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Record Information

Version

5.0

Status

Expected but not Quantified

Creation Date

2012-09-11 18:04:41 UTC

Update Date

2022-03-07 02:53:41 UTC

HMDB ID

HMDB0033362

Secondary Accession Numbers

HMDB33362

Metabolite Identification

Common Name

(S)-Nandigerine

Description

(S)-Nandigerine, also known as hernangerine, belongs to the class of organic compounds known as aporphines. These are quinoline alkaloids containing the dibenzo[de,g]quinoline ring system or a dehydrogenated derivative thereof (S)-Nandigerine is a very strong basic compound (based on its pKa). Outside of the human body, (S)-nandigerine has been detected, but not quantified in, a few different foods, such as herbs and spices, sweet bay, and tea. This could make (S)-nandigerine a potential biomarker for the consumption of these foods.

Structure

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

HMDB0033362
     RDKit          3D
(S)-Nandigerine
 40 44  0  0  0  0  0  0  0  0999 V2000
    3.2796    1.3007   -1.4211 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8494    0.8679   -0.0825 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.2718   -0.3834   -0.0145 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2222   -1.4139   -0.0437 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5618   -1.1146   -0.0892 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8096   -2.7287   -0.0219 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4884   -3.0315    0.0286 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5099   -2.0136    0.0660 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9547   -0.6904    0.0496 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0730    0.3374    0.1560 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3208    1.6791    0.3140 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6836    2.5922    0.5410 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0345    2.2217    0.6175 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3728    0.9272    0.4656 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3754   -0.0393    0.2311 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8685   -1.4189    0.1064 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8921   -2.4530    0.0867 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9331   -1.4989   -0.8955 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9359   -0.4967   -0.7050 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7408    0.3896    0.4985 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1369    3.8618    0.6701 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2494    3.6300    0.9658 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4826    2.3941    0.3221 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.1182    1.9848   -1.2337 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6729    0.4157   -1.9513 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5057    1.7894   -1.9829 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.8880   -0.1788   -0.0754 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5174   -3.5528   -0.0436 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1167   -4.0409    0.0429 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7758    2.9713    0.7949 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4940   -1.5533    1.0845 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0472   -3.1819   -0.8146 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0365   -3.1277    1.0030 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3013   -2.4639   -0.9443 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9134   -1.0372   -0.5324 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0006    0.0937   -1.6495 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4787    1.2175    0.4328 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9225   -0.1671    1.4139 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8540    4.4437    0.5599 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3435    3.4687    2.0497 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
  4  6  1  0
  6  7  2  0
  7  8  1  0
  8  9  2  0
  9 10  1  0
 10 11  2  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
 16 18  1  0
 18 19  1  0
 19 20  1  0
 12 21  1  0
 21 22  1  0
 22 23  1  0
  9  3  1  0
 15 10  1  0
 17  8  1  0
 23 11  1  0
 20 14  1  0
  1 24  1  0
  1 25  1  0
  1 26  1  0
  5 27  1  0
  6 28  1  0
  7 29  1  0
 13 30  1  0
 16 31  1  0
 17 32  1  0
 17 33  1  0
 18 34  1  0
 19 35  1  0
 19 36  1  0
 20 37  1  0
 20 38  1  0
 22 39  1  0
 22 40  1  0
M  END


  Mrv0541 05061307052D          

 23 27  0  0  0  0            999 V2000
    5.0013    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0013   -1.2375    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
    0.7145   -1.2375    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
    1.4289    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1354    2.1307    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
    1.4289    0.0000    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
    5.0013   -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
    2.1434   -0.4125    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
    2.8579    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -1.6500    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.7158    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868    0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.3149    2.0445    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.4710    1.3770    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  3  2  2  0  0  0  0
  5  4  1  0  0  0  0
  9  2  1  0  0  0  0
  9  6  1  0  0  0  0
 10  4  1  0  0  0  0
 10  7  2  0  0  0  0
 11  6  1  0  0  0  0
 12  3  1  0  0  0  0
 13  7  1  0  0  0  0
 14 10  1  0  0  0  0
 14 11  1  0  0  0  0
 15  9  2  0  0  0  0
 16 14  2  0  0  0  0
 16 15  1  0  0  0  0
 17 12  2  0  0  0  0
 17 15  1  0  0  0  0
 18 13  2  0  0  0  0
 18 16  1  0  0  0  0
 19  5  1  0  0  0  0
 19 11  1  0  0  0  0
 20 12  1  0  0  0  0
 21  1  1  0  0  0  0
 21 17  1  0  0  0  0
 22  8  1  0  0  0  0
 22 13  1  0  0  0  0
 23  8  1  0  0  0  0
 23 18  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0033362

> <DATABASE_NAME>
hmdb

> <SMILES>
COC1=C(O)C=CC2=C1C1=C3C(C2)NCCC3=CC2=C1OCO2

> <INCHI_IDENTIFIER>
InChI=1S/C18H17NO4/c1-21-17-12(20)3-2-9-6-11-14-10(4-5-19-11)7-13-18(23-8-22-13)16(14)15(9)17/h2-3,7,11,19-20H,4-6,8H2,1H3

> <INCHI_KEY>
CFUKKPQRQGCLAT-UHFFFAOYSA-N

> <FORMULA>
C18H17NO4

> <MOLECULAR_WEIGHT>
311.3319

> <EXACT_MASS>
311.115758037

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_AVERAGE_POLARIZABILITY>
32.58469807521295

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
18-methoxy-3,5-dioxa-11-azapentacyclo[10.7.1.0²,⁶.0⁸,²⁰.0¹⁴,¹⁹]icosa-1(20),2(6),7,14(19),15,17-hexaen-17-ol

> <ALOGPS_LOGP>
1.49

> <JCHEM_LOGP>
2.088857084552003

> <ALOGPS_LOGS>
-3.24

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA_STRONGEST_ACIDIC>
10.165945195306751

> <JCHEM_PKA_STRONGEST_BASIC>
9.357262952176361

> <JCHEM_POLAR_SURFACE_AREA>
59.95

> <JCHEM_REFRACTIVITY>
84.9426

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.78e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
18-methoxy-3,5-dioxa-11-azapentacyclo[10.7.1.0²,⁶.0⁸,²⁰.0¹⁴,¹⁹]icosa-1(20),2(6),7,14(19),15,17-hexaen-17-ol

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0033362
     RDKit          3D
(S)-Nandigerine
 40 44  0  0  0  0  0  0  0  0999 V2000
    3.2796    1.3007   -1.4211 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8494    0.8679   -0.0825 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.2718   -0.3834   -0.0145 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2222   -1.4139   -0.0437 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5618   -1.1146   -0.0892 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8096   -2.7287   -0.0219 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4884   -3.0315    0.0286 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5099   -2.0136    0.0660 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9547   -0.6904    0.0496 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0730    0.3374    0.1560 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3208    1.6791    0.3140 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6836    2.5922    0.5410 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0345    2.2217    0.6175 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3728    0.9272    0.4656 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3754   -0.0393    0.2311 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8685   -1.4189    0.1064 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8921   -2.4530    0.0867 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9331   -1.4989   -0.8955 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9359   -0.4967   -0.7050 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7408    0.3896    0.4985 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1369    3.8618    0.6701 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2494    3.6300    0.9658 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4826    2.3941    0.3221 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.1182    1.9848   -1.2337 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6729    0.4157   -1.9513 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5057    1.7894   -1.9829 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.8880   -0.1788   -0.0754 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5174   -3.5528   -0.0436 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1167   -4.0409    0.0429 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7758    2.9713    0.7949 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4940   -1.5533    1.0845 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0472   -3.1819   -0.8146 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0365   -3.1277    1.0030 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3013   -2.4639   -0.9443 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9134   -1.0372   -0.5324 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0006    0.0937   -1.6495 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4787    1.2175    0.4328 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9225   -0.1671    1.4139 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8540    4.4437    0.5599 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3435    3.4687    2.0497 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
  4  6  1  0
  6  7  2  0
  7  8  1  0
  8  9  2  0
  9 10  1  0
 10 11  2  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
 16 18  1  0
 18 19  1  0
 19 20  1  0
 12 21  1  0
 21 22  1  0
 22 23  1  0
  9  3  1  0
 15 10  1  0
 17  8  1  0
 23 11  1  0
 20 14  1  0
  1 24  1  0
  1 25  1  0
  1 26  1  0
  5 27  1  0
  6 28  1  0
  7 29  1  0
 13 30  1  0
 16 31  1  0
 17 32  1  0
 17 33  1  0
 18 34  1  0
 19 35  1  0
 19 36  1  0
 20 37  1  0
 20 38  1  0
 22 39  1  0
 22 40  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       9.336   2.310   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       8.002  -3.080   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       9.336  -2.310   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       1.334  -2.310   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       5.335  -3.080   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       5.853   3.977   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       6.668  -2.310   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       2.667   0.000   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       4.001  -2.310   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       9.336  -0.770   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       4.001   2.310   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       6.668  -0.770   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       5.335   0.000   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       8.002   0.000   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       5.335   1.540   0.000  0.00  0.00           C+0
HETATM   19  N   UNK     0       2.667  -3.080   0.000  0.00  0.00           N+0
HETATM   20  O   UNK     0      10.669   0.000   0.000  0.00  0.00           O+0
HETATM   21  O   UNK     0       8.002   1.540   0.000  0.00  0.00           O+0
HETATM   22  O   UNK     0       4.321   3.816   0.000  0.00  0.00           O+0
HETATM   23  O   UNK     0       6.479   2.570   0.000  0.00  0.00           O+0
CONECT    1   21                                                            
CONECT    2    3    9                                                       
CONECT    3    2   12                                                       
CONECT    4    5   10                                                       
CONECT    5    4   19                                                       
CONECT    6    9   11                                                       
CONECT    7   10   13                                                       
CONECT    8   22   23                                                       
CONECT    9    2    6   15                                                  
CONECT   10    4    7   14                                                  
CONECT   11    6   14   19                                                  
CONECT   12    3   17   20                                                  
CONECT   13    7   18   22                                                  
CONECT   14   10   11   16                                                  
CONECT   15    9   16   17                                                  
CONECT   16   14   15   18                                                  
CONECT   17   12   15   21                                                  
CONECT   18   13   16   23                                                  
CONECT   19    5   11                                                       
CONECT   20   12                                                            
CONECT   21    1   17                                                       
CONECT   22    8   13                                                       
CONECT   23    8   18                                                       
MASTER        0    0    0    0    0    0    0    0   23    0   54    0
END

COMPND    HMDB0033362
HETATM    1  C1  UNL     1       3.280   1.301  -1.421  1.00  0.00           C  
HETATM    2  O1  UNL     1       2.849   0.868  -0.082  1.00  0.00           O  
HETATM    3  C2  UNL     1       2.272  -0.383  -0.014  1.00  0.00           C  
HETATM    4  C3  UNL     1       3.222  -1.414  -0.044  1.00  0.00           C  
HETATM    5  O2  UNL     1       4.562  -1.115  -0.089  1.00  0.00           O  
HETATM    6  C4  UNL     1       2.810  -2.729  -0.022  1.00  0.00           C  
HETATM    7  C5  UNL     1       1.488  -3.032   0.029  1.00  0.00           C  
HETATM    8  C6  UNL     1       0.510  -2.014   0.066  1.00  0.00           C  
HETATM    9  C7  UNL     1       0.955  -0.690   0.050  1.00  0.00           C  
HETATM   10  C8  UNL     1      -0.073   0.337   0.156  1.00  0.00           C  
HETATM   11  C9  UNL     1       0.321   1.679   0.314  1.00  0.00           C  
HETATM   12  C10 UNL     1      -0.684   2.592   0.541  1.00  0.00           C  
HETATM   13  C11 UNL     1      -2.034   2.222   0.618  1.00  0.00           C  
HETATM   14  C12 UNL     1      -2.373   0.927   0.466  1.00  0.00           C  
HETATM   15  C13 UNL     1      -1.375  -0.039   0.231  1.00  0.00           C  
HETATM   16  C14 UNL     1      -1.869  -1.419   0.106  1.00  0.00           C  
HETATM   17  C15 UNL     1      -0.892  -2.453   0.087  1.00  0.00           C  
HETATM   18  N1  UNL     1      -2.933  -1.499  -0.895  1.00  0.00           N  
HETATM   19  C16 UNL     1      -3.936  -0.497  -0.705  1.00  0.00           C  
HETATM   20  C17 UNL     1      -3.741   0.390   0.498  1.00  0.00           C  
HETATM   21  O3  UNL     1      -0.137   3.862   0.670  1.00  0.00           O  
HETATM   22  C18 UNL     1       1.249   3.630   0.966  1.00  0.00           C  
HETATM   23  O4  UNL     1       1.483   2.394   0.322  1.00  0.00           O  
HETATM   24  H1  UNL     1       4.118   1.985  -1.234  1.00  0.00           H  
HETATM   25  H2  UNL     1       3.673   0.416  -1.951  1.00  0.00           H  
HETATM   26  H3  UNL     1       2.506   1.789  -1.983  1.00  0.00           H  
HETATM   27  H4  UNL     1       4.888  -0.179  -0.075  1.00  0.00           H  
HETATM   28  H5  UNL     1       3.517  -3.553  -0.044  1.00  0.00           H  
HETATM   29  H6  UNL     1       1.117  -4.041   0.043  1.00  0.00           H  
HETATM   30  H7  UNL     1      -2.776   2.971   0.795  1.00  0.00           H  
HETATM   31  H8  UNL     1      -2.494  -1.553   1.085  1.00  0.00           H  
HETATM   32  H9  UNL     1      -1.047  -3.182  -0.815  1.00  0.00           H  
HETATM   33  H10 UNL     1      -1.037  -3.128   1.003  1.00  0.00           H  
HETATM   34  H11 UNL     1      -3.301  -2.464  -0.944  1.00  0.00           H  
HETATM   35  H12 UNL     1      -4.913  -1.037  -0.532  1.00  0.00           H  
HETATM   36  H13 UNL     1      -4.001   0.094  -1.650  1.00  0.00           H  
HETATM   37  H14 UNL     1      -4.479   1.217   0.433  1.00  0.00           H  
HETATM   38  H15 UNL     1      -3.923  -0.167   1.414  1.00  0.00           H  
HETATM   39  H16 UNL     1       1.854   4.444   0.560  1.00  0.00           H  
HETATM   40  H17 UNL     1       1.344   3.469   2.050  1.00  0.00           H  
CONECT    1    2   24   25   26
CONECT    2    3
CONECT    3    4    4    9
CONECT    4    5    6
CONECT    5   27
CONECT    6    7    7   28
CONECT    7    8   29
CONECT    8    9    9   17
CONECT    9   10
CONECT   10   11   11   15
CONECT   11   12   23
CONECT   12   13   13   21
CONECT   13   14   30
CONECT   14   15   15   20
CONECT   15   16
CONECT   16   17   18   31
CONECT   17   32   33
CONECT   18   19   34
CONECT   19   20   35   36
CONECT   20   37   38
CONECT   21   22
CONECT   22   23   39   40
END

HMDB0033362
     RDKit          3D
(S)-Nandigerine
 40 44  0  0  0  0  0  0  0  0999 V2000
    3.2796    1.3007   -1.4211 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8494    0.8679   -0.0825 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.2718   -0.3834   -0.0145 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2222   -1.4139   -0.0437 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5618   -1.1146   -0.0892 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8096   -2.7287   -0.0219 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4884   -3.0315    0.0286 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5099   -2.0136    0.0660 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9547   -0.6904    0.0496 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0730    0.3374    0.1560 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3208    1.6791    0.3140 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6836    2.5922    0.5410 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0345    2.2217    0.6175 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3728    0.9272    0.4656 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3754   -0.0393    0.2311 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8685   -1.4189    0.1064 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8921   -2.4530    0.0867 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9331   -1.4989   -0.8955 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9359   -0.4967   -0.7050 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7408    0.3896    0.4985 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1369    3.8618    0.6701 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2494    3.6300    0.9658 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4826    2.3941    0.3221 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.1182    1.9848   -1.2337 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6729    0.4157   -1.9513 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5057    1.7894   -1.9829 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.8880   -0.1788   -0.0754 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5174   -3.5528   -0.0436 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1167   -4.0409    0.0429 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7758    2.9713    0.7949 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4940   -1.5533    1.0845 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0472   -3.1819   -0.8146 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0365   -3.1277    1.0030 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3013   -2.4639   -0.9443 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9134   -1.0372   -0.5324 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0006    0.0937   -1.6495 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4787    1.2175    0.4328 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9225   -0.1671    1.4139 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8540    4.4437    0.5599 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3435    3.4687    2.0497 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
  4  6  1  0
  6  7  2  0
  7  8  1  0
  8  9  2  0
  9 10  1  0
 10 11  2  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
 16 18  1  0
 18 19  1  0
 19 20  1  0
 12 21  1  0
 21 22  1  0
 22 23  1  0
  9  3  1  0
 15 10  1  0
 17  8  1  0
 23 11  1  0
 20 14  1  0
  1 24  1  0
  1 25  1  0
  1 26  1  0
  5 27  1  0
  6 28  1  0
  7 29  1  0
 13 30  1  0
 16 31  1  0
 17 32  1  0
 17 33  1  0
 18 34  1  0
 19 35  1  0
 19 36  1  0
 20 37  1  0
 20 38  1  0
 22 39  1  0
 22 40  1  0
M  END

View in JSmol View Stereo Labels

Synonyms

Value	Source
(+)-Nandigerine	HMDB
Hernangerine	HMDB
Nandigerine	HMDB

Chemical Formula

C₁₈H₁₇NO₄

Average Molecular Weight

311.3319

Monoisotopic Molecular Weight

311.115758037

IUPAC Name

18-methoxy-3,5-dioxa-11-azapentacyclo[10.7.1.0²,⁶.0⁸,²⁰.0¹⁴,¹⁹]icosa-1(20),2(6),7,14(19),15,17-hexaen-17-ol

Traditional Name

18-methoxy-3,5-dioxa-11-azapentacyclo[10.7.1.0²,⁶.0⁸,²⁰.0¹⁴,¹⁹]icosa-1(20),2(6),7,14(19),15,17-hexaen-17-ol

CAS Registry Number

31520-97-5

SMILES

COC1=C(O)C=CC2=C1C1=C3C(C2)NCCC3=CC2=C1OCO2

InChI Identifier

InChI=1S/C18H17NO4/c1-21-17-12(20)3-2-9-6-11-14-10(4-5-19-11)7-13-18(23-8-22-13)16(14)15(9)17/h2-3,7,11,19-20H,4-6,8H2,1H3

InChI Key

CFUKKPQRQGCLAT-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as aporphines. These are quinoline alkaloids containing the dibenzo[de,g]quinoline ring system or a dehydrogenated derivative thereof.

Kingdom

Organic compounds

Super Class

Alkaloids and derivatives

Class

Aporphines

Sub Class

Not Available

Direct Parent

Aporphines

Alternative Parents

Substituents

Aporphine
Benzoquinoline
Phenanthrene
2-naphthol
Naphthalene
Tetrahydroisoquinoline
Quinoline
Benzodioxole
Anisole
1-hydroxy-2-unsubstituted benzenoid
Aralkylamine
Alkyl aryl ether
Benzenoid
Organoheterocyclic compound
Azacycle
Ether
Secondary aliphatic amine
Acetal
Oxacycle
Secondary amine
Organopnictogen compound
Organooxygen compound
Organonitrogen compound
Organic nitrogen compound
Hydrocarbon derivative
Amine
Organic oxygen compound
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

Not Available

Ontology

Physiological effect

Not Available

Disposition

Biological location

Cellular substructure

Extracellular (HMDB: HMDB0033362)
Cytoplasm (HMDB: HMDB0033362)

Route of exposure

Enteral

Ingestion (HMDB: HMDB0033362)

Source

Exogenous

Food

Food (HMDB: HMDB0033362)

Tea

Herb and spice

Herb

Sweet bay (FooDB: FOOD00097)

Herbs and Spices (FooDB: FOOD00866)

Endogenous

Plant

Plant (HMDB: HMDB0033362)

Not Available

Nutrient (HMDB: HMDB0033362)

Physical Properties

State

Solid

Experimental Molecular Properties

Property	Value	Reference
Melting Point	176 - 177 °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	0.18 g/L	ALOGPS
logP	1.49	ALOGPS
logP	2.09	ChemAxon
logS	-3.2	ALOGPS
pKa (Strongest Acidic)	10.17	ChemAxon
pKa (Strongest Basic)	9.36	ChemAxon
Physiological Charge	1	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	59.95 Å²	ChemAxon
Rotatable Bond Count	1	ChemAxon
Refractivity	84.94 m³·mol⁻¹	ChemAxon
Polarizability	32.58 Å³	ChemAxon
Number of Rings	5	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]+	172.651	31661259
DarkChem	[M-H]-	170.733	31661259
DeepCCS	[M+H]+	176.65	30932474
DeepCCS	[M-H]-	174.292	30932474
DeepCCS	[M-2H]-	207.179	30932474
DeepCCS	[M+Na]+	182.743	30932474
AllCCS	[M+H]+	172.7	32859911
AllCCS	[M+H-H2O]+	169.3	32859911
AllCCS	[M+NH4]+	175.8	32859911
AllCCS	[M+Na]+	176.8	32859911
AllCCS	[M-H]-	178.9	32859911
AllCCS	[M+Na-2H]-	178.0	32859911
AllCCS	[M+HCOO]-	177.3	32859911

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
(S)-Nandigerine	COC1=C(O)C=CC2=C1C1=C3C(C2)NCCC3=CC2=C1OCO2	4180.8	Standard polar	33892256
(S)-Nandigerine	COC1=C(O)C=CC2=C1C1=C3C(C2)NCCC3=CC2=C1OCO2	2682.4	Standard non polar	33892256
(S)-Nandigerine	COC1=C(O)C=CC2=C1C1=C3C(C2)NCCC3=CC2=C1OCO2	3032.4	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
(S)-Nandigerine,1TMS,isomer #1	COC1=C(O[Si](C)(C)C)C=CC2=C1C1=C3OCOC3=CC3=C1C(C2)NCC3	2897.4	Semi standard non polar	33892256
(S)-Nandigerine,1TMS,isomer #2	COC1=C(O)C=CC2=C1C1=C3OCOC3=CC3=C1C(C2)N([Si](C)(C)C)CC3	2839.9	Semi standard non polar	33892256
(S)-Nandigerine,2TMS,isomer #1	COC1=C(O[Si](C)(C)C)C=CC2=C1C1=C3OCOC3=CC3=C1C(C2)N([Si](C)(C)C)CC3	2832.5	Semi standard non polar	33892256
(S)-Nandigerine,2TMS,isomer #1	COC1=C(O[Si](C)(C)C)C=CC2=C1C1=C3OCOC3=CC3=C1C(C2)N([Si](C)(C)C)CC3	2939.5	Standard non polar	33892256
(S)-Nandigerine,1TBDMS,isomer #1	COC1=C(O[Si](C)(C)C(C)(C)C)C=CC2=C1C1=C3OCOC3=CC3=C1C(C2)NCC3	3140.7	Semi standard non polar	33892256
(S)-Nandigerine,1TBDMS,isomer #2	COC1=C(O)C=CC2=C1C1=C3OCOC3=CC3=C1C(C2)N([Si](C)(C)C(C)(C)C)CC3	3063.8	Semi standard non polar	33892256
(S)-Nandigerine,2TBDMS,isomer #1	COC1=C(O[Si](C)(C)C(C)(C)C)C=CC2=C1C1=C3OCOC3=CC3=C1C(C2)N([Si](C)(C)C(C)(C)C)CC3	3255.9	Semi standard non polar	33892256
(S)-Nandigerine,2TBDMS,isomer #1	COC1=C(O[Si](C)(C)C(C)(C)C)C=CC2=C1C1=C3OCOC3=CC3=C1C(C2)N([Si](C)(C)C(C)(C)C)CC3	3403.7	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)-Nandigerine GC-MS (Non-derivatized) - 70eV, Positive	splash10-001j-0090000000-c316f8069ff05049c88e	2017-09-01	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - (S)-Nandigerine GC-MS (1 TMS) - 70eV, Positive	splash10-01b9-1039000000-3216986572277372a53a	2017-10-06	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - (S)-Nandigerine 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)-Nandigerine 10V, Positive-QTOF	splash10-03di-0129000000-3d9dcb65008d6666ac64	2016-08-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (S)-Nandigerine 20V, Positive-QTOF	splash10-03di-0196000000-79157dbb750c28dc1521	2016-08-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (S)-Nandigerine 40V, Positive-QTOF	splash10-0084-0980000000-20dc1359b1775cc0aa99	2016-08-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (S)-Nandigerine 10V, Negative-QTOF	splash10-03di-0019000000-c37b1f338cdbb6ccf785	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (S)-Nandigerine 20V, Negative-QTOF	splash10-03di-0069000000-f5ddb8357bd02461a43a	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (S)-Nandigerine 40V, Negative-QTOF	splash10-01p6-1190000000-086cf3907f446923abdb	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (S)-Nandigerine 10V, Positive-QTOF	splash10-03di-0009000000-4631b5d1b4d93faf70b7	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (S)-Nandigerine 20V, Positive-QTOF	splash10-03di-0009000000-7f26a29f7533604f9414	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (S)-Nandigerine 40V, Positive-QTOF	splash10-02au-0191000000-154a5edb70a5ddafd123	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (S)-Nandigerine 10V, Negative-QTOF	splash10-03di-0009000000-43e89ef889a2eb4f124e	2021-09-25	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (S)-Nandigerine 20V, Negative-QTOF	splash10-03dl-0098000000-895556af222b2f0b68ee	2021-09-25	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (S)-Nandigerine 40V, Negative-QTOF	splash10-01pc-0090000000-c7d6452be1f2e4b9f599	2021-09-25	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

FDB011390

KNApSAcK ID

C00027566

Chemspider ID

374109

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

422682

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)-Nandigerine (HMDB0033362)

MOL for HMDB0033362 ((S)-Nandigerine)

3D MOL for HMDB0033362 ((S)-Nandigerine)

3D SDF for HMDB0033362 ((S)-Nandigerine)

3D-SDF for HMDB0033362 ((S)-Nandigerine)

PDB for HMDB0033362 ((S)-Nandigerine)

3D PDB for HMDB0033362 ((S)-Nandigerine)

SMILES for HMDB0033362 ((S)-Nandigerine)

INCHI for HMDB0033362 ((S)-Nandigerine)

Structure for HMDB0033362 ((S)-Nandigerine)

3D Structure for HMDB0033362 ((S)-Nandigerine)

Predicted Collision Cross Sections

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra