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Showing NP-Card for Demethylsimmondsin (NP0049807)

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Record Information
Version2.0
Created at2022-03-17 21:18:27 UTC
Updated at2022-03-17 21:18:27 UTC
NP-MRD IDNP0049807
Secondary Accession NumbersNone
Natural Product Identification
Common NameDemethylsimmondsin
DescriptionDe-O-methylsimmondsin 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. De-O-methylsimmondsin is an extremely weak basic (essentially neutral) compound (based on its pKa). Outside of the human body, De-O-methylsimmondsin 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 de-O-methylsimmondsin a potential biomarker for the consumption of these foods.
Structure
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MOLSDFPDBSMILESInChI

MOL for NP0049807 (Demethylsimmondsin)


  Mrv0541 05061312282D          

 25 26  0  0  0  0            999 V2000
    0.0000    3.3000    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
    1.4289    0.8250    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
    6.4302    2.0625    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
    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
    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
    5.7158    3.3000    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
    4.2868    3.3000    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
    4.2868    2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    0.4125    0.0000 N   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
    2.1434    4.5375    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
    6.4302    3.7125    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
    3.5724    3.7125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    3.7125    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
    5.0013    2.0625    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  3  2  1  0  0  0  0
  6  2  2  0  0  0  0
  7  4  1  0  0  0  0
  8  4  1  0  0  0  0
  8  6  1  0  0  0  0
  9  5  1  0  0  0  0
 10  6  1  0  0  0  0
 11  9  1  0  0  0  0
 12 11  1  0  0  0  0
 13 12  1  0  0  0  0
 14  7  1  0  0  0  0
 14 10  1  0  0  0  0
 15 13  1  0  0  0  0
 16  3  3  0  0  0  0
 17  5  1  0  0  0  0
 18  7  1  0  0  0  0
 19 10  1  0  0  0  0
 20 11  1  0  0  0  0
 21 12  1  0  0  0  0
 22 13  1  0  0  0  0
 23  1  1  0  0  0  0
 23 14  1  0  0  0  0
 24  8  1  0  0  0  0
 24 15  1  0  0  0  0
 25  9  1  0  0  0  0
 25 15  1  0  0  0  0
M  END
Download

3D MOL for NP0049807 (Demethylsimmondsin)

Download
3D SDF for NP0049807 (Demethylsimmondsin)

  Mrv0541 05061312282D          

 25 26  0  0  0  0            999 V2000
    0.0000    3.3000    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
    1.4289    0.8250    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
    6.4302    2.0625    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
    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
    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
    5.7158    3.3000    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
    4.2868    3.3000    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
    4.2868    2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    0.4125    0.0000 N   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
    2.1434    4.5375    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
    6.4302    3.7125    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
    3.5724    3.7125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    3.7125    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
    5.0013    2.0625    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  3  2  1  0  0  0  0
  6  2  2  0  0  0  0
  7  4  1  0  0  0  0
  8  4  1  0  0  0  0
  8  6  1  0  0  0  0
  9  5  1  0  0  0  0
 10  6  1  0  0  0  0
 11  9  1  0  0  0  0
 12 11  1  0  0  0  0
 13 12  1  0  0  0  0
 14  7  1  0  0  0  0
 14 10  1  0  0  0  0
 15 13  1  0  0  0  0
 16  3  3  0  0  0  0
 17  5  1  0  0  0  0
 18  7  1  0  0  0  0
 19 10  1  0  0  0  0
 20 11  1  0  0  0  0
 21 12  1  0  0  0  0
 22 13  1  0  0  0  0
 23  1  1  0  0  0  0
 23 14  1  0  0  0  0
 24  8  1  0  0  0  0
 24 15  1  0  0  0  0
 25  9  1  0  0  0  0
 25 15  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0049807

> <DATABASE_NAME>
NP-MRD

> <SMILES>
COC1C(O)CC(OC2OC(CO)C(O)C(O)C2O)\C(=C\C#N)C1O

> <INCHI_IDENTIFIER>
InChI=1S/C15H23NO9/c1-23-14-7(18)4-8(6(2-3-16)10(14)19)24-15-13(22)12(21)11(20)9(5-17)25-15/h2,7-15,17-22H,4-5H2,1H3/b6-2-

> <INCHI_KEY>
SDYUFOBSNZFKRM-KXFIGUGUSA-N

> <FORMULA>
C15H23NO9

> <MOLECULAR_WEIGHT>
361.3444

> <EXACT_MASS>
361.137281339

> <JCHEM_ACCEPTOR_COUNT>
10

> <JCHEM_AVERAGE_POLARIZABILITY>
34.3580443180727

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
6

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

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

> <ALOGPS_LOGP>
-1.59

> <JCHEM_LOGP>
-3.554393311333334

> <ALOGPS_LOGS>
-0.68

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.97772282618682

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.176078726508587

> <JCHEM_PKA_STRONGEST_BASIC>
-2.9810836844765607

> <JCHEM_POLAR_SURFACE_AREA>
172.85999999999999

> <JCHEM_REFRACTIVITY>
81.10190000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
7.56e+01 g/l

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

> <JCHEM_VEBER_RULE>
0

$$$$

Download
3D-SDF for NP0049807 (Demethylsimmondsin)
Download
PDB for NP0049807 (Demethylsimmondsin)
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       0.000   6.160   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       4.001   2.310   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       5.335   6.160   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       4.001   3.850   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      10.669   4.620   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       2.667   4.620   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      10.669   6.160   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       9.336   6.930   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       8.002   6.160   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       2.667   6.160   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       8.002   4.620   0.000  0.00  0.00           C+0
HETATM   16  N   UNK     0       1.334   0.770   0.000  0.00  0.00           N+0
HETATM   17  O   UNK     0      13.337   4.620   0.000  0.00  0.00           O+0
HETATM   18  O   UNK     0       4.001   8.470   0.000  0.00  0.00           O+0
HETATM   19  O   UNK     0       1.334   3.850   0.000  0.00  0.00           O+0
HETATM   20  O   UNK     0      12.003   6.930   0.000  0.00  0.00           O+0
HETATM   21  O   UNK     0       9.336   8.470   0.000  0.00  0.00           O+0
HETATM   22  O   UNK     0       6.668   6.930   0.000  0.00  0.00           O+0
HETATM   23  O   UNK     0       1.334   6.930   0.000  0.00  0.00           O+0
HETATM   24  O   UNK     0       6.668   3.850   0.000  0.00  0.00           O+0
HETATM   25  O   UNK     0       9.336   3.850   0.000  0.00  0.00           O+0
CONECT    1   23                                                            
CONECT    2    3    6                                                       
CONECT    3    2   16                                                       
CONECT    4    7    8                                                       
CONECT    5    9   17                                                       
CONECT    6    2    8   10                                                  
CONECT    7    4   14   18                                                  
CONECT    8    4    6   24                                                  
CONECT    9    5   11   25                                                  
CONECT   10    6   14   19                                                  
CONECT   11    9   12   20                                                  
CONECT   12   11   13   21                                                  
CONECT   13   12   15   22                                                  
CONECT   14    7   10   23                                                  
CONECT   15   13   24   25                                                  
CONECT   16    3                                                            
CONECT   17    5                                                            
CONECT   18    7                                                            
CONECT   19   10                                                            
CONECT   20   11                                                            
CONECT   21   12                                                            
CONECT   22   13                                                            
CONECT   23    1   14                                                       
CONECT   24    8   15                                                       
CONECT   25    9   15                                                       
MASTER        0    0    0    0    0    0    0    0   25    0   52    0
END

Download
3D PDB for NP0049807 (Demethylsimmondsin)
Download
SMILES for NP0049807 (Demethylsimmondsin)
COC1C(O)CC(OC2OC(CO)C(O)C(O)C2O)\C(=C\C#N)C1O
Download
INCHI for NP0049807 (Demethylsimmondsin)
InChI=1S/C15H23NO9/c1-23-14-7(18)4-8(6(2-3-16)10(14)19)24-15-13(22)12(21)11(20)9(5-17)25-15/h2,7-15,17-22H,4-5H2,1H3/b6-2-
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View in JSmol
SynonymsNot Available
Chemical FormulaC15H23NO9
Average Mass361.3444 Da
Monoisotopic Mass361.13728 Da
IUPAC Name2-[(1E)-2,4-dihydroxy-3-methoxy-6-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}cyclohexylidene]acetonitrile
Traditional Name2-[(1E)-2,4-dihydroxy-3-methoxy-6-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}cyclohexylidene]acetonitrile
CAS Registry Number135105-75-8
SMILES
COC1C(O)CC(OC2OC(CO)C(O)C(O)C2O)\C(=C\C#N)C1O
InChI Identifier
InChI=1S/C15H23NO9/c1-23-14-7(18)4-8(6(2-3-16)10(14)19)24-15-13(22)12(21)11(20)9(5-17)25-15/h2,7-15,17-22H,4-5H2,1H3/b6-2-
InChI KeySDYUFOBSNZFKRM-KXFIGUGUSA-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
    • 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 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
    • 

  • Polyol
    • 

  • Acetal
    • 

  • Organoheterocyclic compound
    • 

  • Nitrile
    • 

  • Carbonitrile
    • 

  • Oxacycle
    • 

  • Ether
    • 

  • Dialkyl ether
    • 

  • Organonitrogen compound
    • 

  • Hydrocarbon derivative
    • 

  • Organopnictogen compound
    • 

  • Organic nitrogen compound
    • 

  • Alcohol
    • 

  • Primary alcohol
    • 

  • 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-1.6ALOGPS
logP-3.6ChemAxon
logS-0.68ALOGPS
pKa (Strongest Acidic)12.18ChemAxon
pKa (Strongest Basic)-3ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count10ChemAxon
Hydrogen Donor Count6ChemAxon
Polar Surface Area172.86 ŲChemAxon
Rotatable Bond Count4ChemAxon
Refractivity81.1 m³·mol⁻¹ChemAxon
Polarizability34.36 ųChemAxon
Number of Rings2ChemAxon
BioavailabilityYesChemAxon
Rule of FiveNoChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDHMDB0041208  
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDFDB021107  
KNApSAcK IDNot Available
Chemspider ID4525057  
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound5375609  
PDB IDNot Available
ChEBI IDNot Available
Good Scents IDNot Available
References
General ReferencesNot Available