NP-MRD: Showing NP-Card for (2r)-2-phenyl-2-{[(4s,5s)-3,4,5-trihydroxy-6-({[(3r,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}methyl)oxan-2-yl]oxy}acetonitrile (NP0204297)

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Record Information

Version

2.0

Created at

2022-09-04 23:56:32 UTC

Updated at

2022-09-04 23:56:32 UTC

NP-MRD ID

NP0204297

Secondary Accession Numbers

None

Natural Product Identification

Common Name

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

Description

Amygdalin, also known as laetrile or vitamin B17, belongs to the class of organic compounds known as cyanogenic glycosides. These are glycosides in which the aglycone moiety contains a cyanide group. (2r)-2-phenyl-2-{[(4s,5s)-3,4,5-trihydroxy-6-({[(3r,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}methyl)oxan-2-yl]oxy}acetonitrile is found in Gerbera jamesonii, Oxyanthus pyriformis, Passiflora edulis, Prunus armeniaca, Prunus cerasus, Prunus persica, Prunus salicina and Prunus spinosa. (2r)-2-phenyl-2-{[(4s,5s)-3,4,5-trihydroxy-6-({[(3r,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}methyl)oxan-2-yl]oxy}acetonitrile was first documented in 2022 (PMID: 36047933). Based on a literature review a significant number of articles have been published on amygdalin (PMID: 36044826) (PMID: 36014482) (PMID: 35987015) (PMID: 35977575) (PMID: 35975846) (PMID: 35958222).

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309052201562D          

 32 34  0  0  1  0            999 V2000
   -2.1434    2.8875    0.0000 N   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  2  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
   -1.4289    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434   -0.4125    0.0000 O   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
   -2.8579   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8579   -2.4750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5724   -2.8875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2868   -2.4750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0013   -2.8875    0.0000 C   0  0  2  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
   -6.4302   -2.8875    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0013   -3.7125    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -5.7158   -4.1250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2868   -4.1250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2868   -4.9500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5724   -3.7125    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.8579   -4.1250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289   -1.6500    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.4289   -2.4750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -1.2375    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.0000   -1.6500    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
    0.0000    0.0000    0.0000 O   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
   -2.8579   -0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5724   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2868   -0.0000    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
   -3.5724    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  3  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  6  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  1  1  0  0  0
 13 14  1  0  0  0  0
 12 15  1  0  0  0  0
 15 16  1  6  0  0  0
 15 17  1  0  0  0  0
 17 18  1  0  0  0  0
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 10 19  1  0  0  0  0
 19 20  1  6  0  0  0
  7 21  1  0  0  0  0
 21 22  1  6  0  0  0
 21 23  1  0  0  0  0
 23 24  1  1  0  0  0
 23 25  1  0  0  0  0
  5 25  1  0  0  0  0
 25 26  1  0  0  0  0
  3 27  1  0  0  0  0
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 28 29  1  0  0  0  0
 29 30  2  0  0  0  0
 30 31  1  0  0  0  0
 31 32  2  0  0  0  0
 27 32  1  0  0  0  0
M  END

     RDKit          3D

 59 61  0  0  0  0  0  0  0  0999 V2000
   -6.2857    2.1583   -1.1985 N   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4130    1.5217   -0.7777 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2972    0.6969   -0.2593 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.3601    0.6259   -1.2888 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1359    1.1187   -0.9083 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.1706    0.1576   -1.0250 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0791    0.4884   -0.5507 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.1016    0.3305    0.9483 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2928    0.6134    1.5522 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.3715   -0.1444    1.1899 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.4143    0.6819    0.8400 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.5085    0.0130    0.3087 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.5925    0.4090   -1.1567 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.6561   -0.1988   -1.8068 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.3969   -1.4760    0.4125 C   0  0  1  0  0  0  0  0  0  0  0  0
    5.6727   -2.0166    0.2197 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.8955   -1.9467    1.7460 C   0  0  1  0  0  0  0  0  0  0  0  0
    4.9253   -2.2651    2.6257 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.9004   -0.9816    2.3685 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.6268   -0.1109    3.1754 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5452    1.8573   -0.8965 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.1655    1.7826   -2.1655 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5155    2.9025   -0.9980 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.9347    3.2187    0.3078 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7141    2.3325   -1.7108 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.4418    2.0103   -3.0332 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8812   -0.6291    0.0698 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3049   -1.5067   -0.9131 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.8465   -2.7372   -0.6053 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.9850   -3.1379    0.7094 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5698   -2.2795    1.6923 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0303   -1.0532    1.3802 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8596    1.1317    0.6430 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2271    1.4533    0.1538 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8105   -0.2688   -0.9624 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6482    1.0581    1.3765 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3118   -0.6762    1.2479 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1433   -0.9295    0.4142 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.4258    0.3979    0.8201 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6144    0.1664   -1.6167 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.7202    1.5060   -1.2730 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.4857    0.3619   -1.7719 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7720   -1.8572   -0.4325 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.2653   -1.6634    0.9382 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3355   -2.9056    1.5660 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.2204   -3.2194    2.4823 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0928   -1.4913    2.8978 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9881   -0.5285    3.9797 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3745    2.1677   -0.2032 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9303    2.4058   -2.2224 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1782    3.8203   -1.5140 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3676    4.1240    0.3232 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4963    3.1241   -1.7215 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1946    1.0496   -3.1530 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1858   -1.1685   -1.9369 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.1571   -3.3747   -1.3979 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.4111   -4.1065    0.9742 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6838   -2.6057    2.7325 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7157   -0.4073    2.1932 H   0  0  0  0  0  0  0  0  0  0  0  0
 14 13  1  0
 13 12  1  0
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 10  9  1  0
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  7  6  1  0
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  5  4  1  0
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  3  2  1  0
  2  1  3  0
  3 27  1  0
 27 28  2  0
 28 29  1  0
 29 30  2  0
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 31 32  2  0
  5 25  1  0
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 23 21  1  0
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 10 19  1  0
 19 20  1  0
 19 17  1  0
 17 18  1  0
 17 15  1  0
 15 16  1  0
 15 12  1  0
 21  7  1  0
 32 27  1  0
 14 42  1  0
 13 40  1  0
 13 41  1  0
 12 39  1  1
 10 38  1  6
  8 36  1  0
  8 37  1  0
  7 35  1  6
  5 34  1  1
  3 33  1  1
 28 55  1  0
 29 56  1  0
 30 57  1  0
 31 58  1  0
 32 59  1  0
 25 53  1  6
 26 54  1  0
 23 51  1  6
 24 52  1  0
 21 49  1  1
 22 50  1  0
 19 47  1  1
 20 48  1  0
 17 45  1  6
 18 46  1  0
 15 43  1  6
 16 44  1  0
M  END


  Mrv1652309052201562D          

 32 34  0  0  1  0            999 V2000
   -2.1434    2.8875    0.0000 N   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  2  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
   -1.4289    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434   -0.4125    0.0000 O   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
   -2.8579   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8579   -2.4750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5724   -2.8875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2868   -2.4750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0013   -2.8875    0.0000 C   0  0  2  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
   -6.4302   -2.8875    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0013   -3.7125    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -5.7158   -4.1250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2868   -4.1250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2868   -4.9500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5724   -3.7125    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.8579   -4.1250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289   -1.6500    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.4289   -2.4750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -1.2375    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.0000   -1.6500    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
    0.0000    0.0000    0.0000 O   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
   -2.8579   -0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5724   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2868   -0.0000    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
   -3.5724    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  3  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  6  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  1  1  0  0  0
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 12 15  1  0  0  0  0
 15 16  1  6  0  0  0
 15 17  1  0  0  0  0
 17 18  1  0  0  0  0
 17 19  1  0  0  0  0
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 19 20  1  6  0  0  0
  7 21  1  0  0  0  0
 21 22  1  6  0  0  0
 21 23  1  0  0  0  0
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 23 25  1  0  0  0  0
  5 25  1  0  0  0  0
 25 26  1  0  0  0  0
  3 27  1  0  0  0  0
 27 28  2  0  0  0  0
 28 29  1  0  0  0  0
 29 30  2  0  0  0  0
 30 31  1  0  0  0  0
 31 32  2  0  0  0  0
 27 32  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0204297

> <DATABASE_NAME>
NP-MRD

> <SMILES>
OC[C@H]1OC(OCC2OC(O[C@@H](C#N)C3=CC=CC=C3)C(O)[C@@H](O)[C@@H]2O)[C@H](O)C(O)[C@@H]1O

> <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/t10-,11+,12?,13+,14+,15?,16-,17+,18?,19?,20?/m0/s1

> <INCHI_KEY>
XUCIJNAGGSZNQT-MUXXRXLQSA-N

> <FORMULA>
C20H27NO11

> <MOLECULAR_WEIGHT>
457.432

> <EXACT_MASS>
457.158410693

> <JCHEM_ACCEPTOR_COUNT>
12

> <JCHEM_ATOM_COUNT>
59

> <JCHEM_AVERAGE_POLARIZABILITY>
43.646744599323384

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
7

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

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

> <JCHEM_LOGP>
-2.58788678

> <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>
202.32

> <JCHEM_REFRACTIVITY>
102.50970000000002

> <JCHEM_ROTATABLE_BOND_COUNT>
7

> <JCHEM_RULE_OF_FIVE>
0

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

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 05-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   05-SEP-22         0                                  
HETATM    1  N   UNK     0      -4.001   5.390   0.000  0.00  0.00           N+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  O   UNK     0      -2.667   1.540   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0      -2.667   0.000   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0      -4.001  -0.770   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0      -4.001  -2.310   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -5.335  -3.080   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0      -5.335  -4.620   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0      -6.668  -5.390   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0      -8.002  -4.620   0.000  0.00  0.00           O+0
HETATM   12  C   UNK     0      -9.336  -5.390   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0     -10.669  -4.620   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0     -12.003  -5.390   0.000  0.00  0.00           O+0
HETATM   15  C   UNK     0      -9.336  -6.930   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0     -10.669  -7.700   0.000  0.00  0.00           O+0
HETATM   17  C   UNK     0      -8.002  -7.700   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0      -8.002  -9.240   0.000  0.00  0.00           O+0
HETATM   19  C   UNK     0      -6.668  -6.930   0.000  0.00  0.00           C+0
HETATM   20  O   UNK     0      -5.335  -7.700   0.000  0.00  0.00           O+0
HETATM   21  C   UNK     0      -2.667  -3.080   0.000  0.00  0.00           C+0
HETATM   22  O   UNK     0      -2.667  -4.620   0.000  0.00  0.00           O+0
HETATM   23  C   UNK     0      -1.334  -2.310   0.000  0.00  0.00           C+0
HETATM   24  O   UNK     0       0.000  -3.080   0.000  0.00  0.00           O+0
HETATM   25  C   UNK     0      -1.334  -0.770   0.000  0.00  0.00           C+0
HETATM   26  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   27  C   UNK     0      -5.335   1.540   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0      -5.335  -0.000   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0      -6.668  -0.770   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0      -8.002  -0.000   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0      -8.002   1.540   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0      -6.668   2.310   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4   27                                                  
CONECT    4    3    5                                                       
CONECT    5    4    6   25                                                  
CONECT    6    5    7                                                       
CONECT    7    6    8   21                                                  
CONECT    8    7    9                                                       
CONECT    9    8   10                                                       
CONECT   10    9   11   19                                                  
CONECT   11   10   12                                                       
CONECT   12   11   13   15                                                  
CONECT   13   12   14                                                       
CONECT   14   13                                                            
CONECT   15   12   16   17                                                  
CONECT   16   15                                                            
CONECT   17   15   18   19                                                  
CONECT   18   17                                                            
CONECT   19   17   10   20                                                  
CONECT   20   19                                                            
CONECT   21    7   22   23                                                  
CONECT   22   21                                                            
CONECT   23   21   24   25                                                  
CONECT   24   23                                                            
CONECT   25   23    5   26                                                  
CONECT   26   25                                                            
CONECT   27    3   28   32                                                  
CONECT   28   27   29                                                       
CONECT   29   28   30                                                       
CONECT   30   29   31                                                       
CONECT   31   30   32                                                       
CONECT   32   31   27                                                       
MASTER        0    0    0    0    0    0    0    0   32    0   68    0
END

View in JSmol

Synonyms

Value	Source
Mandelonitrile-beta-gentiobioside	MeSH
Neoamygdalin	MeSH
Amygdaloside	MeSH
Laetrile	MeSH
Mandelonitrile beta gentiobioside	MeSH
Vitamin b17	MeSH

Chemical Formula

C₂₀H₂₇NO₁₁

Average Mass

457.4320 Da

Monoisotopic Mass

457.15841 Da

IUPAC Name

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

Traditional Name

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

CAS Registry Number

Not Available

SMILES

OC[C@H]1OC(OCC2OC(O[C@@H](C#N)C3=CC=CC=C3)C(O)[C@@H](O)[C@@H]2O)[C@H](O)C(O)[C@@H]1O

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/t10-,11+,12?,13+,14+,15?,16-,17+,18?,19?,20?/m0/s1

InChI Key

XUCIJNAGGSZNQT-MUXXRXLQSA-N

Experimental Spectra

Not Available

Predicted Spectra

Spectrum Type	Description	Depositor ID	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹³C NMR Spectrum (1D, 25 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Gerbera jamesonii	LOTUS Database	35616633
Oxyanthus pyriformis	LOTUS Database	35616633
Passiflora edulis	LOTUS Database	35616633
Prunus armeniaca	LOTUS Database	35616633
Prunus cerasus	LOTUS Database	35616633
Prunus persica	LOTUS Database	35616633
Prunus salicina	LOTUS Database	35616633
Prunus spinosa	LOTUS Database	35616633

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
O-glycosyl compound
Disaccharide
Benzenoid
Oxane
Monocyclic benzene moiety
Secondary alcohol
Oxacycle
Organoheterocyclic compound
Polyol
Nitrile
Carbonitrile
Acetal
Organic nitrogen compound
Organopnictogen compound
Hydrocarbon derivative
Primary alcohol
Organonitrogen compound
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	-2.6	ChemAxon
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	43.65 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

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

C00003301

Chemspider ID

78431007

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Amygdalin

METLIN ID

Not Available

PubChem Compound

134694146

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Yang Y, Zhu J, Yao CL, Guo DA, He N, Mei QX, Feng GJ, Chen QH, Yang GY: Determination of six core components from Mahuang Xuanfei Zhike syrup in rat plasma and tissues by UPLC-MS/MS: Application to a pharmacokinetics and tissue distribution study. Biomed Chromatogr. 2022 Dec;36(12):e5496. doi: 10.1002/bmc.5496. Epub 2022 Sep 21. [PubMed:36047933 ]
Permal R, Chia T, Arena G, Fleming C, Chen J, Chen T, Chang WL, Seale B, Hamid N, Kam R: Converting avocado seeds into a ready to eat snack and analysing for persin and amygdalin. Food Chem. 2023 Jan 15;399:134011. doi: 10.1016/j.foodchem.2022.134011. Epub 2022 Aug 25. [PubMed:36044826 ]
Zhou Y, Zhang J, Chen W, Li X, Fu K, Sun W, Liang Y, Xu M, Zhang J, Fan G, Yin H, Wang Z: Identification of Hair Growth Promoting Components in the Kernels of Prunus mira Koehne and Their Mechanism of Action. Molecules. 2022 Aug 17;27(16):5242. doi: 10.3390/molecules27165242. [PubMed:36014482 ]
Fu X, Sun Z, Long Q, Tan W, Ding H, Liu X, Wu L, Wang Y, Zhang W: Glycosides from Buyang Huanwu Decoction inhibit atherosclerotic inflammation via JAK/STAT signaling pathway. Phytomedicine. 2022 Oct;105:154385. doi: 10.1016/j.phymed.2022.154385. Epub 2022 Aug 8. [PubMed:35987015 ]
Ramalingam S, Bahuguna A, Al-Ansari MM, Shanmugam G, Al-Humaid L, Lee JS, Kim M: Whole-genome analysis guided molecular mechanism of cyanogenic glucoside degradation by yeast isolated from Prunus mume fruit syrup. Chemosphere. 2022 Nov;307(Pt 4):136061. doi: 10.1016/j.chemosphere.2022.136061. Epub 2022 Aug 14. [PubMed:35977575 ]
Abdel-Rafei MK, Askar MA, Azab KS, El-Sayyad GS, El Kodous MA, El Fatih NM, Tawill GE, Thabet NM: FA-HA-Amygdalin@Fe(2)O(3) and/or gamma-Rays Affecting SIRT1 Regulation of YAP/TAZ-p53 Signaling and Modulates Tumorigenicity of MDA-MB231 or MCF-7 Cancer Cells. Curr Cancer Drug Targets. 2023;23(2):118-144. doi: 10.2174/1568009622666220816123508. [PubMed:35975846 ]
Iqbal Z, Javad S, Naz S, Shah AA, Shah AN, Paray BA, Gulnaz A, Abdelsalam NR: Elicitation of the in vitro Cultures of Selected Varieties of Vigna radiata L. With Zinc Oxide and Copper Oxide Nanoparticles for Enhanced Phytochemicals Production. Front Plant Sci. 2022 Jul 26;13:908532. doi: 10.3389/fpls.2022.908532. eCollection 2022. [PubMed:35958222 ]
Todorova A, Todorova T: Apricot kernels' extract and amygdalin alter bleomycin-induced Ty1 retrotransposition, mitotic gene conversion in the trp-5 locus and reverse point mutations in ilv1-92 allele in Saccharomyces cerevisiae. Arch Microbiol. 2022 Aug 6;204(9):542. doi: 10.1007/s00203-022-03155-7. [PubMed:35932430 ]
Huang X, Xu J, Gao F, Zhang H, Guo L: Rapid quantitative typing spectra model for distinguishing sweet and bitter apricot kernels. Food Sci Biotechnol. 2022 Jun 23;31(9):1123-1131. doi: 10.1007/s10068-022-01095-y. eCollection 2022 Aug. [PubMed:35919360 ]
Kitic D, Miladinovic B, Randjelovic M, Szopa A, Sharifi-Rad J, Calina D, Seidel V: Anticancer Potential and Other Pharmacological Properties of Prunus armeniaca L.: An Updated Overview. Plants (Basel). 2022 Jul 20;11(14):1885. doi: 10.3390/plants11141885. [PubMed:35890519 ]
LOTUS database [Link]

Showing NP-Card for (2r)-2-phenyl-2-{[(4s,5s)-3,4,5-trihydroxy-6-({[(3r,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}methyl)oxan-2-yl]oxy}acetonitrile (NP0204297)

MOL for NP0204297 ((2r)-2-phenyl-2-{[(4s,5s)-3,4,5-trihydroxy-6-({[(3r,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}methyl)oxan-2-yl]oxy}acetonitrile)

3D MOL for NP0204297 ((2r)-2-phenyl-2-{[(4s,5s)-3,4,5-trihydroxy-6-({[(3r,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}methyl)oxan-2-yl]oxy}acetonitrile)

3D SDF for NP0204297 ((2r)-2-phenyl-2-{[(4s,5s)-3,4,5-trihydroxy-6-({[(3r,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}methyl)oxan-2-yl]oxy}acetonitrile)

3D-SDF for NP0204297 ((2r)-2-phenyl-2-{[(4s,5s)-3,4,5-trihydroxy-6-({[(3r,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}methyl)oxan-2-yl]oxy}acetonitrile)

PDB for NP0204297 ((2r)-2-phenyl-2-{[(4s,5s)-3,4,5-trihydroxy-6-({[(3r,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}methyl)oxan-2-yl]oxy}acetonitrile)

3D PDB for NP0204297 ((2r)-2-phenyl-2-{[(4s,5s)-3,4,5-trihydroxy-6-({[(3r,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}methyl)oxan-2-yl]oxy}acetonitrile)

SMILES for NP0204297 ((2r)-2-phenyl-2-{[(4s,5s)-3,4,5-trihydroxy-6-({[(3r,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}methyl)oxan-2-yl]oxy}acetonitrile)

INCHI for NP0204297 ((2r)-2-phenyl-2-{[(4s,5s)-3,4,5-trihydroxy-6-({[(3r,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}methyl)oxan-2-yl]oxy}acetonitrile)

Structure for NP0204297 ((2r)-2-phenyl-2-{[(4s,5s)-3,4,5-trihydroxy-6-({[(3r,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}methyl)oxan-2-yl]oxy}acetonitrile)

3D Structure for NP0204297 ((2r)-2-phenyl-2-{[(4s,5s)-3,4,5-trihydroxy-6-({[(3r,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}methyl)oxan-2-yl]oxy}acetonitrile)