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Showing NP-Card for Di-demethylsimmondsin 4-alpha-D-glucoside (NP0049068)

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Record Information
Version2.0
Created at2022-03-17 21:06:38 UTC
Updated at2022-03-17 21:06:38 UTC
NP-MRD IDNP0049068
Secondary Accession NumbersNone
Natural Product Identification
Common NameDi-demethylsimmondsin 4-alpha-D-glucoside
DescriptionDide-O-methyl-4-O-alpha-D-glucopyranosylsimmondsin belongs to the class of organic compounds known as o-glycosyl compounds. These are glycoside in which a sugar group is bonded through one carbon to another group via a O-glycosidic bond. Dide-O-methyl-4-O-alpha-D-glucopyranosylsimmondsin is an extremely weak basic (essentially neutral) compound (based on its pKa). Outside of the human body, Dide-O-methyl-4-O-alpha-D-glucopyranosylsimmondsin has been detected, but not quantified in, a few different foods, such as coffee and coffee products, fats and oils, and nuts. This could make dide-O-methyl-4-O-alpha-D-glucopyranosylsimmondsin a potential biomarker for the consumption of these foods.
Structure
Thumb
MOLSDFPDBSMILESInChI

MOL for NP0049068 (Di-demethylsimmondsin 4-alpha-D-glucoside)


  Mrv0541 05061310232D          

 35 37  0  0  0  0            999 V2000
    0.7145    3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    3.3000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579    3.3000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    4.5375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.4302    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    3.3000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434    3.7125    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
    0.0000    4.9500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7158    2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    5.7750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7158    3.3000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    6.1875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0013    3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    5.7750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868    3.3000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    4.9500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868    2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    2.8875    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289    4.9500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.1447    2.4750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    2.0625    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434    1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    6.1875    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.4302    3.7125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    7.0125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.0013    4.5375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434    6.1875    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724    3.7125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434    4.5375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724    2.0625    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    4.5375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.0013    2.0625    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  0  0  0  0
  6  1  2  0  0  0  0
  7  3  1  0  0  0  0
  7  6  1  0  0  0  0
  8  3  1  0  0  0  0
  9  4  1  0  0  0  0
 10  5  1  0  0  0  0
 11  6  1  0  0  0  0
 12  8  1  0  0  0  0
 12 11  1  0  0  0  0
 13  9  1  0  0  0  0
 14 10  1  0  0  0  0
 15 13  1  0  0  0  0
 16 14  1  0  0  0  0
 17 15  1  0  0  0  0
 18 16  1  0  0  0  0
 19 17  1  0  0  0  0
 20 18  1  0  0  0  0
 21  2  3  0  0  0  0
 22  4  1  0  0  0  0
 23  5  1  0  0  0  0
 24 11  1  0  0  0  0
 25 12  1  0  0  0  0
 26 13  1  0  0  0  0
 27 14  1  0  0  0  0
 28 15  1  0  0  0  0
 29 16  1  0  0  0  0
 30 17  1  0  0  0  0
 31 18  1  0  0  0  0
 32  7  1  0  0  0  0
 32 19  1  0  0  0  0
 33  8  1  0  0  0  0
 33 20  1  0  0  0  0
 34  9  1  0  0  0  0
 34 19  1  0  0  0  0
 35 10  1  0  0  0  0
 35 20  1  0  0  0  0
M  END
Download

3D MOL for NP0049068 (Di-demethylsimmondsin 4-alpha-D-glucoside)

Download
3D SDF for NP0049068 (Di-demethylsimmondsin 4-alpha-D-glucoside)

  Mrv0541 05061310232D          

 35 37  0  0  0  0            999 V2000
    0.7145    3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    3.3000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579    3.3000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    4.5375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.4302    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    3.3000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434    3.7125    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
    0.0000    4.9500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7158    2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    5.7750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7158    3.3000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    6.1875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0013    3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    5.7750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868    3.3000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    4.9500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868    2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    2.8875    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289    4.9500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.1447    2.4750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    2.0625    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434    1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    6.1875    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.4302    3.7125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    7.0125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.0013    4.5375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434    6.1875    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724    3.7125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434    4.5375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724    2.0625    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    4.5375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.0013    2.0625    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  0  0  0  0
  6  1  2  0  0  0  0
  7  3  1  0  0  0  0
  7  6  1  0  0  0  0
  8  3  1  0  0  0  0
  9  4  1  0  0  0  0
 10  5  1  0  0  0  0
 11  6  1  0  0  0  0
 12  8  1  0  0  0  0
 12 11  1  0  0  0  0
 13  9  1  0  0  0  0
 14 10  1  0  0  0  0
 15 13  1  0  0  0  0
 16 14  1  0  0  0  0
 17 15  1  0  0  0  0
 18 16  1  0  0  0  0
 19 17  1  0  0  0  0
 20 18  1  0  0  0  0
 21  2  3  0  0  0  0
 22  4  1  0  0  0  0
 23  5  1  0  0  0  0
 24 11  1  0  0  0  0
 25 12  1  0  0  0  0
 26 13  1  0  0  0  0
 27 14  1  0  0  0  0
 28 15  1  0  0  0  0
 29 16  1  0  0  0  0
 30 17  1  0  0  0  0
 31 18  1  0  0  0  0
 32  7  1  0  0  0  0
 32 19  1  0  0  0  0
 33  8  1  0  0  0  0
 33 20  1  0  0  0  0
 34  9  1  0  0  0  0
 34 19  1  0  0  0  0
 35 10  1  0  0  0  0
 35 20  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0049068

> <DATABASE_NAME>
NP-MRD

> <SMILES>
OCC1OC(OC2CC(OC3OC(CO)C(O)C(O)C3O)\C(=C\C#N)C(O)C2O)C(O)C(O)C1O

> <INCHI_IDENTIFIER>
InChI=1S/C20H31NO14/c21-2-1-6-7(32-19-17(30)15(28)13(26)9(4-22)34-19)3-8(12(25)11(6)24)33-20-18(31)16(29)14(27)10(5-23)35-20/h1,7-20,22-31H,3-5H2/b6-1-

> <INCHI_KEY>
XJQKQFRVSPIUIR-BHQIHCQQSA-N

> <FORMULA>
C20H31NO14

> <MOLECULAR_WEIGHT>
509.4584

> <EXACT_MASS>
509.174454705

> <JCHEM_ACCEPTOR_COUNT>
15

> <JCHEM_AVERAGE_POLARIZABILITY>
47.77417185350456

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
10

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2-[(1E)-2,3-dihydroxy-4,6-bis({[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy})cyclohexylidene]acetonitrile

> <ALOGPS_LOGP>
-2.16

> <JCHEM_LOGP>
-5.9683554606666664

> <ALOGPS_LOGS>
-0.60

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.356752597754962

> <JCHEM_PKA_STRONGEST_ACIDIC>
11.873177191920535

> <JCHEM_PKA_STRONGEST_BASIC>
-3.4981311890869513

> <JCHEM_POLAR_SURFACE_AREA>
263.00999999999993

> <JCHEM_REFRACTIVITY>
108.764

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
1.29e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
2-[(1E)-2,3-dihydroxy-4,6-bis({[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy})cyclohexylidene]acetonitrile

> <JCHEM_VEBER_RULE>
0

$$$$

Download
3D-SDF for NP0049068 (Di-demethylsimmondsin 4-alpha-D-glucoside)
Download
PDB for NP0049068 (Di-demethylsimmondsin 4-alpha-D-glucoside)
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       1.334   6.930   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.000   6.160   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       5.335   6.160   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -1.334   8.470   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      12.003   3.850   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       2.667   6.160   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       4.001   6.930   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       5.335   4.620   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       0.000   9.240   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      10.669   4.620   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       2.667   4.620   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       4.001   3.850   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       0.000  10.780   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      10.669   6.160   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       1.334  11.550   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       9.336   6.930   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       2.667  10.780   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       8.002   6.160   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       2.667   9.240   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       8.002   4.620   0.000  0.00  0.00           C+0
HETATM   21  N   UNK     0      -1.334   5.390   0.000  0.00  0.00           N+0
HETATM   22  O   UNK     0      -2.667   9.240   0.000  0.00  0.00           O+0
HETATM   23  O   UNK     0      13.337   4.620   0.000  0.00  0.00           O+0
HETATM   24  O   UNK     0       1.334   3.850   0.000  0.00  0.00           O+0
HETATM   25  O   UNK     0       4.001   2.310   0.000  0.00  0.00           O+0
HETATM   26  O   UNK     0      -1.334  11.550   0.000  0.00  0.00           O+0
HETATM   27  O   UNK     0      12.003   6.930   0.000  0.00  0.00           O+0
HETATM   28  O   UNK     0       1.334  13.090   0.000  0.00  0.00           O+0
HETATM   29  O   UNK     0       9.336   8.470   0.000  0.00  0.00           O+0
HETATM   30  O   UNK     0       4.001  11.550   0.000  0.00  0.00           O+0
HETATM   31  O   UNK     0       6.668   6.930   0.000  0.00  0.00           O+0
HETATM   32  O   UNK     0       4.001   8.470   0.000  0.00  0.00           O+0
HETATM   33  O   UNK     0       6.668   3.850   0.000  0.00  0.00           O+0
HETATM   34  O   UNK     0       1.334   8.470   0.000  0.00  0.00           O+0
HETATM   35  O   UNK     0       9.336   3.850   0.000  0.00  0.00           O+0
CONECT    1    2    6                                                       
CONECT    2    1   21                                                       
CONECT    3    7    8                                                       
CONECT    4    9   22                                                       
CONECT    5   10   23                                                       
CONECT    6    1    7   11                                                  
CONECT    7    3    6   32                                                  
CONECT    8    3   12   33                                                  
CONECT    9    4   13   34                                                  
CONECT   10    5   14   35                                                  
CONECT   11    6   12   24                                                  
CONECT   12    8   11   25                                                  
CONECT   13    9   15   26                                                  
CONECT   14   10   16   27                                                  
CONECT   15   13   17   28                                                  
CONECT   16   14   18   29                                                  
CONECT   17   15   19   30                                                  
CONECT   18   16   20   31                                                  
CONECT   19   17   32   34                                                  
CONECT   20   18   33   35                                                  
CONECT   21    2                                                            
CONECT   22    4                                                            
CONECT   23    5                                                            
CONECT   24   11                                                            
CONECT   25   12                                                            
CONECT   26   13                                                            
CONECT   27   14                                                            
CONECT   28   15                                                            
CONECT   29   16                                                            
CONECT   30   17                                                            
CONECT   31   18                                                            
CONECT   32    7   19                                                       
CONECT   33    8   20                                                       
CONECT   34    9   19                                                       
CONECT   35   10   20                                                       
MASTER        0    0    0    0    0    0    0    0   35    0   74    0
END

Download
3D PDB for NP0049068 (Di-demethylsimmondsin 4-alpha-D-glucoside)
Download
SMILES for NP0049068 (Di-demethylsimmondsin 4-alpha-D-glucoside)
OCC1OC(OC2CC(OC3OC(CO)C(O)C(O)C3O)\C(=C\C#N)C(O)C2O)C(O)C(O)C1O
Download
INCHI for NP0049068 (Di-demethylsimmondsin 4-alpha-D-glucoside)
InChI=1S/C20H31NO14/c21-2-1-6-7(32-19-17(30)15(28)13(26)9(4-22)34-19)3-8(12(25)11(6)24)33-20-18(31)16(29)14(27)10(5-23)35-20/h1,7-20,22-31H,3-5H2/b6-1-
Download
View in JSmol
Synonyms
ValueSource
Dide-O-methyl-4-O-a-D-glucopyranosylsimmondsinGenerator
Dide-O-methyl-4-O-α-D-glucopyranosylsimmondsinGenerator
Di-demethylsimmondsin 4-a-D-glucosideGenerator
Di-demethylsimmondsin 4-α-D-glucosideGenerator
Chemical FormulaC20H31NO14
Average Mass509.4584 Da
Monoisotopic Mass509.17445 Da
IUPAC Name2-[(1E)-2,3-dihydroxy-4,6-bis({[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy})cyclohexylidene]acetonitrile
Traditional Name2-[(1E)-2,3-dihydroxy-4,6-bis({[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy})cyclohexylidene]acetonitrile
CAS Registry Number370068-00-1
SMILES
OCC1OC(OC2CC(OC3OC(CO)C(O)C(O)C3O)\C(=C\C#N)C(O)C2O)C(O)C(O)C1O
InChI Identifier
InChI=1S/C20H31NO14/c21-2-1-6-7(32-19-17(30)15(28)13(26)9(4-22)34-19)3-8(12(25)11(6)24)33-20-18(31)16(29)14(27)10(5-23)35-20/h1,7-20,22-31H,3-5H2/b6-1-
InChI KeyXJQKQFRVSPIUIR-BHQIHCQQSA-N
Experimental Spectra
Not Available
Predicted Spectra
Not Available
Chemical Shift Submissions
Not Available
Species
Species of Origin
Species NameSourceReference
Coffea arabica L.FooDB
    • Shmuel Yannai Dictionary of Food Compounds with CD-ROM: Additives, Flavors, and Ingredients. Chap...
Coffea canephoraFooDB
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Chemical Taxonomy
Description Belongs to the class of organic compounds known as o-glycosyl compounds. These are glycoside in which a sugar group is bonded through one carbon to another group via a O-glycosidic bond.
KingdomOrganic compounds  
Super ClassOrganic oxygen compounds  
ClassOrganooxygen compounds  
Sub ClassCarbohydrates and carbohydrate conjugates  
Direct ParentO-glycosyl compounds  
Alternative Parents
Substituents
  • Hexose monosaccharide
    • 

  • O-glycosyl compound
    • 

  • Cyclitol or derivatives
    • 

  • Monosaccharide
    • 

  • Oxane
    • 

  • Cyclic alcohol
    • 

  • Secondary alcohol
    • 

  • Acetal
    • 

  • Oxacycle
    • 

  • Carbonitrile
    • 

  • Nitrile
    • 

  • Organoheterocyclic compound
    • 

  • Polyol
    • 

  • Alcohol
    • 

  • Organic nitrogen compound
    • 

  • Organopnictogen compound
    • 

  • Organonitrogen compound
    • 

  • Primary alcohol
    • 

  • Hydrocarbon derivative
    • 

  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic heteromonocyclic compounds
External DescriptorsNot Available
Physical Properties
StateNot Available
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
logP-2.2ALOGPS
logP-6ChemAxon
logS-0.6ALOGPS
pKa (Strongest Acidic)11.87ChemAxon
pKa (Strongest Basic)-3.5ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count15ChemAxon
Hydrogen Donor Count10ChemAxon
Polar Surface Area263.01 ŲChemAxon
Rotatable Bond Count6ChemAxon
Refractivity108.76 m³·mol⁻¹ChemAxon
Polarizability47.77 ųChemAxon
Number of Rings3ChemAxon
BioavailabilityNoChemAxon
Rule of FiveNoChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleYesChemAxon
HMDB IDHMDB0038329  
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDFDB017664  
KNApSAcK IDNot Available
Chemspider IDNot Available
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound131752336  
PDB IDNot Available
ChEBI IDNot Available
Good Scents IDNot Available
References
General ReferencesNot Available