Jump To Section:

Identification Taxonomy Ontology Physical properties Spectra Biological properties Concentrations Links References XML

Record Information

Version

5.0

Status

Expected but not Quantified

Creation Date

2012-09-11 19:28:15 UTC

Update Date

2022-03-07 02:54:09 UTC

HMDB ID

HMDB0034593

Secondary Accession Numbers

HMDB34593

Metabolite Identification

Common Name

(S)-Codamine

Description

(S)-Codamine belongs to the class of organic compounds known as benzylisoquinolines. These are organic compounds containing an isoquinoline to which a benzyl group is attached (S)-Codamine is a bitter tasting compound (S)-Codamine has been detected, but not quantified in, opium poppies (Papaver somniferum). This could make (S)-codamine a potential biomarker for the consumption of these foods. Based on a literature review very few articles have been published on (S)-Codamine.

Structure

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

HMDB0034593
     RDKit          3D
(S)-Codamine
 50 52  0  0  0  0  0  0  0  0999 V2000
    6.9670    0.4277    0.7904 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.9462    1.3325    0.4603 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.6147    0.9720    0.3657 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2435   -0.3550    0.6067 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9134   -0.6976    0.5084 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9915    0.2571    0.1811 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3815    1.5882   -0.0588 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7054    1.9508    0.0339 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1387    3.2520   -0.1939 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5709   -0.1376    0.1072 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2825    0.9699   -0.4455 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7188    0.6772   -0.5523 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2801    0.0999   -1.6724 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6258   -0.1640   -1.7823 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4842    0.1410   -0.7644 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.8570   -0.1075   -0.8290 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.3486   -0.7021   -2.0145 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9733    0.7190    0.3757 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8641    1.0253    1.4089 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3181    1.6173    2.5681 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6213    0.9798    0.4765 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4108   -1.3800   -0.5338 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7717   -2.1352   -0.1676 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5089   -2.2750   -0.5301 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4001   -2.0825    0.7193 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.8859    1.0108    1.0689 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.7190   -0.2194    1.6444 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.2733   -0.2027   -0.0679 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.9658   -1.1164    0.8668 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6728    2.3554   -0.3186 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.0940    3.5385   -0.1324 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2166   -0.2759    1.1749 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1779    1.3317   -1.3797 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1971    1.8258    0.2875 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6281   -0.1529   -2.4942 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0578   -0.6216   -2.6749 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.8118   -1.6335   -2.2619 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.4264   -0.8695   -1.9971 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.1391    0.0251   -2.8416 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4869    0.9415    2.8973 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8756    2.6111    2.3611 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0691    1.6555    3.3911 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2084    1.4294    1.3576 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4595   -1.6251    0.5014 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2891   -2.5406   -1.0708 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4156   -3.0412    0.3861 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1735   -2.0419   -1.3878 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2277   -3.3436   -0.6281 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2056   -2.8317    0.6228 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8054   -2.1821    1.6375 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  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
  6 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  2  0
 13 14  1  0
 14 15  2  0
 15 16  1  0
 16 17  1  0
 15 18  1  0
 18 19  1  0
 19 20  1  0
 18 21  2  0
 10 22  1  0
 22 23  1  0
 22 24  1  0
 24 25  1  0
  8  3  1  0
 21 12  1  0
 25  5  1  0
  1 26  1  0
  1 27  1  0
  1 28  1  0
  4 29  1  0
  7 30  1  0
  9 31  1  0
 10 32  1  0
 11 33  1  0
 11 34  1  0
 13 35  1  0
 14 36  1  0
 17 37  1  0
 17 38  1  0
 17 39  1  0
 20 40  1  0
 20 41  1  0
 20 42  1  0
 21 43  1  0
 23 44  1  0
 23 45  1  0
 23 46  1  0
 24 47  1  0
 24 48  1  0
 25 49  1  0
 25 50  1  0
M  END

  Mrv0541 05061307562D          

 25 27  0  0  0  0            999 V2000
    0.0000   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289   -4.9500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -5.3625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -2.8875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -2.8875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -4.1250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -1.2375    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868   -1.6500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289   -4.1250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -4.9500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  6  5  2  0  0  0  0
  8  7  1  0  0  0  0
 13  5  1  0  0  0  0
 13  9  1  0  0  0  0
 13 10  2  0  0  0  0
 14  7  1  0  0  0  0
 14 11  2  0  0  0  0
 15 12  2  0  0  0  0
 15 14  1  0  0  0  0
 16  9  1  0  0  0  0
 16 15  1  0  0  0  0
 17 12  1  0  0  0  0
 18  6  1  0  0  0  0
 19 11  1  0  0  0  0
 19 17  2  0  0  0  0
 20 10  1  0  0  0  0
 20 18  2  0  0  0  0
 21  1  1  0  0  0  0
 21  8  1  0  0  0  0
 21 16  1  0  0  0  0
 22 17  1  0  0  0  0
 23  2  1  0  0  0  0
 23 18  1  0  0  0  0
 24  3  1  0  0  0  0
 24 19  1  0  0  0  0
 25  4  1  0  0  0  0
 25 20  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0034593

> <DATABASE_NAME>
hmdb

> <SMILES>
COC1=C(OC)C=C(CC2N(C)CCC3=CC(OC)=C(O)C=C23)C=C1

> <INCHI_IDENTIFIER>
InChI=1S/C20H25NO4/c1-21-8-7-14-11-19(24-3)17(22)12-15(14)16(21)9-13-5-6-18(23-2)20(10-13)25-4/h5-6,10-12,16,22H,7-9H2,1-4H3

> <INCHI_KEY>
OKORHWXYDBSYNO-UHFFFAOYSA-N

> <FORMULA>
C20H25NO4

> <MOLECULAR_WEIGHT>
343.4168

> <EXACT_MASS>
343.178358293

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_AVERAGE_POLARIZABILITY>
37.84447730381906

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
1-[(3,4-dimethoxyphenyl)methyl]-6-methoxy-2-methyl-1,2,3,4-tetrahydroisoquinolin-7-ol

> <ALOGPS_LOGP>
3.20

> <JCHEM_LOGP>
3.250853363000001

> <ALOGPS_LOGS>
-3.96

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA_STRONGEST_ACIDIC>
10.7898340054934

> <JCHEM_PKA_STRONGEST_BASIC>
7.2210719958196306

> <JCHEM_POLAR_SURFACE_AREA>
51.16000000000001

> <JCHEM_REFRACTIVITY>
98.31859999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
3.73e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
codamine

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0034593
     RDKit          3D
(S)-Codamine
 50 52  0  0  0  0  0  0  0  0999 V2000
    6.9670    0.4277    0.7904 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.9462    1.3325    0.4603 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.6147    0.9720    0.3657 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2435   -0.3550    0.6067 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9134   -0.6976    0.5084 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9915    0.2571    0.1811 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3815    1.5882   -0.0588 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7054    1.9508    0.0339 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1387    3.2520   -0.1939 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5709   -0.1376    0.1072 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2825    0.9699   -0.4455 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7188    0.6772   -0.5523 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2801    0.0999   -1.6724 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6258   -0.1640   -1.7823 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4842    0.1410   -0.7644 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.8570   -0.1075   -0.8290 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.3486   -0.7021   -2.0145 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9733    0.7190    0.3757 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8641    1.0253    1.4089 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3181    1.6173    2.5681 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6213    0.9798    0.4765 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4108   -1.3800   -0.5338 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7717   -2.1352   -0.1676 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5089   -2.2750   -0.5301 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4001   -2.0825    0.7193 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.8859    1.0108    1.0689 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.7190   -0.2194    1.6444 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.2733   -0.2027   -0.0679 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.9658   -1.1164    0.8668 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6728    2.3554   -0.3186 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.0940    3.5385   -0.1324 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2166   -0.2759    1.1749 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1779    1.3317   -1.3797 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1971    1.8258    0.2875 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6281   -0.1529   -2.4942 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0578   -0.6216   -2.6749 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.8118   -1.6335   -2.2619 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.4264   -0.8695   -1.9971 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.1391    0.0251   -2.8416 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4869    0.9415    2.8973 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8756    2.6111    2.3611 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0691    1.6555    3.3911 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2084    1.4294    1.3576 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4595   -1.6251    0.5014 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2891   -2.5406   -1.0708 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4156   -3.0412    0.3861 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1735   -2.0419   -1.3878 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2277   -3.3436   -0.6281 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2056   -2.8317    0.6228 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8054   -2.1821    1.6375 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  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
  6 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  2  0
 13 14  1  0
 14 15  2  0
 15 16  1  0
 16 17  1  0
 15 18  1  0
 18 19  1  0
 19 20  1  0
 18 21  2  0
 10 22  1  0
 22 23  1  0
 22 24  1  0
 24 25  1  0
  8  3  1  0
 21 12  1  0
 25  5  1  0
  1 26  1  0
  1 27  1  0
  1 28  1  0
  4 29  1  0
  7 30  1  0
  9 31  1  0
 10 32  1  0
 11 33  1  0
 11 34  1  0
 13 35  1  0
 14 36  1  0
 17 37  1  0
 17 38  1  0
 17 39  1  0
 20 40  1  0
 20 41  1  0
 20 42  1  0
 21 43  1  0
 23 44  1  0
 23 45  1  0
 23 46  1  0
 24 47  1  0
 24 48  1  0
 25 49  1  0
 25 50  1  0
M  END

HEADER    PROTEIN                                 06-MAY-13   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   06-MAY-13         0                                  
HETATM    1  C   UNK     0       0.000  -3.080   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -2.667  -9.240   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       8.002   1.540   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -1.334 -10.010   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.000  -4.620   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -1.334  -5.390   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       2.667   0.000   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       2.667  -4.620   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       1.334  -6.930   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       5.335   0.000   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       5.335  -3.080   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       1.334  -5.390   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       4.001  -0.770   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       4.001  -2.310   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       2.667  -3.080   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       6.668  -2.310   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      -1.334  -6.930   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       6.668  -0.770   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       0.000  -7.700   0.000  0.00  0.00           C+0
HETATM   21  N   UNK     0       1.334  -2.310   0.000  0.00  0.00           N+0
HETATM   22  O   UNK     0       8.002  -3.080   0.000  0.00  0.00           O+0
HETATM   23  O   UNK     0      -2.667  -7.700   0.000  0.00  0.00           O+0
HETATM   24  O   UNK     0       8.002   0.000   0.000  0.00  0.00           O+0
HETATM   25  O   UNK     0       0.000  -9.240   0.000  0.00  0.00           O+0
CONECT    1   21                                                            
CONECT    2   23                                                            
CONECT    3   24                                                            
CONECT    4   25                                                            
CONECT    5    6   13                                                       
CONECT    6    5   18                                                       
CONECT    7    8   14                                                       
CONECT    8    7   21                                                       
CONECT    9   13   16                                                       
CONECT   10   13   20                                                       
CONECT   11   14   19                                                       
CONECT   12   15   17                                                       
CONECT   13    5    9   10                                                  
CONECT   14    7   11   15                                                  
CONECT   15   12   14   16                                                  
CONECT   16    9   15   21                                                  
CONECT   17   12   19   22                                                  
CONECT   18    6   20   23                                                  
CONECT   19   11   17   24                                                  
CONECT   20   10   18   25                                                  
CONECT   21    1    8   16                                                  
CONECT   22   17                                                            
CONECT   23    2   18                                                       
CONECT   24    3   19                                                       
CONECT   25    4   20                                                       
MASTER        0    0    0    0    0    0    0    0   25    0   54    0
END

COMPND    HMDB0034593
HETATM    1  C1  UNL     1       6.967   0.428   0.790  1.00  0.00           C  
HETATM    2  O1  UNL     1       5.946   1.333   0.460  1.00  0.00           O  
HETATM    3  C2  UNL     1       4.615   0.972   0.366  1.00  0.00           C  
HETATM    4  C3  UNL     1       4.244  -0.355   0.607  1.00  0.00           C  
HETATM    5  C4  UNL     1       2.913  -0.698   0.508  1.00  0.00           C  
HETATM    6  C5  UNL     1       1.992   0.257   0.181  1.00  0.00           C  
HETATM    7  C6  UNL     1       2.382   1.588  -0.059  1.00  0.00           C  
HETATM    8  C7  UNL     1       3.705   1.951   0.034  1.00  0.00           C  
HETATM    9  O2  UNL     1       4.139   3.252  -0.194  1.00  0.00           O  
HETATM   10  C8  UNL     1       0.571  -0.138   0.107  1.00  0.00           C  
HETATM   11  C9  UNL     1      -0.283   0.970  -0.445  1.00  0.00           C  
HETATM   12  C10 UNL     1      -1.719   0.677  -0.552  1.00  0.00           C  
HETATM   13  C11 UNL     1      -2.280   0.100  -1.672  1.00  0.00           C  
HETATM   14  C12 UNL     1      -3.626  -0.164  -1.782  1.00  0.00           C  
HETATM   15  C13 UNL     1      -4.484   0.141  -0.764  1.00  0.00           C  
HETATM   16  O3  UNL     1      -5.857  -0.107  -0.829  1.00  0.00           O  
HETATM   17  C14 UNL     1      -6.349  -0.702  -2.015  1.00  0.00           C  
HETATM   18  C15 UNL     1      -3.973   0.719   0.376  1.00  0.00           C  
HETATM   19  O4  UNL     1      -4.864   1.025   1.409  1.00  0.00           O  
HETATM   20  C16 UNL     1      -4.318   1.617   2.568  1.00  0.00           C  
HETATM   21  C17 UNL     1      -2.621   0.980   0.476  1.00  0.00           C  
HETATM   22  N1  UNL     1       0.411  -1.380  -0.534  1.00  0.00           N  
HETATM   23  C18 UNL     1      -0.772  -2.135  -0.168  1.00  0.00           C  
HETATM   24  C19 UNL     1       1.509  -2.275  -0.530  1.00  0.00           C  
HETATM   25  C20 UNL     1       2.400  -2.083   0.719  1.00  0.00           C  
HETATM   26  H1  UNL     1       7.886   1.011   1.069  1.00  0.00           H  
HETATM   27  H2  UNL     1       6.719  -0.219   1.644  1.00  0.00           H  
HETATM   28  H3  UNL     1       7.273  -0.203  -0.068  1.00  0.00           H  
HETATM   29  H4  UNL     1       4.966  -1.116   0.867  1.00  0.00           H  
HETATM   30  H5  UNL     1       1.673   2.355  -0.319  1.00  0.00           H  
HETATM   31  H6  UNL     1       5.094   3.538  -0.132  1.00  0.00           H  
HETATM   32  H7  UNL     1       0.217  -0.276   1.175  1.00  0.00           H  
HETATM   33  H8  UNL     1       0.178   1.332  -1.380  1.00  0.00           H  
HETATM   34  H9  UNL     1      -0.197   1.826   0.287  1.00  0.00           H  
HETATM   35  H10 UNL     1      -1.628  -0.153  -2.494  1.00  0.00           H  
HETATM   36  H11 UNL     1      -4.058  -0.622  -2.675  1.00  0.00           H  
HETATM   37  H12 UNL     1      -5.812  -1.634  -2.262  1.00  0.00           H  
HETATM   38  H13 UNL     1      -7.426  -0.870  -1.997  1.00  0.00           H  
HETATM   39  H14 UNL     1      -6.139   0.025  -2.842  1.00  0.00           H  
HETATM   40  H15 UNL     1      -3.487   0.942   2.897  1.00  0.00           H  
HETATM   41  H16 UNL     1      -3.876   2.611   2.361  1.00  0.00           H  
HETATM   42  H17 UNL     1      -5.069   1.656   3.391  1.00  0.00           H  
HETATM   43  H18 UNL     1      -2.208   1.429   1.358  1.00  0.00           H  
HETATM   44  H19 UNL     1      -1.460  -1.625   0.501  1.00  0.00           H  
HETATM   45  H20 UNL     1      -1.289  -2.541  -1.071  1.00  0.00           H  
HETATM   46  H21 UNL     1      -0.416  -3.041   0.386  1.00  0.00           H  
HETATM   47  H22 UNL     1       2.173  -2.042  -1.388  1.00  0.00           H  
HETATM   48  H23 UNL     1       1.228  -3.344  -0.628  1.00  0.00           H  
HETATM   49  H24 UNL     1       3.206  -2.832   0.623  1.00  0.00           H  
HETATM   50  H25 UNL     1       1.805  -2.182   1.638  1.00  0.00           H  
CONECT    1    2   26   27   28
CONECT    2    3
CONECT    3    4    4    8
CONECT    4    5   29
CONECT    5    6    6   25
CONECT    6    7   10
CONECT    7    8    8   30
CONECT    8    9
CONECT    9   31
CONECT   10   11   22   32
CONECT   11   12   33   34
CONECT   12   13   13   21
CONECT   13   14   35
CONECT   14   15   15   36
CONECT   15   16   18
CONECT   16   17
CONECT   17   37   38   39
CONECT   18   19   21   21
CONECT   19   20
CONECT   20   40   41   42
CONECT   21   43
CONECT   22   23   24
CONECT   23   44   45   46
CONECT   24   25   47   48
CONECT   25   49   50
END

HMDB0034593
     RDKit          3D
(S)-Codamine
 50 52  0  0  0  0  0  0  0  0999 V2000
    6.9670    0.4277    0.7904 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.9462    1.3325    0.4603 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.6147    0.9720    0.3657 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2435   -0.3550    0.6067 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9134   -0.6976    0.5084 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9915    0.2571    0.1811 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3815    1.5882   -0.0588 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7054    1.9508    0.0339 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1387    3.2520   -0.1939 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5709   -0.1376    0.1072 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2825    0.9699   -0.4455 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7188    0.6772   -0.5523 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2801    0.0999   -1.6724 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6258   -0.1640   -1.7823 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4842    0.1410   -0.7644 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.8570   -0.1075   -0.8290 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.3486   -0.7021   -2.0145 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9733    0.7190    0.3757 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8641    1.0253    1.4089 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3181    1.6173    2.5681 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6213    0.9798    0.4765 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4108   -1.3800   -0.5338 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7717   -2.1352   -0.1676 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5089   -2.2750   -0.5301 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4001   -2.0825    0.7193 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.8859    1.0108    1.0689 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.7190   -0.2194    1.6444 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.2733   -0.2027   -0.0679 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.9658   -1.1164    0.8668 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6728    2.3554   -0.3186 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.0940    3.5385   -0.1324 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2166   -0.2759    1.1749 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1779    1.3317   -1.3797 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1971    1.8258    0.2875 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6281   -0.1529   -2.4942 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0578   -0.6216   -2.6749 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.8118   -1.6335   -2.2619 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.4264   -0.8695   -1.9971 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.1391    0.0251   -2.8416 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4869    0.9415    2.8973 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8756    2.6111    2.3611 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0691    1.6555    3.3911 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2084    1.4294    1.3576 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4595   -1.6251    0.5014 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2891   -2.5406   -1.0708 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4156   -3.0412    0.3861 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1735   -2.0419   -1.3878 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2277   -3.3436   -0.6281 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2056   -2.8317    0.6228 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8054   -2.1821    1.6375 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  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
  6 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  2  0
 13 14  1  0
 14 15  2  0
 15 16  1  0
 16 17  1  0
 15 18  1  0
 18 19  1  0
 19 20  1  0
 18 21  2  0
 10 22  1  0
 22 23  1  0
 22 24  1  0
 24 25  1  0
  8  3  1  0
 21 12  1  0
 25  5  1  0
  1 26  1  0
  1 27  1  0
  1 28  1  0
  4 29  1  0
  7 30  1  0
  9 31  1  0
 10 32  1  0
 11 33  1  0
 11 34  1  0
 13 35  1  0
 14 36  1  0
 17 37  1  0
 17 38  1  0
 17 39  1  0
 20 40  1  0
 20 41  1  0
 20 42  1  0
 21 43  1  0
 23 44  1  0
 23 45  1  0
 23 46  1  0
 24 47  1  0
 24 48  1  0
 25 49  1  0
 25 50  1  0
M  END

View in JSmol View Stereo Labels

Synonyms

Value	Source
(+)-Codamine	HMDB
(.+-.)-codamine	HMDB
Codamine	HMDB
DL-Codamine	HMDB

Chemical Formula

C₂₀H₂₅NO₄

Average Molecular Weight

343.4168

Monoisotopic Molecular Weight

343.178358293

IUPAC Name

1-[(3,4-dimethoxyphenyl)methyl]-6-methoxy-2-methyl-1,2,3,4-tetrahydroisoquinolin-7-ol

Traditional Name

codamine

CAS Registry Number

21040-59-5

SMILES

COC1=C(OC)C=C(CC2N(C)CCC3=CC(OC)=C(O)C=C23)C=C1

InChI Identifier

InChI=1S/C20H25NO4/c1-21-8-7-14-11-19(24-3)17(22)12-15(14)16(21)9-13-5-6-18(23-2)20(10-13)25-4/h5-6,10-12,16,22H,7-9H2,1-4H3

InChI Key

OKORHWXYDBSYNO-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as benzylisoquinolines. These are organic compounds containing an isoquinoline to which a benzyl group is attached.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Isoquinolines and derivatives

Sub Class

Benzylisoquinolines

Direct Parent

Benzylisoquinolines

Alternative Parents

Substituents

Benzylisoquinoline
O-dimethoxybenzene
Dimethoxybenzene
Tetrahydroisoquinoline
Phenoxy compound
Anisole
Phenol ether
Methoxybenzene
Alkyl aryl ether
1-hydroxy-2-unsubstituted benzenoid
Aralkylamine
Monocyclic benzene moiety
Benzenoid
Tertiary aliphatic amine
Tertiary amine
Ether
Azacycle
Organonitrogen compound
Organic nitrogen compound
Hydrocarbon derivative
Organopnictogen compound
Organic oxygen compound
Organooxygen compound
Amine
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

Not Available

Ontology

Physiological effect

Organoleptic effect

Taste

Bitter

Disposition

Biological location

Cellular substructure

Membrane (HMDB: HMDB0034593)
Cell membrane (HMDB: HMDB0034593)

Route of exposure

Enteral

Ingestion (HMDB: HMDB0034593)

Source

Exogenous

Exogenous (HMDB: HMDB0034593)

Food

Food (HMDB: HMDB0034593)

Herb and spice

Spice

Opium poppy (FooDB: FOOD00438)

Endogenous

Plant

Plant (HMDB: HMDB0034593)

Process

Not Available

Role

Biological role

Nutrient (HMDB: HMDB0034593)

Physical Properties

State

Solid

Experimental Molecular Properties

Property	Value	Reference
Melting Point	126 - 127 °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	0.037 g/L	ALOGPS
logP	3.2	ALOGPS
logP	3.25	ChemAxon
logS	-4	ALOGPS
pKa (Strongest Acidic)	10.79	ChemAxon
pKa (Strongest Basic)	7.22	ChemAxon
Physiological Charge	1	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	51.16 Å²	ChemAxon
Rotatable Bond Count	5	ChemAxon
Refractivity	98.32 m³·mol⁻¹	ChemAxon
Polarizability	37.84 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
DarkChem	[M+H]+	180.836	31661259
DarkChem	[M-H]-	182.015	31661259
DeepCCS	[M-2H]-	219.14	30932474
DeepCCS	[M+Na]+	195.43	30932474
AllCCS	[M+H]+	184.7	32859911
AllCCS	[M+H-H2O]+	181.6	32859911
AllCCS	[M+NH4]+	187.6	32859911
AllCCS	[M+Na]+	188.5	32859911
AllCCS	[M-H]-	189.8	32859911
AllCCS	[M+Na-2H]-	189.8	32859911
AllCCS	[M+HCOO]-	190.0	32859911

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
(S)-Codamine	COC1=C(OC)C=C(CC2N(C)CCC3=CC(OC)=C(O)C=C23)C=C1	4238.7	Standard polar	33892256
(S)-Codamine	COC1=C(OC)C=C(CC2N(C)CCC3=CC(OC)=C(O)C=C23)C=C1	2779.5	Standard non polar	33892256
(S)-Codamine	COC1=C(OC)C=C(CC2N(C)CCC3=CC(OC)=C(O)C=C23)C=C1	2776.0	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
(S)-Codamine,1TMS,isomer #1	COC1=CC=C(CC2C3=CC(O[Si](C)(C)C)=C(OC)C=C3CCN2C)C=C1OC	2723.0	Semi standard non polar	33892256
(S)-Codamine,1TBDMS,isomer #1	COC1=CC=C(CC2C3=CC(O[Si](C)(C)C(C)(C)C)=C(OC)C=C3CCN2C)C=C1OC	2952.7	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 - (S)-Codamine GC-MS (Non-derivatized) - 70eV, Positive	splash10-0006-0900000000-a3142469441c07edcd5a	2017-09-01	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - (S)-Codamine GC-MS (1 TMS) - 70eV, Positive	splash10-03di-1390100000-f97311c09a25829bde87	2017-10-06	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - (S)-Codamine 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 - (S)-Codamine 10V, Positive-QTOF	splash10-0006-0009000000-5c1d1aba4a29acdb0ee4	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (S)-Codamine 20V, Positive-QTOF	splash10-01ox-0917000000-734f92f58de9ca320440	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (S)-Codamine 40V, Positive-QTOF	splash10-0j4m-1931000000-41e3e8efe8cc738fb82a	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (S)-Codamine 10V, Negative-QTOF	splash10-0006-0009000000-cd691319c35409992f87	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (S)-Codamine 20V, Negative-QTOF	splash10-002f-0019000000-928877f61eee6f97ef10	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (S)-Codamine 40V, Negative-QTOF	splash10-007k-1092000000-82ee3833247cb7dc9801	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (S)-Codamine 10V, Negative-QTOF	splash10-0006-0009000000-5a516184c230fa2e7a58	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (S)-Codamine 20V, Negative-QTOF	splash10-01ox-0139000000-31112d91d662727c16db	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (S)-Codamine 40V, Negative-QTOF	splash10-00xv-0391000000-f73013eb114d2efdaa0d	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (S)-Codamine 10V, Positive-QTOF	splash10-0006-0009000000-4c99d939ca6eae6febd1	2021-09-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (S)-Codamine 20V, Positive-QTOF	splash10-0006-0924000000-22cd306df90bfa420c1b	2021-09-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (S)-Codamine 40V, Positive-QTOF	splash10-0ikd-0912000000-ba986575b3938984d9e9	2021-09-24	Wishart Lab	View Spectrum

Biological Properties

Cellular Locations

Membrane

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

FDB013109

KNApSAcK ID

C00025654

Chemspider ID

80700

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

89421

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 (S)-Codamine (HMDB0034593)

MOL for HMDB0034593 ((S)-Codamine)

3D MOL for HMDB0034593 ((S)-Codamine)

3D SDF for HMDB0034593 ((S)-Codamine)

3D-SDF for HMDB0034593 ((S)-Codamine)

PDB for HMDB0034593 ((S)-Codamine)

3D PDB for HMDB0034593 ((S)-Codamine)

SMILES for HMDB0034593 ((S)-Codamine)

INCHI for HMDB0034593 ((S)-Codamine)

Structure for HMDB0034593 ((S)-Codamine)

3D Structure for HMDB0034593 ((S)-Codamine)

Predicted Collision Cross Sections

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra