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Record Information

Version

5.0

Status

Detected but not Quantified

Creation Date

2021-09-11 22:01:24 UTC

Update Date

2022-11-23 21:39:02 UTC

HMDB ID

HMDB0259446

Secondary Accession Numbers

None

Metabolite Identification

Common Name

(3R)-Palonosetron

Description

3-{1-azabicyclo[2.2.2]octan-3-yl}-3-azatricyclo[7.3.1.0⁵,¹³]trideca-1(12),9(13),10-trien-2-one belongs to the class of organic compounds known as isoquinolones and derivatives. These are aromatic polycyclic compounds containing a ketone bearing isoquinoline moiety. Based on a literature review very few articles have been published on 3-{1-azabicyclo[2.2.2]octan-3-yl}-3-azatricyclo[7.3.1.0⁵,¹³]trideca-1(12),9(13),10-trien-2-one. This compound has been identified in human blood as reported by (PMID: 31557052 ). (3r)-palonosetron is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically (3R)-Palonosetron is part of the human exposome. The exposome can be defined as the collection of all the exposures of an individual in a lifetime and how those exposures relate to health. An individual's exposure begins before birth and includes insults from environmental and occupational sources.

Structure

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

HMDB0259446
     RDKit          3D
Palonosetron, (3R)-
 46 50  0  0  0  0  0  0  0  0999 V2000
   -0.5860    2.3704   -0.0655 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1036    1.3565   -0.1382 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4621    1.3601    0.4504 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8902    2.5320    1.0660 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1560    2.5260    1.6087 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9413    1.3923    1.5297 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4889    0.2509    0.9150 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2148    0.2183    0.3543 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6819   -0.9689   -0.3057 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6908   -1.9267   -0.8528 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1065   -1.6575   -0.5056 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3035   -0.9828    0.8160 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6616   -0.6646   -1.3553 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3912    0.2124   -0.7735 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7285   -0.1492   -0.8669 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7162    0.7616   -1.4589 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8978    0.9717   -0.6196 N   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6029   -0.2929   -0.5571 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6572   -1.3677   -0.0905 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3430   -0.7395    0.4190 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6428    0.3391    1.3883 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5466    1.3487    0.7273 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2248    3.3591    1.0839 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5251    3.4316    2.1009 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.9446    1.4169    1.9707 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1190   -1.5388    0.4968 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4524   -2.9895   -0.5824 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6222   -1.9189   -1.9795 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.5965   -1.0483   -1.2916 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.6703   -2.6172   -0.4749 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.3688   -0.6809    0.8923 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1040   -1.6539    1.6813 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1279   -0.1309   -2.2016 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1863   -1.6137   -1.6512 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7410   -1.1101   -1.5113 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1653    0.3583   -2.4089 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3023    1.7497   -1.7977 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4868   -0.2253    0.1184 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0077   -0.4861   -1.5682 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1148   -1.8923    0.7683 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4293   -2.1186   -0.8520 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7327   -1.5666    0.8028 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1560   -0.1342    2.2815 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7051    0.7871    1.7632 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5072    1.3390    1.3017 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1825    2.3932    0.8134 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  5  6  2  0
  6  7  1  0
  7  8  2  0
  8  9  1  0
  9 10  1  0
 10 11  1  0
 11 12  1  0
  9 13  1  0
 13 14  1  0
 14 15  1  0
 15 16  1  0
 16 17  1  0
 17 18  1  0
 18 19  1  0
 19 20  1  0
 20 21  1  0
 21 22  1  0
 14  2  1  0
 20 15  1  0
  8  3  1  0
 22 17  1  0
 12  7  1  0
  4 23  1  0
  5 24  1  0
  6 25  1  0
  9 26  1  0
 10 27  1  0
 10 28  1  0
 11 29  1  0
 11 30  1  0
 12 31  1  0
 12 32  1  0
 13 33  1  0
 13 34  1  0
 15 35  1  0
 16 36  1  0
 16 37  1  0
 18 38  1  0
 18 39  1  0
 19 40  1  0
 19 41  1  0
 20 42  1  0
 21 43  1  0
 21 44  1  0
 22 45  1  0
 22 46  1  0
M  END


  Mrv1652309122100012D          

 22 26  0  0  0  0            999 V2000
   -2.5694   -6.4334    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8549   -6.0209    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8549   -5.1959    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1405   -4.7834    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1405   -3.9584    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8549   -3.5459    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8549   -2.7209    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5694   -3.9584    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5694   -4.7834    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2839   -5.1959    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9983   -4.7834    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9983   -3.9584    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2839   -3.5459    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2839   -6.0209    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4260   -3.5459    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4260   -2.7209    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2885   -2.3084    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.0030   -2.7209    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0030   -3.5459    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2885   -3.9584    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4260   -3.4084    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4260   -2.8584    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  2  0  0  0  0
  6  8  1  0  0  0  0
  8  9  2  0  0  0  0
  3  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  2  0  0  0  0
 11 12  1  0  0  0  0
 12 13  2  0  0  0  0
  8 13  1  0  0  0  0
 10 14  1  0  0  0  0
  1 14  1  0  0  0  0
  5 15  1  0  0  0  0
 15 16  1  0  0  0  0
 16 17  1  0  0  0  0
 17 18  1  0  0  0  0
 18 19  1  0  0  0  0
 19 20  1  0  0  0  0
 15 20  1  0  0  0  0
 20 21  1  0  0  0  0
 21 22  1  0  0  0  0
 17 22  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0259446

> <DATABASE_NAME>
hmdb

> <SMILES>
O=C1N(CC2CCCC3=CC=CC1=C23)C1CN2CCC1CC2

> <INCHI_IDENTIFIER>
InChI=1S/C19H24N2O/c22-19-16-6-2-4-14-3-1-5-15(18(14)16)11-21(19)17-12-20-9-7-13(17)8-10-20/h2,4,6,13,15,17H,1,3,5,7-12H2

> <INCHI_KEY>
CPZBLNMUGSZIPR-UHFFFAOYSA-N

> <FORMULA>
C19H24N2O

> <MOLECULAR_WEIGHT>
296.414

> <EXACT_MASS>
296.188863401

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_ATOM_COUNT>
46

> <JCHEM_AVERAGE_POLARIZABILITY>
34.16013599093088

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
3-{1-azabicyclo[2.2.2]octan-3-yl}-3-azatricyclo[7.3.1.0^{5,13}]trideca-1(13),9,11-trien-2-one

> <ALOGPS_LOGP>
2.72

> <JCHEM_LOGP>
2.5460127283333343

> <ALOGPS_LOGS>
-2.81

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA_STRONGEST_BASIC>
7.973688632702442

> <JCHEM_POLAR_SURFACE_AREA>
23.550000000000004

> <JCHEM_REFRACTIVITY>
88.5213

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
4.64e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
3-{1-azabicyclo[2.2.2]octan-3-yl}-3-azatricyclo[7.3.1.0^{5,13}]trideca-1(13),9,11-trien-2-one

> <JCHEM_VEBER_RULE>
1

$$$$

HMDB0259446
     RDKit          3D
Palonosetron, (3R)-
 46 50  0  0  0  0  0  0  0  0999 V2000
   -0.5860    2.3704   -0.0655 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1036    1.3565   -0.1382 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4621    1.3601    0.4504 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8902    2.5320    1.0660 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1560    2.5260    1.6087 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9413    1.3923    1.5297 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4889    0.2509    0.9150 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2148    0.2183    0.3543 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6819   -0.9689   -0.3057 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6908   -1.9267   -0.8528 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1065   -1.6575   -0.5056 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3035   -0.9828    0.8160 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6616   -0.6646   -1.3553 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3912    0.2124   -0.7735 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7285   -0.1492   -0.8669 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7162    0.7616   -1.4589 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8978    0.9717   -0.6196 N   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6029   -0.2929   -0.5571 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6572   -1.3677   -0.0905 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3430   -0.7395    0.4190 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6428    0.3391    1.3883 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5466    1.3487    0.7273 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2248    3.3591    1.0839 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5251    3.4316    2.1009 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.9446    1.4169    1.9707 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1190   -1.5388    0.4968 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4524   -2.9895   -0.5824 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6222   -1.9189   -1.9795 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.5965   -1.0483   -1.2916 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.6703   -2.6172   -0.4749 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.3688   -0.6809    0.8923 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1040   -1.6539    1.6813 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1279   -0.1309   -2.2016 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1863   -1.6137   -1.6512 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7410   -1.1101   -1.5113 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1653    0.3583   -2.4089 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3023    1.7497   -1.7977 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4868   -0.2253    0.1184 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0077   -0.4861   -1.5682 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1148   -1.8923    0.7683 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4293   -2.1186   -0.8520 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7327   -1.5666    0.8028 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1560   -0.1342    2.2815 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7051    0.7871    1.7632 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5072    1.3390    1.3017 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1825    2.3932    0.8134 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  5  6  2  0
  6  7  1  0
  7  8  2  0
  8  9  1  0
  9 10  1  0
 10 11  1  0
 11 12  1  0
  9 13  1  0
 13 14  1  0
 14 15  1  0
 15 16  1  0
 16 17  1  0
 17 18  1  0
 18 19  1  0
 19 20  1  0
 20 21  1  0
 21 22  1  0
 14  2  1  0
 20 15  1  0
  8  3  1  0
 22 17  1  0
 12  7  1  0
  4 23  1  0
  5 24  1  0
  6 25  1  0
  9 26  1  0
 10 27  1  0
 10 28  1  0
 11 29  1  0
 11 30  1  0
 12 31  1  0
 12 32  1  0
 13 33  1  0
 13 34  1  0
 15 35  1  0
 16 36  1  0
 16 37  1  0
 18 38  1  0
 18 39  1  0
 19 40  1  0
 19 41  1  0
 20 42  1  0
 21 43  1  0
 21 44  1  0
 22 45  1  0
 22 46  1  0
M  END

HEADER    PROTEIN                                 12-SEP-21   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   12-SEP-21         0                                  
HETATM    1  C   UNK     0      -4.796 -12.009   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -3.463 -11.239   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -3.463  -9.699   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -2.129  -8.929   0.000  0.00  0.00           C+0
HETATM    5  N   UNK     0      -2.129  -7.389   0.000  0.00  0.00           N+0
HETATM    6  C   UNK     0      -3.463  -6.619   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0      -3.463  -5.079   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0      -4.796  -7.389   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -4.796  -8.929   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -6.130  -9.699   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      -7.464  -8.929   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      -7.464  -7.389   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      -6.130  -6.619   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      -6.130 -11.239   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      -0.795  -6.619   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      -0.795  -5.079   0.000  0.00  0.00           C+0
HETATM   17  N   UNK     0       0.539  -4.309   0.000  0.00  0.00           N+0
HETATM   18  C   UNK     0       1.872  -5.079   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       1.872  -6.619   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       0.539  -7.389   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       0.795  -6.362   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       0.795  -5.336   0.000  0.00  0.00           C+0
CONECT    1    2   14                                                       
CONECT    2    1    3                                                       
CONECT    3    2    4    9                                                  
CONECT    4    3    5                                                       
CONECT    5    4    6   15                                                  
CONECT    6    5    7    8                                                  
CONECT    7    6                                                            
CONECT    8    6    9   13                                                  
CONECT    9    8    3   10                                                  
CONECT   10    9   11   14                                                  
CONECT   11   10   12                                                       
CONECT   12   11   13                                                       
CONECT   13   12    8                                                       
CONECT   14   10    1                                                       
CONECT   15    5   16   20                                                  
CONECT   16   15   17                                                       
CONECT   17   16   18   22                                                  
CONECT   18   17   19                                                       
CONECT   19   18   20                                                       
CONECT   20   19   15   21                                                  
CONECT   21   20   22                                                       
CONECT   22   21   17                                                       
MASTER        0    0    0    0    0    0    0    0   22    0   52    0
END

COMPND    HMDB0259446
HETATM    1  O1  UNL     1      -0.586   2.370  -0.065  1.00  0.00           O  
HETATM    2  C1  UNL     1       0.104   1.357  -0.138  1.00  0.00           C  
HETATM    3  C2  UNL     1       1.462   1.360   0.450  1.00  0.00           C  
HETATM    4  C3  UNL     1       1.890   2.532   1.066  1.00  0.00           C  
HETATM    5  C4  UNL     1       3.156   2.526   1.609  1.00  0.00           C  
HETATM    6  C5  UNL     1       3.941   1.392   1.530  1.00  0.00           C  
HETATM    7  C6  UNL     1       3.489   0.251   0.915  1.00  0.00           C  
HETATM    8  C7  UNL     1       2.215   0.218   0.354  1.00  0.00           C  
HETATM    9  C8  UNL     1       1.682  -0.969  -0.306  1.00  0.00           C  
HETATM   10  C9  UNL     1       2.691  -1.927  -0.853  1.00  0.00           C  
HETATM   11  C10 UNL     1       4.106  -1.657  -0.506  1.00  0.00           C  
HETATM   12  C11 UNL     1       4.303  -0.983   0.816  1.00  0.00           C  
HETATM   13  C12 UNL     1       0.662  -0.665  -1.355  1.00  0.00           C  
HETATM   14  N1  UNL     1      -0.391   0.212  -0.774  1.00  0.00           N  
HETATM   15  C13 UNL     1      -1.729  -0.149  -0.867  1.00  0.00           C  
HETATM   16  C14 UNL     1      -2.716   0.762  -1.459  1.00  0.00           C  
HETATM   17  N2  UNL     1      -3.898   0.972  -0.620  1.00  0.00           N  
HETATM   18  C15 UNL     1      -4.603  -0.293  -0.557  1.00  0.00           C  
HETATM   19  C16 UNL     1      -3.657  -1.368  -0.091  1.00  0.00           C  
HETATM   20  C17 UNL     1      -2.343  -0.739   0.419  1.00  0.00           C  
HETATM   21  C18 UNL     1      -2.643   0.339   1.388  1.00  0.00           C  
HETATM   22  C19 UNL     1      -3.547   1.349   0.727  1.00  0.00           C  
HETATM   23  H1  UNL     1       1.225   3.359   1.084  1.00  0.00           H  
HETATM   24  H2  UNL     1       3.525   3.432   2.101  1.00  0.00           H  
HETATM   25  H3  UNL     1       4.945   1.417   1.971  1.00  0.00           H  
HETATM   26  H4  UNL     1       1.119  -1.539   0.497  1.00  0.00           H  
HETATM   27  H5  UNL     1       2.452  -2.990  -0.582  1.00  0.00           H  
HETATM   28  H6  UNL     1       2.622  -1.919  -1.979  1.00  0.00           H  
HETATM   29  H7  UNL     1       4.597  -1.048  -1.292  1.00  0.00           H  
HETATM   30  H8  UNL     1       4.670  -2.617  -0.475  1.00  0.00           H  
HETATM   31  H9  UNL     1       5.369  -0.681   0.892  1.00  0.00           H  
HETATM   32  H10 UNL     1       4.104  -1.654   1.681  1.00  0.00           H  
HETATM   33  H11 UNL     1       1.128  -0.131  -2.202  1.00  0.00           H  
HETATM   34  H12 UNL     1       0.186  -1.614  -1.651  1.00  0.00           H  
HETATM   35  H13 UNL     1      -1.741  -1.110  -1.511  1.00  0.00           H  
HETATM   36  H14 UNL     1      -3.165   0.358  -2.409  1.00  0.00           H  
HETATM   37  H15 UNL     1      -2.302   1.750  -1.798  1.00  0.00           H  
HETATM   38  H16 UNL     1      -5.487  -0.225   0.118  1.00  0.00           H  
HETATM   39  H17 UNL     1      -5.008  -0.486  -1.568  1.00  0.00           H  
HETATM   40  H18 UNL     1      -4.115  -1.892   0.768  1.00  0.00           H  
HETATM   41  H19 UNL     1      -3.429  -2.119  -0.852  1.00  0.00           H  
HETATM   42  H20 UNL     1      -1.733  -1.567   0.803  1.00  0.00           H  
HETATM   43  H21 UNL     1      -3.156  -0.134   2.281  1.00  0.00           H  
HETATM   44  H22 UNL     1      -1.705   0.787   1.763  1.00  0.00           H  
HETATM   45  H23 UNL     1      -4.507   1.339   1.302  1.00  0.00           H  
HETATM   46  H24 UNL     1      -3.183   2.393   0.813  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3   14
CONECT    3    4    4    8
CONECT    4    5   23
CONECT    5    6    6   24
CONECT    6    7   25
CONECT    7    8    8   12
CONECT    8    9
CONECT    9   10   13   26
CONECT   10   11   27   28
CONECT   11   12   29   30
CONECT   12   31   32
CONECT   13   14   33   34
CONECT   14   15
CONECT   15   16   20   35
CONECT   16   17   36   37
CONECT   17   18   22
CONECT   18   19   38   39
CONECT   19   20   40   41
CONECT   20   21   42
CONECT   21   22   43   44
CONECT   22   45   46
END

HMDB0259446
     RDKit          3D
Palonosetron, (3R)-
 46 50  0  0  0  0  0  0  0  0999 V2000
   -0.5860    2.3704   -0.0655 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1036    1.3565   -0.1382 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4621    1.3601    0.4504 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8902    2.5320    1.0660 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1560    2.5260    1.6087 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9413    1.3923    1.5297 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4889    0.2509    0.9150 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2148    0.2183    0.3543 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6819   -0.9689   -0.3057 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6908   -1.9267   -0.8528 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1065   -1.6575   -0.5056 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3035   -0.9828    0.8160 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6616   -0.6646   -1.3553 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3912    0.2124   -0.7735 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7285   -0.1492   -0.8669 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7162    0.7616   -1.4589 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8978    0.9717   -0.6196 N   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6029   -0.2929   -0.5571 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6572   -1.3677   -0.0905 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3430   -0.7395    0.4190 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6428    0.3391    1.3883 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5466    1.3487    0.7273 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2248    3.3591    1.0839 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5251    3.4316    2.1009 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.9446    1.4169    1.9707 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1190   -1.5388    0.4968 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4524   -2.9895   -0.5824 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6222   -1.9189   -1.9795 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.5965   -1.0483   -1.2916 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.6703   -2.6172   -0.4749 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.3688   -0.6809    0.8923 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1040   -1.6539    1.6813 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1279   -0.1309   -2.2016 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1863   -1.6137   -1.6512 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7410   -1.1101   -1.5113 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1653    0.3583   -2.4089 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3023    1.7497   -1.7977 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4868   -0.2253    0.1184 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0077   -0.4861   -1.5682 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1148   -1.8923    0.7683 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4293   -2.1186   -0.8520 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7327   -1.5666    0.8028 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1560   -0.1342    2.2815 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7051    0.7871    1.7632 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5072    1.3390    1.3017 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1825    2.3932    0.8134 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  5  6  2  0
  6  7  1  0
  7  8  2  0
  8  9  1  0
  9 10  1  0
 10 11  1  0
 11 12  1  0
  9 13  1  0
 13 14  1  0
 14 15  1  0
 15 16  1  0
 16 17  1  0
 17 18  1  0
 18 19  1  0
 19 20  1  0
 20 21  1  0
 21 22  1  0
 14  2  1  0
 20 15  1  0
  8  3  1  0
 22 17  1  0
 12  7  1  0
  4 23  1  0
  5 24  1  0
  6 25  1  0
  9 26  1  0
 10 27  1  0
 10 28  1  0
 11 29  1  0
 11 30  1  0
 12 31  1  0
 12 32  1  0
 13 33  1  0
 13 34  1  0
 15 35  1  0
 16 36  1  0
 16 37  1  0
 18 38  1  0
 18 39  1  0
 19 40  1  0
 19 41  1  0
 20 42  1  0
 21 43  1  0
 21 44  1  0
 22 45  1  0
 22 46  1  0
M  END

View in JSmol View Stereo Labels

Synonyms

Not Available

Chemical Formula

C₁₉H₂₄N₂O

Average Molecular Weight

296.414

Monoisotopic Molecular Weight

296.188863401

IUPAC Name

3-{1-azabicyclo[2.2.2]octan-3-yl}-3-azatricyclo[7.3.1.0^{5,13}]trideca-1(13),9,11-trien-2-one

Traditional Name

3-{1-azabicyclo[2.2.2]octan-3-yl}-3-azatricyclo[7.3.1.0^{5,13}]trideca-1(13),9,11-trien-2-one

CAS Registry Number

Not Available

SMILES

O=C1N(CC2CCCC3=CC=CC1=C23)C1CN2CCC1CC2

InChI Identifier

InChI=1S/C19H24N2O/c22-19-16-6-2-4-14-3-1-5-15(18(14)16)11-21(19)17-12-20-9-7-13(17)8-10-20/h2,4,6,13,15,17H,1,3,5,7-12H2

InChI Key

CPZBLNMUGSZIPR-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as isoquinolones and derivatives. These are aromatic polycyclic compounds containing a ketone bearing isoquinoline moiety.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Isoquinolines and derivatives

Sub Class

Isoquinolones and derivatives

Direct Parent

Isoquinolones and derivatives

Alternative Parents

Substituents

Isoquinolone
Tetrahydroisoquinoline
Tetralin
Quinuclidine
Piperidine
Benzenoid
Tertiary carboxylic acid amide
Amino acid or derivatives
Tertiary aliphatic amine
Carboxamide group
Lactam
Tertiary amine
Azacycle
Carboxylic acid derivative
Organooxygen compound
Organonitrogen compound
Organopnictogen compound
Organic nitrogen compound
Hydrocarbon derivative
Organic oxide
Amine
Organic oxygen compound
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

Not Available

Ontology

Physiological effect

Not Available

Disposition

Biological location

Non-excretory biofluid

Biofluid or Excreta

Blood (PMID: 31557052)

Process

Not Available

Role

Not Available

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	2.72	ALOGPS
logP	2.55	ChemAxon
logS	-2.8	ALOGPS
pKa (Strongest Basic)	7.97	ChemAxon
Physiological Charge	1	ChemAxon
Hydrogen Acceptor Count	2	ChemAxon
Hydrogen Donor Count	0	ChemAxon
Polar Surface Area	23.55 Å²	ChemAxon
Rotatable Bond Count	1	ChemAxon
Refractivity	88.52 m³·mol⁻¹	ChemAxon
Polarizability	34.16 Å³	ChemAxon
Number of Rings	5	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	Yes	ChemAxon
MDDR-like Rule	No	ChemAxon

Predicted Chromatographic Properties

Predicted Collision Cross Sections

Predictor	Adduct Type	CCS Value (Å²)	Reference
DeepCCS	[M-2H]-	201.389	30932474
DeepCCS	[M+Na]+	176.954	30932474
AllCCS	[M+H]+	171.5	32859911
AllCCS	[M+H-H2O]+	168.4	32859911
AllCCS	[M+NH4]+	174.4	32859911
AllCCS	[M+Na]+	175.2	32859911
AllCCS	[M-H]-	175.7	32859911
AllCCS	[M+Na-2H]-	175.3	32859911
AllCCS	[M+HCOO]-	174.9	32859911

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
Palonosetron, (3R)-	O=C1N(CC2CCCC3=CC=CC1=C23)C1CN2CCC1CC2	3540.8	Standard polar	33892256
Palonosetron, (3R)-	O=C1N(CC2CCCC3=CC=CC1=C23)C1CN2CCC1CC2	2679.0	Standard non polar	33892256
Palonosetron, (3R)-	O=C1N(CC2CCCC3=CC=CC1=C23)C1CN2CCC1CC2	2793.0	Semi standard non polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted GC-MS	Predicted GC-MS Spectrum - (3R)-Palonosetron GC-MS (Non-derivatized) - 70eV, Positive	splash10-0bt9-0920000000-c32d60d5f7240bc355ba	2021-09-24	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - (3R)-Palonosetron GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Blood

Tissue Locations

Not Available

Pathways

Not Available

Name	SMPDB/PathBank	KEGG

Normal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Blood	Detected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	31557052	details

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

Not Available

KNApSAcK ID

Not Available

Chemspider ID

8058347

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

9882672

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

Barupal DK, Fiehn O: Generating the Blood Exposome Database Using a Comprehensive Text Mining and Database Fusion Approach. Environ Health Perspect. 2019 Sep;127(9):97008. doi: 10.1289/EHP4713. Epub 2019 Sep 26. [PubMed:31557052 ]

Showing metabocard for (3R)-Palonosetron (HMDB0259446)

MOL for HMDB0259446 ((3R)-Palonosetron)

3D MOL for HMDB0259446 ((3R)-Palonosetron)

3D SDF for HMDB0259446 ((3R)-Palonosetron)

3D-SDF for HMDB0259446 ((3R)-Palonosetron)

PDB for HMDB0259446 ((3R)-Palonosetron)

3D PDB for HMDB0259446 ((3R)-Palonosetron)

SMILES for HMDB0259446 ((3R)-Palonosetron)

INCHI for HMDB0259446 ((3R)-Palonosetron)

Structure for HMDB0259446 ((3R)-Palonosetron)

3D Structure for HMDB0259446 ((3R)-Palonosetron)

Predicted Collision Cross Sections

Predicted Kovats Retention Indices

Underivatized

GC-MS Spectra