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Record Information

Version

5.0

Status

Expected but not Quantified

Creation Date

2012-09-12 02:42:24 UTC

Update Date

2022-03-07 02:56:52 UTC

HMDB ID

HMDB0041061

Secondary Accession Numbers

HMDB41061

Metabolite Identification

Common Name

Nigellidine

Description

Nigellidine belongs to the class of organic compounds known as pyridazinoindazoles. Pyridazinoindazoles are compounds containing a pyridazinoindazole moiety, which consists of a pyridazine ring fused to an indazole. Nigellidine is an extremely weak basic (essentially neutral) compound (based on its pKa). Outside of the human body, nigellidine has been detected, but not quantified in, herbs and spices. This could make nigellidine a potential biomarker for the consumption of these foods.

Structure

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

HMDB0041061
     RDKit          3D
Nigellidine
 40 43  0  0  0  0  0  0  0  0999 V2000
   -4.1262    3.2746   -0.6380 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8621    2.5364   -0.4235 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6608    3.2095   -0.4551 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4823    2.4826   -0.2491 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6975    3.2014   -0.2786 O   0  0  0  0  0  1  0  0  0  0  0  0
   -0.4725    1.1228   -0.0188 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4928    0.1733    0.2354 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9352    0.3094    0.1524 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7420   -0.4516    1.0018 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1111   -0.4304    0.8645 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7612    0.3137   -0.0815 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.1509    0.3266   -0.2086 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.9782    1.0690   -0.9260 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5799    1.0569   -0.8001 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1312   -1.0282    0.4205 N   0  0  0  0  0  4  0  0  0  0  0  0
   -1.4187   -0.7927    0.2760 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6954    0.4876    0.0074 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8966    1.1767   -0.1930 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3773   -1.8998    0.4090 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7951   -3.0214   -0.4389 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5237   -3.4465    0.1964 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3739   -2.3632    0.6957 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4634    3.2301   -1.7015 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9819    4.3437   -0.4029 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9580    2.9019   -0.0082 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6554    4.2639   -0.6348 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2650   -1.0423    1.7955 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.7046   -1.0359    1.5426 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.7401   -0.2196    0.4002 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.4714    1.6636   -1.6789 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0429    1.6284   -1.5313 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8347    0.6259   -0.1630 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3584   -2.2088    1.4629 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3755   -1.6423    0.0628 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6345   -2.6646   -1.4774 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5155   -3.8609   -0.3996 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0742   -4.0922   -0.5112 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8044   -4.1769    1.0134 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3757   -2.4600    0.2107 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5269   -2.5607    1.7793 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  0
  3  4  1  0
  4  5  1  0
  4  6  2  0
  6  7  1  0
  7  8  1  0
  8  9  2  0
  9 10  1  0
 10 11  2  0
 11 12  1  0
 11 13  1  0
 13 14  2  0
  7 15  2  0
 15 16  1  0
 16 17  1  0
 17 18  2  0
 16 19  1  0
 19 20  1  0
 20 21  1  0
 21 22  1  0
 18  2  1  0
 17  6  1  0
 14  8  1  0
 22 15  1  0
  1 23  1  0
  1 24  1  0
  1 25  1  0
  3 26  1  0
  9 27  1  0
 10 28  1  0
 12 29  1  0
 13 30  1  0
 14 31  1  0
 18 32  1  0
 19 33  1  0
 19 34  1  0
 20 35  1  0
 20 36  1  0
 21 37  1  0
 21 38  1  0
 22 39  1  0
 22 40  1  0
M  CHG  2   5  -1  15   1
M  END


  Mrv0541 02241215062D          

 22 25  0  0  0  0            999 V2000
    2.1704    1.3992    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9190    2.1860    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1128    2.3620    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5593    1.7515    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.8107    0.9647    0.0000 N   0  3  0  0  0  0  0  0  0  0  0  0
    1.6152    0.7896    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2657    1.7553    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5229    0.9721    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1399    0.4859    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8145    2.3691    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6195    2.2014    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8761    1.4214    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3277    0.8090    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1348   -0.3395    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5856   -0.7446    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5947   -1.5713    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1176   -1.9912    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8372   -1.5834    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8444   -0.7559    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1099   -2.8174    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5874    0.0250    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
   -2.1704    2.8174    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  6  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
  4  7  1  0  0  0  0
  5  6  1  0  0  0  0
  5  9  2  0  0  0  0
  7  8  2  0  0  0  0
  7 10  1  0  0  0  0
  8  9  1  0  0  0  0
  8 13  1  0  0  0  0
  9 14  1  0  0  0  0
 10 11  2  0  0  0  0
 11 12  1  0  0  0  0
 11 22  1  0  0  0  0
 12 13  2  0  0  0  0
 13 21  1  0  0  0  0
 14 15  1  0  0  0  0
 14 19  2  0  0  0  0
 15 16  2  0  0  0  0
 16 17  1  0  0  0  0
 17 18  2  0  0  0  0
 17 20  1  0  0  0  0
 18 19  1  0  0  0  0
M  CHG  2   5   1  21  -1
M  END
> <DATABASE_ID>
HMDB0041061

> <DATABASE_NAME>
hmdb

> <SMILES>
CC1=CC2=C(C(C3=CC=C(O)C=C3)=[N+]3CCCCN23)C([O-])=C1

> <INCHI_IDENTIFIER>
InChI=1S/C18H18N2O2/c1-12-10-15-17(16(22)11-12)18(13-4-6-14(21)7-5-13)20-9-3-2-8-19(15)20/h4-7,10-11H,2-3,8-9H2,1H3,(H,21,22)

> <INCHI_KEY>
BYNDPWUDABJNCH-UHFFFAOYSA-N

> <FORMULA>
C18H18N2O2

> <MOLECULAR_WEIGHT>
294.3477

> <EXACT_MASS>
294.13682783

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_AVERAGE_POLARIZABILITY>
32.946763094083366

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
11-(4-hydroxyphenyl)-3-methyl-6H,7H,8H,9H-10λ⁵-pyridazino[1,2-a]indazol-10-ylium-1-olate

> <ALOGPS_LOGP>
0.48

> <JCHEM_LOGP>
0.12612580852825434

> <ALOGPS_LOGS>
-4.77

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
9.101753248457753

> <JCHEM_PKA_STRONGEST_ACIDIC>
5.719995810297655

> <JCHEM_PKA_STRONGEST_BASIC>
-5.537146541106499

> <JCHEM_POLAR_SURFACE_AREA>
52.099999999999994

> <JCHEM_REFRACTIVITY>
118.9371

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
5.84e-03 g/l

> <JCHEM_TRADITIONAL_IUPAC>
11-(4-hydroxyphenyl)-3-methyl-6H,7H,8H,9H-10λ⁵-pyridazino[1,2-a]indazol-10-ylium-1-olate

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0041061
     RDKit          3D
Nigellidine
 40 43  0  0  0  0  0  0  0  0999 V2000
   -4.1262    3.2746   -0.6380 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8621    2.5364   -0.4235 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6608    3.2095   -0.4551 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4823    2.4826   -0.2491 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6975    3.2014   -0.2786 O   0  0  0  0  0  1  0  0  0  0  0  0
   -0.4725    1.1228   -0.0188 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4928    0.1733    0.2354 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9352    0.3094    0.1524 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7420   -0.4516    1.0018 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1111   -0.4304    0.8645 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7612    0.3137   -0.0815 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.1509    0.3266   -0.2086 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.9782    1.0690   -0.9260 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5799    1.0569   -0.8001 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1312   -1.0282    0.4205 N   0  0  0  0  0  4  0  0  0  0  0  0
   -1.4187   -0.7927    0.2760 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6954    0.4876    0.0074 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8966    1.1767   -0.1930 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3773   -1.8998    0.4090 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7951   -3.0214   -0.4389 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5237   -3.4465    0.1964 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3739   -2.3632    0.6957 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4634    3.2301   -1.7015 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9819    4.3437   -0.4029 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9580    2.9019   -0.0082 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6554    4.2639   -0.6348 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2650   -1.0423    1.7955 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.7046   -1.0359    1.5426 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.7401   -0.2196    0.4002 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.4714    1.6636   -1.6789 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0429    1.6284   -1.5313 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8347    0.6259   -0.1630 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3584   -2.2088    1.4629 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3755   -1.6423    0.0628 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6345   -2.6646   -1.4774 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5155   -3.8609   -0.3996 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0742   -4.0922   -0.5112 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8044   -4.1769    1.0134 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3757   -2.4600    0.2107 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5269   -2.5607    1.7793 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  0
  3  4  1  0
  4  5  1  0
  4  6  2  0
  6  7  1  0
  7  8  1  0
  8  9  2  0
  9 10  1  0
 10 11  2  0
 11 12  1  0
 11 13  1  0
 13 14  2  0
  7 15  2  0
 15 16  1  0
 16 17  1  0
 17 18  2  0
 16 19  1  0
 19 20  1  0
 20 21  1  0
 21 22  1  0
 18  2  1  0
 17  6  1  0
 14  8  1  0
 22 15  1  0
  1 23  1  0
  1 24  1  0
  1 25  1  0
  3 26  1  0
  9 27  1  0
 10 28  1  0
 12 29  1  0
 13 30  1  0
 14 31  1  0
 18 32  1  0
 19 33  1  0
 19 34  1  0
 20 35  1  0
 20 36  1  0
 21 37  1  0
 21 38  1  0
 22 39  1  0
 22 40  1  0
M  CHG  2   5  -1  15   1
M  END

HEADER    PROTEIN                                 24-FEB-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-FEB-12         0                                  
HETATM    1  C   UNK     0       4.051   2.612   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       3.582   4.081   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       2.077   4.409   0.000  0.00  0.00           C+0
HETATM    4  N   UNK     0       1.044   3.269   0.000  0.00  0.00           N+0
HETATM    5  N   UNK     0       1.513   1.801   0.000  0.00  0.00           N+1
HETATM    6  C   UNK     0       3.015   1.474   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -0.496   3.277   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -0.976   1.815   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       0.261   0.907   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -1.520   4.422   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      -3.023   4.109   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      -3.502   2.653   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      -2.478   1.510   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       0.252  -0.634   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      -1.093  -1.390   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      -1.110  -2.933   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       0.220  -3.717   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       1.563  -2.956   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       1.576  -1.411   0.000  0.00  0.00           C+0
HETATM   20  O   UNK     0       0.205  -5.259   0.000  0.00  0.00           O+0
HETATM   21  O   UNK     0      -2.963   0.047   0.000  0.00  0.00           O-1
HETATM   22  C   UNK     0      -4.051   5.259   0.000  0.00  0.00           C+0
CONECT    1    2    6                                                       
CONECT    2    1    3                                                       
CONECT    3    2    4                                                       
CONECT    4    3    5    7                                                  
CONECT    5    4    6    9                                                  
CONECT    6    1    5                                                       
CONECT    7    4    8   10                                                  
CONECT    8    7    9   13                                                  
CONECT    9    5    8   14                                                  
CONECT   10    7   11                                                       
CONECT   11   10   12   22                                                  
CONECT   12   11   13                                                       
CONECT   13    8   12   21                                                  
CONECT   14    9   15   19                                                  
CONECT   15   14   16                                                       
CONECT   16   15   17                                                       
CONECT   17   16   18   20                                                  
CONECT   18   17   19                                                       
CONECT   19   14   18                                                       
CONECT   20   17                                                            
CONECT   21   13                                                            
CONECT   22   11                                                            
MASTER        0    0    0    0    0    0    0    0   22    0   50    0
END

COMPND    HMDB0041061
HETATM    1  C1  UNL     1      -4.126   3.275  -0.638  1.00  0.00           C  
HETATM    2  C2  UNL     1      -2.862   2.536  -0.423  1.00  0.00           C  
HETATM    3  C3  UNL     1      -1.661   3.210  -0.455  1.00  0.00           C  
HETATM    4  C4  UNL     1      -0.482   2.483  -0.249  1.00  0.00           C  
HETATM    5  O1  UNL     1       0.698   3.201  -0.279  1.00  0.00           O1-
HETATM    6  C5  UNL     1      -0.473   1.123  -0.019  1.00  0.00           C  
HETATM    7  C6  UNL     1       0.493   0.173   0.235  1.00  0.00           C  
HETATM    8  C7  UNL     1       1.935   0.309   0.152  1.00  0.00           C  
HETATM    9  C8  UNL     1       2.742  -0.452   1.002  1.00  0.00           C  
HETATM   10  C9  UNL     1       4.111  -0.430   0.864  1.00  0.00           C  
HETATM   11  C10 UNL     1       4.761   0.314  -0.081  1.00  0.00           C  
HETATM   12  O2  UNL     1       6.151   0.327  -0.209  1.00  0.00           O  
HETATM   13  C11 UNL     1       3.978   1.069  -0.926  1.00  0.00           C  
HETATM   14  C12 UNL     1       2.580   1.057  -0.800  1.00  0.00           C  
HETATM   15  N1  UNL     1      -0.131  -1.028   0.421  1.00  0.00           N1+
HETATM   16  N2  UNL     1      -1.419  -0.793   0.276  1.00  0.00           N  
HETATM   17  C13 UNL     1      -1.695   0.488   0.007  1.00  0.00           C  
HETATM   18  C14 UNL     1      -2.897   1.177  -0.193  1.00  0.00           C  
HETATM   19  C15 UNL     1      -2.377  -1.900   0.409  1.00  0.00           C  
HETATM   20  C16 UNL     1      -1.795  -3.021  -0.439  1.00  0.00           C  
HETATM   21  C17 UNL     1      -0.524  -3.446   0.196  1.00  0.00           C  
HETATM   22  C18 UNL     1       0.374  -2.363   0.696  1.00  0.00           C  
HETATM   23  H1  UNL     1      -4.463   3.230  -1.702  1.00  0.00           H  
HETATM   24  H2  UNL     1      -3.982   4.344  -0.403  1.00  0.00           H  
HETATM   25  H3  UNL     1      -4.958   2.902  -0.008  1.00  0.00           H  
HETATM   26  H4  UNL     1      -1.655   4.264  -0.635  1.00  0.00           H  
HETATM   27  H5  UNL     1       2.265  -1.042   1.795  1.00  0.00           H  
HETATM   28  H6  UNL     1       4.705  -1.036   1.543  1.00  0.00           H  
HETATM   29  H7  UNL     1       6.740  -0.220   0.400  1.00  0.00           H  
HETATM   30  H8  UNL     1       4.471   1.664  -1.679  1.00  0.00           H  
HETATM   31  H9  UNL     1       2.043   1.628  -1.531  1.00  0.00           H  
HETATM   32  H10 UNL     1      -3.835   0.626  -0.163  1.00  0.00           H  
HETATM   33  H11 UNL     1      -2.358  -2.209   1.463  1.00  0.00           H  
HETATM   34  H12 UNL     1      -3.375  -1.642   0.063  1.00  0.00           H  
HETATM   35  H13 UNL     1      -1.634  -2.665  -1.477  1.00  0.00           H  
HETATM   36  H14 UNL     1      -2.515  -3.861  -0.400  1.00  0.00           H  
HETATM   37  H15 UNL     1       0.074  -4.092  -0.511  1.00  0.00           H  
HETATM   38  H16 UNL     1      -0.804  -4.177   1.013  1.00  0.00           H  
HETATM   39  H17 UNL     1       1.376  -2.460   0.211  1.00  0.00           H  
HETATM   40  H18 UNL     1       0.527  -2.561   1.779  1.00  0.00           H  
CONECT    1    2   23   24   25
CONECT    2    3    3   18
CONECT    3    4   26
CONECT    4    5    6    6
CONECT    6    7   17
CONECT    7    8   15   15
CONECT    8    9    9   14
CONECT    9   10   27
CONECT   10   11   11   28
CONECT   11   12   13
CONECT   12   29
CONECT   13   14   14   30
CONECT   14   31
CONECT   15   16   22
CONECT   16   17   19
CONECT   17   18   18
CONECT   18   32
CONECT   19   20   33   34
CONECT   20   21   35   36
CONECT   21   22   37   38
CONECT   22   39   40
END

HMDB0041061
     RDKit          3D
Nigellidine
 40 43  0  0  0  0  0  0  0  0999 V2000
   -4.1262    3.2746   -0.6380 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8621    2.5364   -0.4235 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6608    3.2095   -0.4551 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4823    2.4826   -0.2491 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6975    3.2014   -0.2786 O   0  0  0  0  0  1  0  0  0  0  0  0
   -0.4725    1.1228   -0.0188 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4928    0.1733    0.2354 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9352    0.3094    0.1524 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7420   -0.4516    1.0018 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1111   -0.4304    0.8645 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7612    0.3137   -0.0815 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.1509    0.3266   -0.2086 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.9782    1.0690   -0.9260 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5799    1.0569   -0.8001 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1312   -1.0282    0.4205 N   0  0  0  0  0  4  0  0  0  0  0  0
   -1.4187   -0.7927    0.2760 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6954    0.4876    0.0074 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8966    1.1767   -0.1930 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3773   -1.8998    0.4090 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7951   -3.0214   -0.4389 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5237   -3.4465    0.1964 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3739   -2.3632    0.6957 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4634    3.2301   -1.7015 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9819    4.3437   -0.4029 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9580    2.9019   -0.0082 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6554    4.2639   -0.6348 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2650   -1.0423    1.7955 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.7046   -1.0359    1.5426 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.7401   -0.2196    0.4002 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.4714    1.6636   -1.6789 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0429    1.6284   -1.5313 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8347    0.6259   -0.1630 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3584   -2.2088    1.4629 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3755   -1.6423    0.0628 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6345   -2.6646   -1.4774 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5155   -3.8609   -0.3996 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0742   -4.0922   -0.5112 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8044   -4.1769    1.0134 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3757   -2.4600    0.2107 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5269   -2.5607    1.7793 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  0
  3  4  1  0
  4  5  1  0
  4  6  2  0
  6  7  1  0
  7  8  1  0
  8  9  2  0
  9 10  1  0
 10 11  2  0
 11 12  1  0
 11 13  1  0
 13 14  2  0
  7 15  2  0
 15 16  1  0
 16 17  1  0
 17 18  2  0
 16 19  1  0
 19 20  1  0
 20 21  1  0
 21 22  1  0
 18  2  1  0
 17  6  1  0
 14  8  1  0
 22 15  1  0
  1 23  1  0
  1 24  1  0
  1 25  1  0
  3 26  1  0
  9 27  1  0
 10 28  1  0
 12 29  1  0
 13 30  1  0
 14 31  1  0
 18 32  1  0
 19 33  1  0
 19 34  1  0
 20 35  1  0
 20 36  1  0
 21 37  1  0
 21 38  1  0
 22 39  1  0
 22 40  1  0
M  CHG  2   5  -1  15   1
M  END

View in JSmol View Stereo Labels

Synonyms

Value	Source
6,7,8,9-Tetrahydro-1-hydroxy-11-(4-hydroxyphenyl)-3-methylpyridazino[1,2-a]indazol-5-ium inner salt, 9ci	HMDB

Chemical Formula

C₁₈H₁₈N₂O₂

Average Molecular Weight

294.3477

Monoisotopic Molecular Weight

294.13682783

IUPAC Name

11-(4-hydroxyphenyl)-3-methyl-6H,7H,8H,9H-10λ⁵-pyridazino[1,2-a]indazol-10-ylium-1-olate

Traditional Name

11-(4-hydroxyphenyl)-3-methyl-6H,7H,8H,9H-10λ⁵-pyridazino[1,2-a]indazol-10-ylium-1-olate

CAS Registry Number

120993-86-4

SMILES

CC1=CC2=C(C(C3=CC=C(O)C=C3)=[N+]3CCCCN23)C([O-])=C1

InChI Identifier

InChI=1S/C18H18N2O2/c1-12-10-15-17(16(22)11-12)18(13-4-6-14(21)7-5-13)20-9-3-2-8-19(15)20/h4-7,10-11H,2-3,8-9H2,1H3,(H,21,22)

InChI Key

BYNDPWUDABJNCH-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as pyridazinoindazoles. Pyridazinoindazoles are compounds containing a pyridazinoindazole moiety, which consists of a pyridazine ring fused to an indazole.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Benzopyrazoles

Sub Class

Indazoles

Direct Parent

Pyridazinoindazoles

Alternative Parents

Not Available

Substituents

Not Available

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

Not Available

Ontology

Physiological effect

Not Available

Disposition

Biological location

Cellular substructure

Extracellular (HMDB: HMDB0041061)
Cytoplasm (HMDB: HMDB0041061)

Route of exposure

Enteral

Ingestion (HMDB: HMDB0041061)

Source

Exogenous

Food

Food (HMDB: HMDB0041061)

Herb and spice

Herbs and Spices (FooDB: FOOD00866)

Endogenous

Plant

Plant (HMDB: HMDB0041061)

Not Available

Nutrient (HMDB: HMDB0041061)

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
Water Solubility	0.0058 g/L	ALOGPS
logP	0.48	ALOGPS
logP	0.13	ChemAxon
logS	-4.8	ALOGPS
pKa (Strongest Acidic)	5.72	ChemAxon
pKa (Strongest Basic)	-5.5	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	2	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	52.1 Å²	ChemAxon
Rotatable Bond Count	1	ChemAxon
Refractivity	118.94 m³·mol⁻¹	ChemAxon
Polarizability	32.95 Å³	ChemAxon
Number of Rings	4	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Predicted Chromatographic Properties

Predicted Collision Cross Sections

Predictor	Adduct Type	CCS Value (Å²)	Reference
DeepCCS	[M-2H]-	208.873	30932474
DeepCCS	[M+Na]+	184.101	30932474
AllCCS	[M+H]+	169.4	32859911
AllCCS	[M+H-H2O]+	165.9	32859911
AllCCS	[M+NH4]+	172.7	32859911
AllCCS	[M+Na]+	173.7	32859911
AllCCS	[M-H]-	176.8	32859911
AllCCS	[M+Na-2H]-	176.4	32859911
AllCCS	[M+HCOO]-	176.0	32859911

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
Nigellidine	CC1=CC2=C(C(C3=CC=C(O)C=C3)=[N+]3CCCCN23)C([O-])=C1	3793.2	Standard polar	33892256
Nigellidine	CC1=CC2=C(C(C3=CC=C(O)C=C3)=[N+]3CCCCN23)C([O-])=C1	2802.8	Standard non polar	33892256
Nigellidine	CC1=CC2=C(C(C3=CC=C(O)C=C3)=[N+]3CCCCN23)C([O-])=C1	3398.0	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
Nigellidine,1TMS,isomer #1	CC1=CC([O-])=C2C(C3=CC=C(O[Si](C)(C)C)C=C3)=[N+]3CCCCN3C2=C1	3018.9	Semi standard non polar	33892256
Nigellidine,1TBDMS,isomer #1	CC1=CC([O-])=C2C(C3=CC=C(O[Si](C)(C)C(C)(C)C)C=C3)=[N+]3CCCCN3C2=C1	3270.7	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 - Nigellidine GC-MS (Non-derivatized) - 70eV, Positive	splash10-092c-0190000000-e8c8f7f449e0bd68b06e	2017-09-01	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Nigellidine GC-MS (1 TMS) - 70eV, Positive	splash10-0gi0-3197000000-18d441b61280df2a4541	2017-10-06	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Nigellidine 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 - Nigellidine 10V, Positive-QTOF	splash10-0002-0090000000-802b1dc93b8407a6e39c	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Nigellidine 20V, Positive-QTOF	splash10-0002-0090000000-e89820ef6d7f8e715254	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Nigellidine 40V, Positive-QTOF	splash10-001i-1940000000-f0728845f6d71dfe336a	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Nigellidine 10V, Negative-QTOF	splash10-0006-0090000000-9e7159a937079a8591b1	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Nigellidine 20V, Negative-QTOF	splash10-0006-0090000000-960d23c08713f87a4e7a	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Nigellidine 40V, Negative-QTOF	splash10-000i-1090000000-29aede27d94026376ab9	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Nigellidine 10V, Negative-QTOF	splash10-0006-0090000000-0d9320ff24c77d3dc094	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Nigellidine 20V, Negative-QTOF	splash10-0006-0090000000-0d9320ff24c77d3dc094	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Nigellidine 40V, Negative-QTOF	splash10-0a6r-0490000000-03797346662478c55bfc	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Nigellidine 10V, Positive-QTOF	splash10-0002-0090000000-8151dfcb83bc7c9712c9	2021-09-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Nigellidine 20V, Positive-QTOF	splash10-0002-0090000000-8151dfcb83bc7c9712c9	2021-09-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Nigellidine 40V, Positive-QTOF	splash10-0bt9-5890000000-b53d888ab348b7fdf951	2021-09-24	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

FDB020935

KNApSAcK ID

C00028687

Chemspider ID

Not Available

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

Not Available

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 Nigellidine (HMDB0041061)

MOL for HMDB0041061 (Nigellidine)

3D MOL for HMDB0041061 (Nigellidine)

3D SDF for HMDB0041061 (Nigellidine)

3D-SDF for HMDB0041061 (Nigellidine)

PDB for HMDB0041061 (Nigellidine)

3D PDB for HMDB0041061 (Nigellidine)

SMILES for HMDB0041061 (Nigellidine)

INCHI for HMDB0041061 (Nigellidine)

Structure for HMDB0041061 (Nigellidine)

3D Structure for HMDB0041061 (Nigellidine)

Predicted Collision Cross Sections

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra