QTOF	splash10-014i-0095000000-ea4ede504476185992e9	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (±)-Pandamarine 40V, Positive-QTOF	splash10-014l-1960000000-f02c727567a2826846b1	2021-09-23	Wishart Lab	View Spectrum

Biological Properties

Cellular Locations

Cytoplasm
Extracellular

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

FDB020115

KNApSAcK ID

Not Available

Chemspider ID

35014937

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

131752803

PDB ID

Not Available

ChEBI ID

Not Available

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

(). Yannai, Shmuel. (2004) Dictionary of food compounds with CD-ROM: Additives, flavors, and ingredients. Boca Raton: Chapman & Hall/CRC.. .

Showing metabocard for (±)-Pandamarine (HMDB0040383)

MOL for HMDB0040383 ((±)-Pandamarine)

3D MOL for HMDB0040383 ((±)-Pandamarine)

3D SDF for HMDB0040383 ((±)-Pandamarine)

3D-SDF for HMDB0040383 ((±)-Pandamarine)

PDB for HMDB0040383 ((±)-Pandamarine)

3D PDB for HMDB0040383 ((±)-Pandamarine)

SMILES for HMDB0040383 ((±)-Pandamarine)

INCHI for HMDB0040383 ((±)-Pandamarine)

Structure for HMDB0040383 ((±)-Pandamarine)

3D Structure for HMDB0040383 ((±)-Pandamarine)

Predicted Collision Cross Sections

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra