NP-MRD: Showing NP-Card for Methyl lucidenate F (NP0048508)

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Record Information

Version

2.0

Created at

2022-03-17 20:57:34 UTC

Updated at

2022-03-17 20:57:34 UTC

NP-MRD ID

NP0048508

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Methyl lucidenate F

Description

Dhurrin 6'-glucoside belongs to the class of organic compounds known as cyanogenic glycosides. These are glycosides in which the aglycone moiety contains a cyanide group. Dhurrin 6'-glucoside is an extremely weak basic (essentially neutral) compound (based on its pKa). Outside of the human body, Dhurrin 6'-glucoside has been detected, but not quantified in, cereals and cereal products. Methyl lucidenate F is found in Ganoderma lucidum (FR.)KARST. . This could make dhurrin 6'-glucoside a potential biomarker for the consumption of these foods.

Structure

MOL SDF PDB SMILES InChI


  Mrv0541 02241210292D          

 34 37  0  0  0  0            999 V2000
   -3.2494   -1.0048    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2494   -1.8312    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5345   -2.2445    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8208   -1.8312    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8208   -1.0048    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5345   -0.5929    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1060   -2.2445    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3925   -1.8312    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3925   -1.0048    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1060   -0.5929    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3196   -0.5929    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3196    0.2293    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3925    0.6398    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1060    0.2293    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1005   -0.8464    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5813   -0.1812    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1005    0.4813    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1005    1.3079    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3842    1.7210    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8167    1.7210    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5331    1.3079    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2494    1.7210    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9655    1.3079    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.2494    2.5476    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3567   -1.6314    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3196    1.0558    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3196   -1.4194    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8208    0.6398    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3196   -2.2445    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9476   -2.9607    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1213   -2.9607    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9655   -2.2445    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8208   -0.1812    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5331    2.9607    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
  2 32  2  0  0  0  0
  3  4  1  0  0  0  0
  3 30  1  0  0  0  0
  3 31  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 10  1  0  0  0  0
  5 33  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  8 29  2  0  0  0  0
  9 10  2  0  0  0  0
  9 11  1  0  0  0  0
 10 14  1  0  0  0  0
 11 12  1  0  0  0  0
 11 15  1  0  0  0  0
 11 27  1  0  0  0  0
 12 13  1  0  0  0  0
 12 17  1  0  0  0  0
 12 26  1  0  0  0  0
 13 14  1  0  0  0  0
 14 28  2  0  0  0  0
 15 16  1  0  0  0  0
 15 25  2  0  0  0  0
 16 17  1  0  0  0  0
 17 18  1  0  0  0  0
 18 19  1  0  0  0  0
 18 20  1  0  0  0  0
 20 21  1  0  0  0  0
 21 22  1  0  0  0  0
 22 23  2  0  0  0  0
 22 24  1  0  0  0  0
 24 34  1  0  0  0  0
M  END


  Mrv0541 02241210292D          

 34 37  0  0  0  0            999 V2000
   -3.2494   -1.0048    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2494   -1.8312    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5345   -2.2445    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8208   -1.8312    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8208   -1.0048    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5345   -0.5929    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1060   -2.2445    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3925   -1.8312    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3925   -1.0048    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1060   -0.5929    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3196   -0.5929    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3196    0.2293    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3925    0.6398    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1060    0.2293    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1005   -0.8464    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5813   -0.1812    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1005    0.4813    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1005    1.3079    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3842    1.7210    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8167    1.7210    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5331    1.3079    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2494    1.7210    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9655    1.3079    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.2494    2.5476    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3567   -1.6314    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3196    1.0558    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3196   -1.4194    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8208    0.6398    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3196   -2.2445    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9476   -2.9607    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1213   -2.9607    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9655   -2.2445    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8208   -0.1812    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5331    2.9607    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
  2 32  2  0  0  0  0
  3  4  1  0  0  0  0
  3 30  1  0  0  0  0
  3 31  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 10  1  0  0  0  0
  5 33  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  8 29  2  0  0  0  0
  9 10  2  0  0  0  0
  9 11  1  0  0  0  0
 10 14  1  0  0  0  0
 11 12  1  0  0  0  0
 11 15  1  0  0  0  0
 11 27  1  0  0  0  0
 12 13  1  0  0  0  0
 12 17  1  0  0  0  0
 12 26  1  0  0  0  0
 13 14  1  0  0  0  0
 14 28  2  0  0  0  0
 15 16  1  0  0  0  0
 15 25  2  0  0  0  0
 16 17  1  0  0  0  0
 17 18  1  0  0  0  0
 18 19  1  0  0  0  0
 18 20  1  0  0  0  0
 20 21  1  0  0  0  0
 21 22  1  0  0  0  0
 22 23  2  0  0  0  0
 22 24  1  0  0  0  0
 24 34  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0048508

> <DATABASE_NAME>
NP-MRD

> <SMILES>
COC(=O)CCC(C)C1CC(=O)C2(C)C3=C(C(=O)CC12C)C1(C)CCC(=O)C(C)(C)C1CC3=O

> <INCHI_IDENTIFIER>
InChI=1S/C28H38O6/c1-15(8-9-22(33)34-7)16-12-21(32)28(6)24-17(29)13-19-25(2,3)20(31)10-11-26(19,4)23(24)18(30)14-27(16,28)5/h15-16,19H,8-14H2,1-7H3

> <INCHI_KEY>
ZXYSCJISDAKHPX-UHFFFAOYSA-N

> <FORMULA>
C28H38O6

> <MOLECULAR_WEIGHT>
470.5977

> <EXACT_MASS>
470.266838948

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_AVERAGE_POLARIZABILITY>
51.50060754926325

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
methyl 4-{2,6,6,11,15-pentamethyl-5,9,12,17-tetraoxotetracyclo[8.7.0.0²,⁷.0¹¹,¹⁵]heptadec-1(10)-en-14-yl}pentanoate

> <ALOGPS_LOGP>
3.82

> <JCHEM_LOGP>
4.323425488666668

> <ALOGPS_LOGS>
-5.14

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
19.547233676234498

> <JCHEM_PKA_STRONGEST_ACIDIC>
18.91577657271087

> <JCHEM_PKA_STRONGEST_BASIC>
-6.75838544173817

> <JCHEM_POLAR_SURFACE_AREA>
94.58000000000001

> <JCHEM_REFRACTIVITY>
127.63589999999994

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
3.44e-03 g/l

> <JCHEM_TRADITIONAL_IUPAC>
methyl 4-{2,6,6,11,15-pentamethyl-5,9,12,17-tetraoxotetracyclo[8.7.0.0²,⁷.0¹¹,¹⁵]heptadec-1(10)-en-14-yl}pentanoate

> <JCHEM_VEBER_RULE>
0

$$$$

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      -6.065  -1.876   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -6.065  -3.418   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -4.731  -4.190   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -3.399  -3.418   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -3.399  -1.876   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -4.731  -1.107   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -2.065  -4.190   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -0.733  -3.418   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -0.733  -1.876   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -2.065  -1.107   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       0.597  -1.107   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       0.597   0.428   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      -0.733   1.194   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      -2.065   0.428   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       2.054  -1.580   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       2.952  -0.338   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       2.054   0.898   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       2.054   2.441   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       0.717   3.213   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       3.391   3.213   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       4.728   2.441   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       6.065   3.213   0.000  0.00  0.00           C+0
HETATM   23  O   UNK     0       7.402   2.441   0.000  0.00  0.00           O+0
HETATM   24  O   UNK     0       6.065   4.756   0.000  0.00  0.00           O+0
HETATM   25  O   UNK     0       2.533  -3.045   0.000  0.00  0.00           O+0
HETATM   26  C   UNK     0       0.597   1.971   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0       0.597  -2.650   0.000  0.00  0.00           C+0
HETATM   28  O   UNK     0      -3.399   1.194   0.000  0.00  0.00           O+0
HETATM   29  O   UNK     0       0.597  -4.190   0.000  0.00  0.00           O+0
HETATM   30  C   UNK     0      -5.502  -5.527   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0      -3.960  -5.527   0.000  0.00  0.00           C+0
HETATM   32  O   UNK     0      -7.402  -4.190   0.000  0.00  0.00           O+0
HETATM   33  C   UNK     0      -3.399  -0.338   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0       4.728   5.527   0.000  0.00  0.00           C+0
CONECT    1    2    6                                                       
CONECT    2    1    3   32                                                  
CONECT    3    2    4   30   31                                             
CONECT    4    3    5    7                                                  
CONECT    5    4    6   10   33                                             
CONECT    6    1    5                                                       
CONECT    7    4    8                                                       
CONECT    8    7    9   29                                                  
CONECT    9    8   10   11                                                  
CONECT   10    5    9   14                                                  
CONECT   11    9   12   15   27                                             
CONECT   12   11   13   17   26                                             
CONECT   13   12   14                                                       
CONECT   14   10   13   28                                                  
CONECT   15   11   16   25                                                  
CONECT   16   15   17                                                       
CONECT   17   12   16   18                                                  
CONECT   18   17   19   20                                                  
CONECT   19   18                                                            
CONECT   20   18   21                                                       
CONECT   21   20   22                                                       
CONECT   22   21   23   24                                                  
CONECT   23   22                                                            
CONECT   24   22   34                                                       
CONECT   25   15                                                            
CONECT   26   12                                                            
CONECT   27   11                                                            
CONECT   28   14                                                            
CONECT   29    8                                                            
CONECT   30    3                                                            
CONECT   31    3                                                            
CONECT   32    2                                                            
CONECT   33    5                                                            
CONECT   34   24                                                            
MASTER        0    0    0    0    0    0    0    0   34    0   74    0
END

View in JSmol

Synonyms

Value	Source
(+)-Methyl lucidenic acid F	HMDB
Methyl 4-{2,6,6,11,15-pentamethyl-5,9,12,17-tetraoxotetracyclo[8.7.0.0²,⁷.0¹¹,¹⁵]heptadec-1(10)-en-14-yl}pentanoic acid	Generator
Methyl lucidenic acid F	Generator

Chemical Formula

C₂₈H₃₈O₆

Average Mass

470.5977 Da

Monoisotopic Mass

470.26684 Da

IUPAC Name

methyl 4-{2,6,6,11,15-pentamethyl-5,9,12,17-tetraoxotetracyclo[8.7.0.0²,⁷.0¹¹,¹⁵]heptadec-1(10)-en-14-yl}pentanoate

Traditional Name

methyl 4-{2,6,6,11,15-pentamethyl-5,9,12,17-tetraoxotetracyclo[8.7.0.0²,⁷.0¹¹,¹⁵]heptadec-1(10)-en-14-yl}pentanoate

CAS Registry Number

98665-10-2

SMILES

COC(=O)CCC(C)C1CC(=O)C2(C)C3=C(C(=O)CC12C)C1(C)CCC(=O)C(C)(C)C1CC3=O

InChI Identifier

InChI=1S/C28H38O6/c1-15(8-9-22(33)34-7)16-12-21(32)28(6)24-17(29)13-19-25(2,3)20(31)10-11-26(19,4)23(24)18(30)14-27(16,28)5/h15-16,19H,8-14H2,1-7H3

InChI Key

ZXYSCJISDAKHPX-UHFFFAOYSA-N

Experimental Spectra

Not Available

Predicted Spectra

Not Available

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Agaricus bisporus	FooDB	Shmuel Yannai Dictionary of Food Compounds with CD-ROM: Additives, Flavors, and Ingredients. Chap...
Ganoderma lucidum (FR.)KARST.	Fungi	KNApSAcK
Pleurotus ostreatus	FooDB	Shmuel Yannai Dictionary of Food Compounds with CD-ROM: Additives, Flavors, and Ingredients. Chap...

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as cyanogenic glycosides. These are glycosides in which the aglycone moiety contains a cyanide group.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Carbohydrates and carbohydrate conjugates

Direct Parent

Cyanogenic glycosides

Alternative Parents

Substituents

Cyanogenic glycoside
Disaccharide
O-glycosyl compound
1-hydroxy-2-unsubstituted benzenoid
Phenol
Benzenoid
Monocyclic benzene moiety
Oxane
Secondary alcohol
Organoheterocyclic compound
Oxacycle
Polyol
Acetal
Carbonitrile
Nitrile
Hydrocarbon derivative
Organopnictogen compound
Organonitrogen compound
Organic nitrogen compound
Alcohol
Primary alcohol
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

Not Available

Physical Properties

State

Not Available

Experimental 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

Predicted Properties

Property	Value	Source
logP	3.82	ALOGPS
logP	4.32	ChemAxon
logS	-5.1	ALOGPS
pKa (Strongest Acidic)	18.92	ChemAxon
pKa (Strongest Basic)	-6.8	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	0	ChemAxon
Polar Surface Area	94.58 Å²	ChemAxon
Rotatable Bond Count	5	ChemAxon
Refractivity	127.64 m³·mol⁻¹	ChemAxon
Polarizability	51.5 Å³	ChemAxon
Number of Rings	4	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

External Links

HMDB ID

HMDB0029776

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

FDB000983

KNApSAcK ID

Not Available

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

131750898

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Not Available

Showing NP-Card for Methyl lucidenate F (NP0048508)

MOL for NP0048508 (Methyl lucidenate F)

3D MOL for NP0048508 (Methyl lucidenate F)

3D SDF for NP0048508 (Methyl lucidenate F)

3D-SDF for NP0048508 (Methyl lucidenate F)

PDB for NP0048508 (Methyl lucidenate F)

3D PDB for NP0048508 (Methyl lucidenate F)

SMILES for NP0048508 (Methyl lucidenate F)

INCHI for NP0048508 (Methyl lucidenate F)

Structure for NP0048508 (Methyl lucidenate F)

3D Structure for NP0048508 (Methyl lucidenate F)