NP-MRD: Showing NP-Card for Amygdalin (NP0048111)

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Record Information

Version

2.0

Created at

2022-03-17 20:51:15 UTC

Updated at

2025-07-16 00:03:48 UTC

NP-MRD ID

NP0048111

Natural Product DOI

https://doi.org/10.57994/1436

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Amygdalin

Description

Amygdalin, also known as (R)-amygdaloside or (R)-laenitrile, belongs to the class of organic compounds known as cyanogenic glycosides. These are glycosides in which the aglycone moiety contains a cyanide group. Amygdalin is an extremely weak basic (essentially neutral) compound (based on its pKa). Outside of the human body, Amygdalin is found, on average, in the highest concentration within a few different foods, such as apricots, peachs, and european plums and in a lower concentration in apples and quinces. Amygdalin has also been detected, but not quantified in, several different foods, such as almonds, fruits, pears, passion fruits, and common chokecherries. This could make amygdalin a potential biomarker for the consumption of these foods. Amygdalin can also be found in passion fruit. Amygdalin is a bitter glycoside of the Rosaceae, found in sources such as kernels of cherries, peaches and apricots. Amygdalin is found in Clerodendrum grayi, Elsholtzia rugulosa Hemsl., Gerbera jamesonii, Perilla frutescens , Prunus avium , Prunus ilicifolia , Prunus laurocerasus , Prunus lyonii, Prunus padus , Prunus serotina , Prunus spinosa , Rosaceae and Sorbus commixta . Amygdalin was first documented in 2006 (PMID: 16880611). Present in cold pressed bitter almond oil from the these sources prior to enzymic hydolysis and steam distillation for food use (PMID: 18670089).

Structure

MOL SDF PDB SMILES InChI


  Mrv0541 05061308122D          

 32 34  0  0  0  0            999 V2000
    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
    0.7145    3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434    4.5375    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
    0.7145    6.1875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0013   11.9625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724    8.6625    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
    1.4289    5.7750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0013   11.1375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579    8.2500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7158   10.7250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434    8.6625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7158    9.9000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    8.2500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0013    9.4875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    7.4250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868    9.9000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434    7.0125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    6.6000    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.7158   12.3750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.4302   11.1375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434    9.4875    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.4302    9.4875    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    8.6625    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.0013    8.6625    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
    3.5724    9.4875    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
    4.2868   10.7250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579    7.4250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  2  0  0  0  0
  3  1  1  0  0  0  0
  4  2  1  0  0  0  0
  5  3  2  0  0  0  0
  9  4  2  0  0  0  0
  9  5  1  0  0  0  0
 10  6  1  0  0  0  0
 10  9  1  0  0  0  0
 11  7  1  0  0  0  0
 12  8  1  0  0  0  0
 13 11  1  0  0  0  0
 14 12  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  6  3  0  0  0  0
 22  7  1  0  0  0  0
 23 13  1  0  0  0  0
 24 14  1  0  0  0  0
 25 15  1  0  0  0  0
 26 16  1  0  0  0  0
 27 17  1  0  0  0  0
 28 18  1  0  0  0  0
 29  8  1  0  0  0  0
 29 19  1  0  0  0  0
 30 10  1  0  0  0  0
 30 20  1  0  0  0  0
 31 11  1  0  0  0  0
 31 19  1  0  0  0  0
 32 12  1  0  0  0  0
 32 20  1  0  0  0  0
M  END


  Mrv0541 05061308122D          

 32 34  0  0  0  0            999 V2000
    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
    0.7145    3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434    4.5375    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
    0.7145    6.1875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0013   11.9625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724    8.6625    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
    1.4289    5.7750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0013   11.1375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579    8.2500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7158   10.7250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434    8.6625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7158    9.9000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    8.2500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0013    9.4875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    7.4250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868    9.9000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434    7.0125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    6.6000    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.7158   12.3750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.4302   11.1375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434    9.4875    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.4302    9.4875    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    8.6625    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.0013    8.6625    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
    3.5724    9.4875    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
    4.2868   10.7250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579    7.4250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  2  0  0  0  0
  3  1  1  0  0  0  0
  4  2  1  0  0  0  0
  5  3  2  0  0  0  0
  9  4  2  0  0  0  0
  9  5  1  0  0  0  0
 10  6  1  0  0  0  0
 10  9  1  0  0  0  0
 11  7  1  0  0  0  0
 12  8  1  0  0  0  0
 13 11  1  0  0  0  0
 14 12  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  6  3  0  0  0  0
 22  7  1  0  0  0  0
 23 13  1  0  0  0  0
 24 14  1  0  0  0  0
 25 15  1  0  0  0  0
 26 16  1  0  0  0  0
 27 17  1  0  0  0  0
 28 18  1  0  0  0  0
 29  8  1  0  0  0  0
 29 19  1  0  0  0  0
 30 10  1  0  0  0  0
 30 20  1  0  0  0  0
 31 11  1  0  0  0  0
 31 19  1  0  0  0  0
 32 12  1  0  0  0  0
 32 20  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0048111

> <DATABASE_NAME>
NP-MRD

> <SMILES>
OCC1OC(OCC2OC(OC(C#N)C3=CC=CC=C3)C(O)C(O)C2O)C(O)C(O)C1O

> <INCHI_IDENTIFIER>
InChI=1S/C20H27NO11/c21-6-10(9-4-2-1-3-5-9)30-20-18(28)16(26)14(24)12(32-20)8-29-19-17(27)15(25)13(23)11(7-22)31-19/h1-5,10-20,22-28H,7-8H2

> <INCHI_KEY>
XUCIJNAGGSZNQT-UHFFFAOYSA-N

> <FORMULA>
C20H27NO11

> <MOLECULAR_WEIGHT>
457.4285

> <EXACT_MASS>
457.158410711

> <JCHEM_ACCEPTOR_COUNT>
12

> <JCHEM_AVERAGE_POLARIZABILITY>
44.60557454000434

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
7

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2-phenyl-2-{[3,4,5-trihydroxy-6-({[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}methyl)oxan-2-yl]oxy}acetonitrile

> <ALOGPS_LOGP>
-1.29

> <JCHEM_LOGP>
-2.58788678

> <ALOGPS_LOGS>
-1.11

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.43099750787811

> <JCHEM_PKA_STRONGEST_ACIDIC>
11.909080174553063

> <JCHEM_PKA_STRONGEST_BASIC>
-2.981083422322401

> <JCHEM_POLAR_SURFACE_AREA>
202.31999999999996

> <JCHEM_REFRACTIVITY>
102.50969999999998

> <JCHEM_ROTATABLE_BOND_COUNT>
7

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
3.53e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
amygdalin

> <JCHEM_VEBER_RULE>
0

$$$$

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       2.667   6.160   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       4.001   6.930   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       1.334   6.930   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       4.001   8.470   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       1.334   8.470   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       1.334  11.550   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       9.336  22.330   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       6.668  16.170   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       2.667   9.240   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       2.667  10.780   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       9.336  20.790   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       5.335  15.400   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      10.669  20.020   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       4.001  16.170   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      10.669  18.480   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       2.667  15.400   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       9.336  17.710   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       2.667  13.860   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       8.002  18.480   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       4.001  13.090   0.000  0.00  0.00           C+0
HETATM   21  N   UNK     0       0.000  12.320   0.000  0.00  0.00           N+0
HETATM   22  O   UNK     0      10.669  23.100   0.000  0.00  0.00           O+0
HETATM   23  O   UNK     0      12.003  20.790   0.000  0.00  0.00           O+0
HETATM   24  O   UNK     0       4.001  17.710   0.000  0.00  0.00           O+0
HETATM   25  O   UNK     0      12.003  17.710   0.000  0.00  0.00           O+0
HETATM   26  O   UNK     0       1.334  16.170   0.000  0.00  0.00           O+0
HETATM   27  O   UNK     0       9.336  16.170   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       6.668  17.710   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       8.002  20.020   0.000  0.00  0.00           O+0
HETATM   32  O   UNK     0       5.335  13.860   0.000  0.00  0.00           O+0
CONECT    1    2    3                                                       
CONECT    2    1    4                                                       
CONECT    3    1    5                                                       
CONECT    4    2    9                                                       
CONECT    5    3    9                                                       
CONECT    6   10   21                                                       
CONECT    7   11   22                                                       
CONECT    8   12   29                                                       
CONECT    9    4    5   10                                                  
CONECT   10    6    9   30                                                  
CONECT   11    7   13   31                                                  
CONECT   12    8   14   32                                                  
CONECT   13   11   15   23                                                  
CONECT   14   12   16   24                                                  
CONECT   15   13   17   25                                                  
CONECT   16   14   18   26                                                  
CONECT   17   15   19   27                                                  
CONECT   18   16   20   28                                                  
CONECT   19   17   29   31                                                  
CONECT   20   18   30   32                                                  
CONECT   21    6                                                            
CONECT   22    7                                                            
CONECT   23   13                                                            
CONECT   24   14                                                            
CONECT   25   15                                                            
CONECT   26   16                                                            
CONECT   27   17                                                            
CONECT   28   18                                                            
CONECT   29    8   19                                                       
CONECT   30   10   20                                                       
CONECT   31   11   19                                                       
CONECT   32   12   20                                                       
MASTER        0    0    0    0    0    0    0    0   32    0   68    0
END

View in JSmol

Synonyms

Value	Source
(-)-D-Mandelonitrile beta-D-gentiobioside	HMDB
(R)-Amygdalin	HMDB
(R)-Amygdaloside	HMDB
(R)-Laenitrile	HMDB
Amygdaloside	HMDB
D(-)-Mandelonitrile-beta-D-gentiobioside	HMDB
D(-)-Mandelonitrile-β-D-gentiobioside	HMDB
D-Amygdalin	HMDB
D-Mandelonitrile-beta-D-glucosido-6-beta-D-glucoside	HMDB
Glucoprunasin	HMDB
Mandelonitrile gentiobioside	HMDB
Mandelonitrile-β-gentiobioside	HMDB
NSC 15780	HMDB
Mandelonitrile-beta-gentiobioside	HMDB
Neoamygdalin	HMDB
Laetrile	HMDB
Mandelonitrile beta gentiobioside	HMDB
Amygdalin	MeSH

Chemical Formula

C₂₀H₂₇NO₁₁

Average Mass

457.4285 Da

Monoisotopic Mass

457.15841 Da

IUPAC Name

2-phenyl-2-{[3,4,5-trihydroxy-6-({[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}methyl)oxan-2-yl]oxy}acetonitrile

Traditional Name

amygdalin

CAS Registry Number

29883-15-6

SMILES

OCC1OC(OCC2OC(OC(C#N)C3=CC=CC=C3)C(O)C(O)C2O)C(O)C(O)C1O

InChI Identifier

InChI=1S/C20H27NO11/c21-6-10(9-4-2-1-3-5-9)30-20-18(28)16(26)14(24)12(32-20)8-29-19-17(27)15(25)13(23)11(7-22)31-19/h1-5,10-20,22-28H,7-8H2

InChI Key

XUCIJNAGGSZNQT-UHFFFAOYSA-N

Experimental Spectra

Spectrum Type	Description	Depositor Email	Depositor Organization	Depositor	Deposition Date	View
HMBC NMR	[¹H, ¹³C] NMR Spectrum (2D, 600 MHz, D2O, experimental)	rjm4kd@umsystem.edu	Sumner lab, University of Missouri	Ronald Myers	2025-07-14	View Spectrum
COSY NMR	[¹H, ¹H] NMR Spectrum (2D, 600 MHz, D2O, experimental)	rjm4kd@umsystem.edu	Sumner lab, University of Missouri	Ronald Myers	2025-07-14	View Spectrum
HSQC NMR	[¹H, ¹³C] NMR Spectrum (2D, 600 MHz, D2O, experimental)	rjm4kd@umsystem.edu	Sumner lab, University of Missouri	Ronald Myers	2025-07-14	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D2O, experimental)	rjm4kd@umsystem.edu	Sumner lab, University of Missouri	Ronald Myers	2025-07-14	View Spectrum
HMBC NMR	[¹H, ¹³C] NMR Spectrum (2D, 600 MHz, CD3OD, experimental)	bgnzk@missouri.edu	MU Metabolomics Center, University of Missouri, Columbia. MO, USA	Dr. Bharat Goel	2024-05-02	View Spectrum
HSQC NMR	[¹H, ¹³C] NMR Spectrum (2D, 600 MHz, CD3OD, experimental)	bgnzk@missouri.edu	MU Metabolomics Center, University of Missouri, Columbia. MO, USA	Dr. Bharat Goel	2024-05-02	View Spectrum
COSY NMR	[¹H, ¹H] NMR Spectrum (2D, 600 MHz, CD3OD, experimental)	bgnzk@missouri.edu	MU Metabolomics Center, University of Missouri, Columbia. MO, USA	Dr. Bharat Goel	2024-05-02	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, CD3OD, experimental)	bgnzk@missouri.edu	MU Metabolomics Center, University of Missouri, Columbia. MO, USA	Dr. Bharat Goel	2024-05-02	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, CD3OD, experimental)	bgnzk@missouri.edu	MU Metabolomics Center, University of Missouri, Columbia. MO, USA	Dr. Bharat Goel	2024-05-02	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600.0 MHz, D₂O, experimental)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum

Predicted Spectra

Spectrum Type	Description	Depositor ID	Depositor Organization	Depositor	Deposition Date	View

Chemical Shift Submissions

Spectrum Type	Description	Depositor Email	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹H NMR Spectrum (1D, 600.0, D₂O, simulated)	rjm4kd@umsystem.edu	Sumner lab, University of Missouri	Ronald Myers	2025-07-14	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600.133705802, CD₃OD, simulated)	bgnzk@missouri.edu	Sumner Lab, MU Metabolomics Center, University of Missouri, Columbia. MO, USA	Dr. Bharat Goel	2024-05-02	View Spectrum

Species

Species of Origin

Species Name	Source	Reference
Clerodendrum grayi	Plant	KNApSAcK
Cydonia oblonga	FooDB	Dr. Duke's Phytochemical and Ethnobotanical Databases
Elsholtzia rugulosa Hemsl.	Plant	KNApSAcK
Eriobotrya japonica	FooDB	Dr. Duke's Phytochemical and Ethnobotanical Databases
Gerbera jamesonii	Plant	KNApSAcK
Malus pumila	FooDB	Dr. Duke's Phytochemical and Ethnobotanical Databases
Passiflora edulis	FooDB	KNAPSACK
Perilla frutescens	Plant	KNApSAcK
Phaseolus lunatus	FooDB	Dr. Duke's Phytochemical and Ethnobotanical Databases
Prunus armeniaca	FooDB	Dr. Duke's Phytochemical and Ethnobotanical Databases
Prunus avium	Plant	KNApSAcK
Prunus cerasus	FooDB	Dr. Duke's Phytochemical and Ethnobotanical Databases
Prunus domestica	FooDB	Dr. Duke's Phytochemical and Ethnobotanical Databases
Prunus dulcis	FooDB	KNAPSACK
Prunus ilicifolia	Plant	KNApSAcK
Prunus laurocerasus	Plant	KNApSAcK
Prunus lyonii	Plant	KNApSAcK
Prunus padus	Plant	KNApSAcK
Prunus persica	FooDB	Dr. Duke's Phytochemical and Ethnobotanical Databases
Prunus serotina	Plant	KNApSAcK
Prunus spinosa	Plant	KNApSAcK
Prunus virginiana	FooDB	KNAPSACK
Pyrus communis	FooDB	Dr. Duke's Phytochemical and Ethnobotanical Databases
Rosaceae	-	KNApSAcK
Sorbus commixta	Plant	KNApSAcK

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
Monocyclic benzene moiety
Oxane
Benzenoid
Secondary alcohol
Polyol
Nitrile
Carbonitrile
Acetal
Organoheterocyclic compound
Oxacycle
Primary alcohol
Alcohol
Organonitrogen compound
Hydrocarbon derivative
Organopnictogen compound
Organic nitrogen compound
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

a small molecule (CPD-1125 )

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	-1.3	ALOGPS
logP	-2.6	ChemAxon
logS	-1.1	ALOGPS
pKa (Strongest Acidic)	11.91	ChemAxon
pKa (Strongest Basic)	-3	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	12	ChemAxon
Hydrogen Donor Count	7	ChemAxon
Polar Surface Area	202.32 Å²	ChemAxon
Rotatable Bond Count	7	ChemAxon
Refractivity	102.51 m³·mol⁻¹	ChemAxon
Polarizability	44.61 Å³	ChemAxon
Number of Rings	3	ChemAxon
Bioavailability	No	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	Yes	ChemAxon

External Links

HMDB ID

HMDB0035030

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

KNApSAcK ID

Chemspider ID

KEGG Compound ID

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Amygdalin

METLIN ID

Not Available

PubChem Compound

2180

PDB ID

Not Available

ChEBI ID

27613

Good Scents ID

Not Available

References

General References

Hwang HJ, Kim P, Kim CJ, Lee HJ, Shim I, Yin CS, Yang Y, Hahm DH: Antinociceptive effect of amygdalin isolated from Prunus armeniaca on formalin-induced pain in rats. Biol Pharm Bull. 2008 Aug;31(8):1559-64. doi: 10.1248/bpb.31.1559. [PubMed:18670089 ]
Chang HK, Shin MS, Yang HY, Lee JW, Kim YS, Lee MH, Kim J, Kim KH, Kim CJ: Amygdalin induces apoptosis through regulation of Bax and Bcl-2 expressions in human DU145 and LNCaP prostate cancer cells. Biol Pharm Bull. 2006 Aug;29(8):1597-602. doi: 10.1248/bpb.29.1597. [PubMed:16880611 ]

Showing NP-Card for Amygdalin (NP0048111)

MOL for NP0048111 (Amygdalin)

3D MOL for NP0048111 (Amygdalin)

3D SDF for NP0048111 (Amygdalin)

3D-SDF for NP0048111 (Amygdalin)

PDB for NP0048111 (Amygdalin)

3D PDB for NP0048111 (Amygdalin)

SMILES for NP0048111 (Amygdalin)

INCHI for NP0048111 (Amygdalin)

Structure for NP0048111 (Amygdalin)

3D Structure for NP0048111 (Amygdalin)