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Showing metabocard for Cnicin (HMDB0341297)

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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2022-09-09 20:15:08 UTC
Update Date2022-09-22 18:34:46 UTC
HMDB IDHMDB0341297
Secondary Accession NumbersNone
Metabolite Identification
Common NameCnicin
Description(+)-Cnicin belongs to the class of organic compounds known as germacranolides and derivatives. These are sesquiterpene lactones with a structure based on the germacranolide skeleton, characterized by a gamma lactone fused to a 1,7-dimethylcyclodec-1-ene moiety. Based on a literature review a significant number of articles have been published on (+)-Cnicin.
Structure
Thumb
MOLSDFPDBSMILESInChI

MOL for HMDB0341297 (Cnicin)


  Mrv1652309092222532D          

 33 34  0  0  1  0            999 V2000
   -1.4289    2.4750    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434    2.0625    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
   -2.9639    1.3237    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
   -1.4289    0.0000    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.4289   -0.8250    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0000    0.8250    0.0000 O   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
    1.4289    0.0000    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.7145    0.4125    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.8250    0.0000 O   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
    2.8579    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434   -0.4125    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.1434    0.4125    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3149   -1.2195    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7629   -1.8326    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1354   -1.3057    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5479   -2.0202    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4710   -0.5520    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8579   -0.0000    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.6116    0.3356    0.0000 H   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
   -3.6826    0.8034    0.0000 H   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
   -4.2868    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0013    1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5724    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8579    2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  2  0  0  0  0
  3  4  1  0  0  0  0
  3  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  1  0  0  0
  6  8  1  6  0  0  0
  8  9  1  0  0  0  0
  9 10  2  0  0  0  0
  9 11  1  0  0  0  0
 11 12  2  0  0  0  0
 11 13  1  0  0  0  0
 13 14  1  6  0  0  0
 13 15  1  1  0  0  0
 13 16  1  0  0  0  0
 16 17  1  0  0  0  0
  6 18  1  0  0  0  0
 18 19  1  6  0  0  0
 18 20  1  0  0  0  0
 20 21  2  0  0  0  0
 20 22  1  0  0  0  0
 22 23  2  0  0  0  0
 22 24  1  0  0  0  0
 24 25  1  0  0  0  0
 18 25  1  0  0  0  0
 25 26  1  1  0  0  0
 25 27  1  0  0  0  0
 27 28  1  0  0  0  0
 27 29  2  0  0  0  0
 29 30  1  0  0  0  0
 30 31  1  0  0  0  0
 29 32  1  0  0  0  0
 32 33  1  0  0  0  0
  2 33  1  0  0  0  0
M  END
Download

3D MOL for HMDB0341297 (Cnicin)

Download
3D SDF for HMDB0341297 (Cnicin)

  Mrv1652309092222532D          

 33 34  0  0  1  0            999 V2000
   -1.4289    2.4750    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434    2.0625    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
   -2.9639    1.3237    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
   -1.4289    0.0000    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.4289   -0.8250    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0000    0.8250    0.0000 O   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
    1.4289    0.0000    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.7145    0.4125    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.8250    0.0000 O   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
    2.8579    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434   -0.4125    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.1434    0.4125    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3149   -1.2195    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7629   -1.8326    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1354   -1.3057    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5479   -2.0202    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4710   -0.5520    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8579   -0.0000    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.6116    0.3356    0.0000 H   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
   -3.6826    0.8034    0.0000 H   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
   -4.2868    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0013    1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5724    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8579    2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  2  0  0  0  0
  3  4  1  0  0  0  0
  3  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  1  0  0  0
  6  8  1  6  0  0  0
  8  9  1  0  0  0  0
  9 10  2  0  0  0  0
  9 11  1  0  0  0  0
 11 12  2  0  0  0  0
 11 13  1  0  0  0  0
 13 14  1  6  0  0  0
 13 15  1  1  0  0  0
 13 16  1  0  0  0  0
 16 17  1  0  0  0  0
  6 18  1  0  0  0  0
 18 19  1  6  0  0  0
 18 20  1  0  0  0  0
 20 21  2  0  0  0  0
 20 22  1  0  0  0  0
 22 23  2  0  0  0  0
 22 24  1  0  0  0  0
 24 25  1  0  0  0  0
 18 25  1  0  0  0  0
 25 26  1  1  0  0  0
 25 27  1  0  0  0  0
 27 28  1  0  0  0  0
 27 29  2  0  0  0  0
 29 30  1  0  0  0  0
 30 31  1  0  0  0  0
 29 32  1  0  0  0  0
 32 33  1  0  0  0  0
  2 33  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0341297

> <DATABASE_NAME>
hmdb

> <SMILES>
[H]\C1=C(C)/C[C@]([H])(OC(=O)C(=C)[C@@]([H])(O)CO)[C@@]2([H])C(=C)C(=O)O[C@]2([H])C([H])=C(CO)CC1

> <INCHI_IDENTIFIER>
InChI=1S/C20H26O7/c1-11-5-4-6-14(9-21)8-17-18(13(3)20(25)27-17)16(7-11)26-19(24)12(2)15(23)10-22/h5,8,15-18,21-23H,2-4,6-7,9-10H2,1H3/b11-5+,14-8+/t15-,16-,17+,18+/m0/s1

> <INCHI_KEY>
ZTDFZLVUIVPZDU-HOGDEQLHSA-N

> <FORMULA>
C20H26O7

> <MOLECULAR_WEIGHT>
378.421

> <EXACT_MASS>
378.167853177

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
53

> <JCHEM_AVERAGE_POLARIZABILITY>
38.303642138959745

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(3aR,4S,11aR)-10-(hydroxymethyl)-6-methyl-3-methylidene-2-oxo-2H,3H,3aH,4H,5H,8H,9H,11aH-cyclodeca[b]furan-4-yl (3R)-3,4-dihydroxy-2-methylidenebutanoate

> <JCHEM_LOGP>
1.1054298313333335

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
15.01379948012794

> <JCHEM_PKA_STRONGEST_ACIDIC>
13.52151690532435

> <JCHEM_PKA_STRONGEST_BASIC>
-2.734788470651095

> <JCHEM_POLAR_SURFACE_AREA>
113.29000000000002

> <JCHEM_REFRACTIVITY>
99.18529999999997

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
cnicin

> <JCHEM_VEBER_RULE>
0

$$$$

Download
3D-SDF for HMDB0341297 (Cnicin)
Download
PDB for HMDB0341297 (Cnicin)
HEADER    PROTEIN                                 09-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   09-SEP-22         0                                  
HETATM    1  H   UNK     0      -2.667   4.620   0.000  0.00  0.00           H+0
HETATM    2  C   UNK     0      -4.001   3.850   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -4.001   2.310   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -5.533   2.471   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -2.667   1.540   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -2.667   0.000   0.000  0.00  0.00           C+0
HETATM    7  H   UNK     0      -2.667  -1.540   0.000  0.00  0.00           H+0
HETATM    8  O   UNK     0      -1.334  -0.770   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0      -0.000   0.000   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0      -0.000   1.540   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       1.334  -2.310   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       2.667   0.000   0.000  0.00  0.00           C+0
HETATM   14  H   UNK     0       1.334   0.770   0.000  0.00  0.00           H+0
HETATM   15  O   UNK     0       2.667   1.540   0.000  0.00  0.00           O+0
HETATM   16  C   UNK     0       4.001  -0.770   0.000  0.00  0.00           C+0
HETATM   17  O   UNK     0       5.335   0.000   0.000  0.00  0.00           O+0
HETATM   18  C   UNK     0      -4.001  -0.770   0.000  0.00  0.00           C+0
HETATM   19  H   UNK     0      -4.001   0.770   0.000  0.00  0.00           H+0
HETATM   20  C   UNK     0      -4.321  -2.276   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      -3.291  -3.421   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      -5.853  -2.437   0.000  0.00  0.00           C+0
HETATM   23  O   UNK     0      -6.623  -3.771   0.000  0.00  0.00           O+0
HETATM   24  O   UNK     0      -6.479  -1.030   0.000  0.00  0.00           O+0
HETATM   25  C   UNK     0      -5.335  -0.000   0.000  0.00  0.00           C+0
HETATM   26  H   UNK     0      -6.742   0.626   0.000  0.00  0.00           H+0
HETATM   27  C   UNK     0      -5.335   1.540   0.000  0.00  0.00           C+0
HETATM   28  H   UNK     0      -6.874   1.500   0.000  0.00  0.00           H+0
HETATM   29  C   UNK     0      -6.668   2.310   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0      -8.002   1.540   0.000  0.00  0.00           C+0
HETATM   31  O   UNK     0      -9.336   2.310   0.000  0.00  0.00           O+0
HETATM   32  C   UNK     0      -6.668   3.850   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0      -5.335   4.620   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3   33                                                  
CONECT    3    2    4    5                                                  
CONECT    4    3                                                            
CONECT    5    3    6                                                       
CONECT    6    5    7    8   18                                             
CONECT    7    6                                                            
CONECT    8    6    9                                                       
CONECT    9    8   10   11                                                  
CONECT   10    9                                                            
CONECT   11    9   12   13                                                  
CONECT   12   11                                                            
CONECT   13   11   14   15   16                                             
CONECT   14   13                                                            
CONECT   15   13                                                            
CONECT   16   13   17                                                       
CONECT   17   16                                                            
CONECT   18    6   19   20   25                                             
CONECT   19   18                                                            
CONECT   20   18   21   22                                                  
CONECT   21   20                                                            
CONECT   22   20   23   24                                                  
CONECT   23   22                                                            
CONECT   24   22   25                                                       
CONECT   25   24   18   26   27                                             
CONECT   26   25                                                            
CONECT   27   25   28   29                                                  
CONECT   28   27                                                            
CONECT   29   27   30   32                                                  
CONECT   30   29   31                                                       
CONECT   31   30                                                            
CONECT   32   29   33                                                       
CONECT   33   32    2                                                       
MASTER        0    0    0    0    0    0    0    0   33    0   68    0
END

Download
3D PDB for HMDB0341297 (Cnicin)
Download
SMILES for HMDB0341297 (Cnicin)
[H]\C1=C(C)/C[C@]([H])(OC(=O)C(=C)[C@@]([H])(O)CO)[C@@]2([H])C(=C)C(=O)O[C@]2([H])C([H])=C(CO)CC1
Download
INCHI for HMDB0341297 (Cnicin)
InChI=1S/C20H26O7/c1-11-5-4-6-14(9-21)8-17-18(13(3)20(25)27-17)16(7-11)26-19(24)12(2)15(23)10-22/h5,8,15-18,21-23H,2-4,6-7,9-10H2,1H3/b11-5+,14-8+/t15-,16-,17+,18+/m0/s1
Download
View in JSmolView Stereo Labels
SynonymsNot Available
Chemical FormulaC20H26O7
Average Molecular Weight378.421
Monoisotopic Molecular Weight378.167853177
IUPAC Name(3aR,4S,11aR)-10-(hydroxymethyl)-6-methyl-3-methylidene-2-oxo-2H,3H,3aH,4H,5H,8H,9H,11aH-cyclodeca[b]furan-4-yl (3R)-3,4-dihydroxy-2-methylidenebutanoate
Traditional Namecnicin
CAS Registry NumberNot Available
SMILES
[H]\C1=C(C)/C[C@]([H])(OC(=O)C(=C)[C@@]([H])(O)CO)[C@@]2([H])C(=C)C(=O)O[C@]2([H])C([H])=C(CO)CC1
InChI Identifier
InChI=1S/C20H26O7/c1-11-5-4-6-14(9-21)8-17-18(13(3)20(25)27-17)16(7-11)26-19(24)12(2)15(23)10-22/h5,8,15-18,21-23H,2-4,6-7,9-10H2,1H3/b11-5+,14-8+/t15-,16-,17+,18+/m0/s1
InChI KeyZTDFZLVUIVPZDU-HOGDEQLHSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as germacranolides and derivatives. These are sesquiterpene lactones with a structure based on the germacranolide skeleton, characterized by a gamma lactone fused to a 1,7-dimethylcyclodec-1-ene moiety.
KingdomOrganic compounds  
Super ClassLipids and lipid-like molecules  
ClassPrenol lipids  
Sub ClassTerpene lactones  
Direct ParentGermacranolides and derivatives  
Alternative Parents
Substituents
  • Germacranolide
    • 

  • Germacrane sesquiterpenoid
    • 

  • Sesquiterpenoid
    • 

  • Beta-hydroxy acid
    • 

  • Fatty acid ester
    • 

  • Dicarboxylic acid or derivatives
    • 

  • Gamma butyrolactone
    • 

  • Fatty acyl
    • 

  • Hydroxy acid
    • 

  • Alpha,beta-unsaturated carboxylic ester
    • 

  • Enoate ester
    • 

  • Tetrahydrofuran
    • 

  • Lactone
    • 

  • Carboxylic acid ester
    • 

  • Secondary alcohol
    • 

  • Organoheterocyclic compound
    • 

  • Oxacycle
    • 

  • Carboxylic acid derivative
    • 

  • Organooxygen compound
    • 

  • Alcohol
    • 

  • Hydrocarbon derivative
    • 

  • Organic oxide
    • 

  • Carbonyl group
    • 

  • Primary alcohol
    • 

  • Organic oxygen compound
    • 

  • Aliphatic heteropolycyclic compound
Molecular FrameworkAliphatic heteropolycyclic compounds
External DescriptorsNot Available
Ontology
Not AvailableNot Available
Physical Properties
StateNot Available
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
logP1.11ChemAxon
pKa (Strongest Acidic)13.52ChemAxon
pKa (Strongest Basic)-2.7ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count5ChemAxon
Hydrogen Donor Count3ChemAxon
Polar Surface Area113.29 ŲChemAxon
Rotatable Bond Count6ChemAxon
Refractivity99.19 m³·mol⁻¹ChemAxon
Polarizability38.3 ųChemAxon
Number of Rings2ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties
Predicted Kovats Retention Indices
Not Available
Spectra
Biological Properties
Cellular LocationsNot Available
Biospecimen Locations
  • Blood
    • 

  • Urine
Tissue LocationsNot Available
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodExpected but not QuantifiedNot QuantifiedNot SpecifiedNot SpecifiedCancer patients undergoing total body irradiation  details
UrineDetected but not QuantifiedNot QuantifiedNot SpecifiedNot SpecifiedCancer patients undergoing total body irradiation  details
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDNot Available
KNApSAcK IDNot Available
Chemspider IDNot Available
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound98300196  
PDB IDNot Available
ChEBI IDNot Available
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General References
  1. Simon-Manso Y, Marupaka R, Yan X, Liang Y, Telu KH, Mirokhin Y, Stein SE: Mass Spectrometry Fingerprints of Small-Molecule Metabolites in Biofluids: Building a Spectral Library of Recurrent Spectra for Urine Analysis. Anal Chem. 2019 Sep 17;91(18):12021-12029. doi: 10.1021/acs.analchem.9b02977. Epub 2019 Aug 30. [PubMed:31424920  ]