NP-MRD: Showing NP-Card for 3-{[(2s,3r,4s,5s,6r)-4,5-dihydroxy-6-(hydroxymethyl)-3-{[(2s,3r,4s,5r)-3,4,5-trihydroxyoxan-2-yl]oxy}oxan-2-yl]oxy}-5,7-dihydroxy-2-(3,4,5-trihydroxyphenyl)-1λ⁴-chromen-1-ylium (NP0242582)

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Record Information

Version

2.0

Created at

2022-09-07 02:55:45 UTC

Updated at

2022-09-07 02:55:45 UTC

NP-MRD ID

NP0242582

Secondary Accession Numbers

None

Natural Product Identification

Common Name

3-{[(2s,3r,4s,5s,6r)-4,5-dihydroxy-6-(hydroxymethyl)-3-{[(2s,3r,4s,5r)-3,4,5-trihydroxyoxan-2-yl]oxy}oxan-2-yl]oxy}-5,7-dihydroxy-2-(3,4,5-trihydroxyphenyl)-1λ⁴-chromen-1-ylium

Description

Delphinidin 3-O-beta-D-sambubioside belongs to the class of organic compounds known as anthocyanidin-3-o-glycosides. These are phenolic compounds containing one anthocyanidin moiety which is O-glycosidically linked to a carbohydrate moiety at the C3-position. Thus, delphinidin 3-O-beta-D-sambubioside is considered to be a flavonoid. Delphinidin 3-O-beta-D-sambubioside is a primary metabolite. Primary metabolites are metabolically or physiologically essential metabolites. They are directly involved in an organism’s growth, development or reproduction. 3-{[(2s,3r,4s,5s,6r)-4,5-dihydroxy-6-(hydroxymethyl)-3-{[(2s,3r,4s,5r)-3,4,5-trihydroxyoxan-2-yl]oxy}oxan-2-yl]oxy}-5,7-dihydroxy-2-(3,4,5-trihydroxyphenyl)-1λ⁴-chromen-1-ylium is found in Vaccinium padifolium. Based on a literature review very few articles have been published on delphinidin 3-O-beta-D-sambubioside.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309072204552D          

 42 46  0  0  1  0            999 V2000
    2.1434    2.0625    0.0000 O   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
    0.7145    2.0625    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.7145    1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 C   0  0  1  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
    0.7145   -0.4125    0.0000 C   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 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
    2.8579    0.8250    0.0000 O   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
    3.5724   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868   -1.6500    0.0000 O   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
    2.1434   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -1.6500    0.0000 O   0  3  0  0  0  0  0  0  0  0  0  0
    0.7145   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -2.8875    0.0000 C   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
   -1.4289   -2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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   -2.1434   -1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
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   -1.4289    0.8250    0.0000 O   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
   -2.1434    2.0625    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
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   -3.5724    2.0625    0.0000 C   0  0  1  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
   -3.5724    1.2375    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -4.2868    0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8579    0.8250    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.8579    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    2.0625    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
    0.0000    2.4750    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.0000    3.3000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  3  2  1  1  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  1  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  2  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
 10 12  2  0  0  0  0
 12 13  1  0  0  0  0
 13 14  1  0  0  0  0
 13 15  2  0  0  0  0
 15 16  1  0  0  0  0
  9 16  1  0  0  0  0
 16 17  2  0  0  0  0
 17 18  1  0  0  0  0
  7 18  2  0  0  0  0
 18 19  1  0  0  0  0
 19 20  2  0  0  0  0
 20 21  1  0  0  0  0
 21 22  1  0  0  0  0
 21 23  2  0  0  0  0
 23 24  1  0  0  0  0
 23 25  1  0  0  0  0
 25 26  1  0  0  0  0
 25 27  2  0  0  0  0
 19 27  1  0  0  0  0
  5 28  1  0  0  0  0
 28 29  1  6  0  0  0
 30 29  1  1  0  0  0
 30 31  1  0  0  0  0
 31 32  1  0  0  0  0
 32 33  1  0  0  0  0
 33 34  1  6  0  0  0
 33 35  1  0  0  0  0
 35 36  1  1  0  0  0
 35 37  1  0  0  0  0
 30 37  1  0  0  0  0
 37 38  1  6  0  0  0
 28 39  1  0  0  0  0
 39 40  1  1  0  0  0
 39 41  1  0  0  0  0
  3 41  1  0  0  0  0
 41 42  1  6  0  0  0
M  CHG  1  17   1
M  END

     RDKit          3D

 71 75  0  0  0  0  0  0  0  0999 V2000
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    1.7813   -4.3383    2.3201 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8509   -3.0212    1.6266 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.6042   -2.5538    1.2813 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.6063   -1.4880    0.4114 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.5466   -0.7432    0.6425 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6709   -0.5136   -0.0518 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8497   -1.1088   -1.3178 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9999   -0.8508   -1.9878 C   0  0  0  0  0  0  0  0  0  0  0  0
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   -5.1022    0.2212   -2.1137 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9409   -0.0267   -1.4148 C   0  0  0  0  0  0  0  0  0  0  0  0
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   -3.7006    2.4534    3.3157 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8113    3.2512    3.6208 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6615    2.3469    4.2095 C   0  0  0  0  0  0  0  0  0  0  0  0
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   -1.5770    1.5562    3.8898 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5136    1.4286    4.7706 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5303    0.8663    2.6673 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8509   -0.6606    0.3802 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.4214   -0.6834   -0.9084 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.3773    0.5108   -1.5657 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.6412    0.3798   -2.7426 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9928    1.2869   -3.7108 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5811    2.5620   -3.1799 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.6356    3.3272   -2.5199 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.8319    2.3280   -2.3657 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.9951    2.5336   -3.1035 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.8119    0.8671   -1.9570 C   0  0  1  0  0  0  0  0  0  0  0  0
    4.7296    0.5578   -0.9757 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8525   -0.8668    1.4485 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.1682    0.3022    2.1479 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4737   -1.9215    2.4626 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.6059   -2.3576    3.1453 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7107   -5.2744    0.5972 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2996   -4.3350    3.2965 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8375   -4.7222    2.4276 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4287   -3.1691    0.6828 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5041   -1.9477   -0.5941 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0605   -1.7497   -1.7047 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4024   -2.5457   -3.5025 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5412   -1.5999   -4.8865 H   0  0  0  0  0  0  0  0  0  0  0  0
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   -0.5364    1.9184    5.6504 H   0  0  0  0  0  0  0  0  0  0  0  0
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    1.5030    0.4148    0.4883 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9047    1.3340   -1.0014 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6327    0.8656   -4.5212 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0369    1.5847   -4.2346 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8995    3.1636   -4.0785 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0275    4.2157   -2.3033 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8264    2.9533   -1.4363 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.6380    2.9838   -2.4992 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.0780    0.2553   -2.8566 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.9803   -0.3913   -1.0777 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8406   -1.2289    1.0260 H   0  0  0  0  0  0  0  0  0  0  0  0
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    1.7557   -1.5561    3.2150 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4299   -3.1877    3.6360 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7 18  1  0
 18 17  2  0
 17 16  1  0
 16 15  2  0
 15 13  1  0
 13 14  1  0
 13 12  2  0
 12 10  1  0
 10 11  1  0
 10  9  2  0
  9  8  1  0
 18 19  1  0
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 21 23  2  0
 23 24  1  0
 23 25  1  0
 25 26  1  0
 25 27  2  0
  5 28  1  0
 28 29  1  0
 29 30  1  0
 30 31  1  0
 31 32  1  0
 32 33  1  0
 33 34  1  0
 33 35  1  0
 35 36  1  0
 35 37  1  0
 37 38  1  0
 28 39  1  0
 39 40  1  0
 39 41  1  0
 41 42  1  0
 41  3  1  0
  8  7  2  0
 27 19  1  0
 37 30  1  0
  9 16  1  0
  1 43  1  0
  2 44  1  0
  2 45  1  0
  3 46  1  6
  5 47  1  6
 15 52  1  0
 14 51  1  0
 12 50  1  0
 11 49  1  0
  8 48  1  0
 20 53  1  0
 22 54  1  0
 24 55  1  0
 26 56  1  0
 27 57  1  0
 28 58  1  1
 30 59  1  1
 32 60  1  0
 32 61  1  0
 33 62  1  6
 34 63  1  0
 35 64  1  1
 36 65  1  0
 37 66  1  6
 38 67  1  0
 39 68  1  6
 40 69  1  0
 41 70  1  1
 42 71  1  0
M  CHG  1  17   1
M  END


  Mrv1652309072204552D          

 42 46  0  0  1  0            999 V2000
    2.1434    2.0625    0.0000 O   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
    0.7145    2.0625    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.7145    1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 C   0  0  1  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
    0.7145   -0.4125    0.0000 C   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 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
    2.8579    0.8250    0.0000 O   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
    3.5724   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868   -1.6500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
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    1.4289   -1.6500    0.0000 O   0  3  0  0  0  0  0  0  0  0  0  0
    0.7145   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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   -1.4289    0.8250    0.0000 O   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
   -2.1434    2.0625    0.0000 O   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
   -3.5724    2.0625    0.0000 C   0  0  1  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
   -3.5724    1.2375    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -4.2868    0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8579    0.8250    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.8579    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    2.0625    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
    0.0000    2.4750    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.0000    3.3000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  3  2  1  1  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  1  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  2  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
 10 12  2  0  0  0  0
 12 13  1  0  0  0  0
 13 14  1  0  0  0  0
 13 15  2  0  0  0  0
 15 16  1  0  0  0  0
  9 16  1  0  0  0  0
 16 17  2  0  0  0  0
 17 18  1  0  0  0  0
  7 18  2  0  0  0  0
 18 19  1  0  0  0  0
 19 20  2  0  0  0  0
 20 21  1  0  0  0  0
 21 22  1  0  0  0  0
 21 23  2  0  0  0  0
 23 24  1  0  0  0  0
 23 25  1  0  0  0  0
 25 26  1  0  0  0  0
 25 27  2  0  0  0  0
 19 27  1  0  0  0  0
  5 28  1  0  0  0  0
 28 29  1  6  0  0  0
 30 29  1  1  0  0  0
 30 31  1  0  0  0  0
 31 32  1  0  0  0  0
 32 33  1  0  0  0  0
 33 34  1  6  0  0  0
 33 35  1  0  0  0  0
 35 36  1  1  0  0  0
 35 37  1  0  0  0  0
 30 37  1  0  0  0  0
 37 38  1  6  0  0  0
 28 39  1  0  0  0  0
 39 40  1  1  0  0  0
 39 41  1  0  0  0  0
  3 41  1  0  0  0  0
 41 42  1  6  0  0  0
M  CHG  1  17   1
M  END
> <DATABASE_ID>
NP0242582

> <DATABASE_NAME>
NP-MRD

> <SMILES>
OC[C@H]1O[C@@H](OC2=C([O+]=C3C=C(O)C=C(O)C3=C2)C2=CC(O)=C(O)C(O)=C2)[C@H](O[C@@H]2OC[C@@H](O)[C@H](O)[C@H]2O)[C@@H](O)[C@@H]1O

> <INCHI_IDENTIFIER>
InChI=1S/C26H28O16/c27-6-17-20(35)21(36)24(42-25-22(37)19(34)14(32)7-38-25)26(41-17)40-16-5-10-11(29)3-9(28)4-15(10)39-23(16)8-1-12(30)18(33)13(31)2-8/h1-5,14,17,19-22,24-27,32,34-37H,6-7H2,(H4-,28,29,30,31,33)/p+1/t14-,17-,19+,20-,21+,22-,24-,25+,26-/m1/s1

> <INCHI_KEY>
TWYYVOVDSNRIJM-AFAGGVQESA-O

> <FORMULA>
C26H29O16

> <MOLECULAR_WEIGHT>
597.501

> <EXACT_MASS>
597.145011274

> <JCHEM_ACCEPTOR_COUNT>
16

> <JCHEM_ATOM_COUNT>
71

> <JCHEM_AVERAGE_POLARIZABILITY>
55.55973303080417

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
11

> <JCHEM_FORMAL_CHARGE>
1

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
3-{[(2S,3R,4S,5S,6R)-4,5-dihydroxy-6-(hydroxymethyl)-3-{[(2S,3R,4S,5R)-3,4,5-trihydroxyoxan-2-yl]oxy}oxan-2-yl]oxy}-5,7-dihydroxy-2-(3,4,5-trihydroxyphenyl)-1lambda4-chromen-1-ylium

> <JCHEM_LOGP>
-1.3416000000000003

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
7.293529135205347

> <JCHEM_PKA_STRONGEST_ACIDIC>
6.366606855198211

> <JCHEM_PKA_STRONGEST_BASIC>
-3.6726879805135386

> <JCHEM_POLAR_SURFACE_AREA>
272.5899999999999

> <JCHEM_REFRACTIVITY>
144.68920000000003

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
3-{[(2S,3R,4S,5S,6R)-4,5-dihydroxy-6-(hydroxymethyl)-3-{[(2S,3R,4S,5R)-3,4,5-trihydroxyoxan-2-yl]oxy}oxan-2-yl]oxy}-5,7-dihydroxy-2-(3,4,5-trihydroxyphenyl)-1lambda4-chromen-1-ylium

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 07-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   07-SEP-22         0                                  
HETATM    1  O   UNK     0       4.001   3.850   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0       2.667   4.620   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       1.334   3.850   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0       1.334   2.310   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       2.667   0.000   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       4.001  -0.770   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       5.335   0.000   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0       5.335   1.540   0.000  0.00  0.00           O+0
HETATM   12  C   UNK     0       6.668  -0.770   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       6.668  -2.310   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0       8.002  -3.080   0.000  0.00  0.00           O+0
HETATM   15  C   UNK     0       5.335  -3.080   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       4.001  -2.310   0.000  0.00  0.00           C+0
HETATM   17  O   UNK     0       2.667  -3.080   0.000  0.00  0.00           O+1
HETATM   18  C   UNK     0       1.334  -2.310   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       0.000  -3.080   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       0.000  -4.620   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      -1.334  -5.390   0.000  0.00  0.00           C+0
HETATM   22  O   UNK     0      -1.334  -6.930   0.000  0.00  0.00           O+0
HETATM   23  C   UNK     0      -2.667  -4.620   0.000  0.00  0.00           C+0
HETATM   24  O   UNK     0      -4.001  -5.390   0.000  0.00  0.00           O+0
HETATM   25  C   UNK     0      -2.667  -3.080   0.000  0.00  0.00           C+0
HETATM   26  O   UNK     0      -4.001  -2.310   0.000  0.00  0.00           O+0
HETATM   27  C   UNK     0      -1.334  -2.310   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0      -1.334   2.310   0.000  0.00  0.00           C+0
HETATM   29  O   UNK     0      -2.667   1.540   0.000  0.00  0.00           O+0
HETATM   30  C   UNK     0      -4.001   2.310   0.000  0.00  0.00           C+0
HETATM   31  O   UNK     0      -4.001   3.850   0.000  0.00  0.00           O+0
HETATM   32  C   UNK     0      -5.335   4.620   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0      -6.668   3.850   0.000  0.00  0.00           C+0
HETATM   34  O   UNK     0      -8.002   4.620   0.000  0.00  0.00           O+0
HETATM   35  C   UNK     0      -6.668   2.310   0.000  0.00  0.00           C+0
HETATM   36  O   UNK     0      -8.002   1.540   0.000  0.00  0.00           O+0
HETATM   37  C   UNK     0      -5.335   1.540   0.000  0.00  0.00           C+0
HETATM   38  O   UNK     0      -5.335   0.000   0.000  0.00  0.00           O+0
HETATM   39  C   UNK     0      -1.334   3.850   0.000  0.00  0.00           C+0
HETATM   40  O   UNK     0      -2.667   4.620   0.000  0.00  0.00           O+0
HETATM   41  C   UNK     0       0.000   4.620   0.000  0.00  0.00           C+0
HETATM   42  O   UNK     0      -0.000   6.160   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4   41                                                  
CONECT    4    3    5                                                       
CONECT    5    4    6   28                                                  
CONECT    6    5    7                                                       
CONECT    7    6    8   18                                                  
CONECT    8    7    9                                                       
CONECT    9    8   10   16                                                  
CONECT   10    9   11   12                                                  
CONECT   11   10                                                            
CONECT   12   10   13                                                       
CONECT   13   12   14   15                                                  
CONECT   14   13                                                            
CONECT   15   13   16                                                       
CONECT   16   15    9   17                                                  
CONECT   17   16   18                                                       
CONECT   18   17    7   19                                                  
CONECT   19   18   20   27                                                  
CONECT   20   19   21                                                       
CONECT   21   20   22   23                                                  
CONECT   22   21                                                            
CONECT   23   21   24   25                                                  
CONECT   24   23                                                            
CONECT   25   23   26   27                                                  
CONECT   26   25                                                            
CONECT   27   25   19                                                       
CONECT   28    5   29   39                                                  
CONECT   29   28   30                                                       
CONECT   30   29   31   37                                                  
CONECT   31   30   32                                                       
CONECT   32   31   33                                                       
CONECT   33   32   34   35                                                  
CONECT   34   33                                                            
CONECT   35   33   36   37                                                  
CONECT   36   35                                                            
CONECT   37   35   30   38                                                  
CONECT   38   37                                                            
CONECT   39   28   40   41                                                  
CONECT   40   39                                                            
CONECT   41   39    3   42                                                  
CONECT   42   41                                                            
MASTER        0    0    0    0    0    0    0    0   42    0   92    0
END

View in JSmol

Synonyms

Value	Source
Delphinidin 3-sambubioside	ChEBI
Delphinidin 3-O-b-D-sambubioside	Generator
Delphinidin 3-O-β-D-sambubioside	Generator

Chemical Formula

C₂₆H₂₉O₁₆

Average Mass

597.5010 Da

Monoisotopic Mass

597.14501 Da

IUPAC Name

3-{[(2S,3R,4S,5S,6R)-4,5-dihydroxy-6-(hydroxymethyl)-3-{[(2S,3R,4S,5R)-3,4,5-trihydroxyoxan-2-yl]oxy}oxan-2-yl]oxy}-5,7-dihydroxy-2-(3,4,5-trihydroxyphenyl)-1lambda4-chromen-1-ylium

Traditional Name

3-{[(2S,3R,4S,5S,6R)-4,5-dihydroxy-6-(hydroxymethyl)-3-{[(2S,3R,4S,5R)-3,4,5-trihydroxyoxan-2-yl]oxy}oxan-2-yl]oxy}-5,7-dihydroxy-2-(3,4,5-trihydroxyphenyl)-1lambda4-chromen-1-ylium

CAS Registry Number

Not Available

SMILES

OC[C@H]1O[C@@H](OC2=C([O+]=C3C=C(O)C=C(O)C3=C2)C2=CC(O)=C(O)C(O)=C2)[C@H](O[C@@H]2OC[C@@H](O)[C@H](O)[C@H]2O)[C@@H](O)[C@@H]1O

InChI Identifier

InChI=1S/C26H28O16/c27-6-17-20(35)21(36)24(42-25-22(37)19(34)14(32)7-38-25)26(41-17)40-16-5-10-11(29)3-9(28)4-15(10)39-23(16)8-1-12(30)18(33)13(31)2-8/h1-5,14,17,19-22,24-27,32,34-37H,6-7H2,(H4-,28,29,30,31,33)/p+1/t14-,17-,19+,20-,21+,22-,24-,25+,26-/m1/s1

InChI Key

TWYYVOVDSNRIJM-AFAGGVQESA-O

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
Vaccinium padifolium	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as anthocyanidin-3-o-glycosides. These are phenolic compounds containing one anthocyanidin moiety which is O-glycosidically linked to a carbohydrate moiety at the C3-position.

Kingdom

Organic compounds

Super Class

Phenylpropanoids and polyketides

Class

Flavonoids

Sub Class

Flavonoid glycosides

Direct Parent

Anthocyanidin-3-O-glycosides

Alternative Parents

Substituents

Anthocyanidin-3-o-glycoside
Flavonoid-3-o-glycoside
5-hydroxyflavonoid
7-hydroxyflavonoid
4'-hydroxyflavonoid
3'-hydroxyflavonoid
Hydroxyflavonoid
Anthocyanidin
Disaccharide
Glycosyl compound
O-glycosyl compound
Benzopyran
1-benzopyran
Benzenetriol
Pyrogallol derivative
1-hydroxy-4-unsubstituted benzenoid
1-hydroxy-2-unsubstituted benzenoid
Phenol
Benzenoid
Monocyclic benzene moiety
Oxane
Heteroaromatic compound
Secondary alcohol
Polyol
Organoheterocyclic compound
Oxacycle
Acetal
Primary alcohol
Hydrocarbon derivative
Organic oxygen compound
Alcohol
Organooxygen compound
Organic cation
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

anthocyanidin 3-O-beta-D-sambubioside (CHEBI:74810 )

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	ChemAxon
pKa (Strongest Acidic)	6.37	ChemAxon
pKa (Strongest Basic)	-3.7	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	16	ChemAxon
Hydrogen Donor Count	11	ChemAxon
Polar Surface Area	272.59 Å²	ChemAxon
Rotatable Bond Count	6	ChemAxon
Refractivity	144.69 m³·mol⁻¹	ChemAxon
Polarizability	55.56 Å³	ChemAxon
Number of Rings	5	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

C00006704

Chemspider ID

8372337

KEGG Compound ID

C20491

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

10196837

PDB ID

Not Available

ChEBI ID

74810

Good Scents ID

rw1701161

References

General References

LOTUS database [Link]

Showing NP-Card for 3-{[(2s,3r,4s,5s,6r)-4,5-dihydroxy-6-(hydroxymethyl)-3-{[(2s,3r,4s,5r)-3,4,5-trihydroxyoxan-2-yl]oxy}oxan-2-yl]oxy}-5,7-dihydroxy-2-(3,4,5-trihydroxyphenyl)-1λ⁴-chromen-1-ylium (NP0242582)

MOL for NP0242582 (3-{[(2s,3r,4s,5s,6r)-4,5-dihydroxy-6-(hydroxymethyl)-3-{[(2s,3r,4s,5r)-3,4,5-trihydroxyoxan-2-yl]oxy}oxan-2-yl]oxy}-5,7-dihydroxy-2-(3,4,5-trihydroxyphenyl)-1λ⁴-chromen-1-ylium)

3D MOL for NP0242582 (3-{[(2s,3r,4s,5s,6r)-4,5-dihydroxy-6-(hydroxymethyl)-3-{[(2s,3r,4s,5r)-3,4,5-trihydroxyoxan-2-yl]oxy}oxan-2-yl]oxy}-5,7-dihydroxy-2-(3,4,5-trihydroxyphenyl)-1λ⁴-chromen-1-ylium)

3D SDF for NP0242582 (3-{[(2s,3r,4s,5s,6r)-4,5-dihydroxy-6-(hydroxymethyl)-3-{[(2s,3r,4s,5r)-3,4,5-trihydroxyoxan-2-yl]oxy}oxan-2-yl]oxy}-5,7-dihydroxy-2-(3,4,5-trihydroxyphenyl)-1λ⁴-chromen-1-ylium)

3D-SDF for NP0242582 (3-{[(2s,3r,4s,5s,6r)-4,5-dihydroxy-6-(hydroxymethyl)-3-{[(2s,3r,4s,5r)-3,4,5-trihydroxyoxan-2-yl]oxy}oxan-2-yl]oxy}-5,7-dihydroxy-2-(3,4,5-trihydroxyphenyl)-1λ⁴-chromen-1-ylium)

PDB for NP0242582 (3-{[(2s,3r,4s,5s,6r)-4,5-dihydroxy-6-(hydroxymethyl)-3-{[(2s,3r,4s,5r)-3,4,5-trihydroxyoxan-2-yl]oxy}oxan-2-yl]oxy}-5,7-dihydroxy-2-(3,4,5-trihydroxyphenyl)-1λ⁴-chromen-1-ylium)

3D PDB for NP0242582 (3-{[(2s,3r,4s,5s,6r)-4,5-dihydroxy-6-(hydroxymethyl)-3-{[(2s,3r,4s,5r)-3,4,5-trihydroxyoxan-2-yl]oxy}oxan-2-yl]oxy}-5,7-dihydroxy-2-(3,4,5-trihydroxyphenyl)-1λ⁴-chromen-1-ylium)

SMILES for NP0242582 (3-{[(2s,3r,4s,5s,6r)-4,5-dihydroxy-6-(hydroxymethyl)-3-{[(2s,3r,4s,5r)-3,4,5-trihydroxyoxan-2-yl]oxy}oxan-2-yl]oxy}-5,7-dihydroxy-2-(3,4,5-trihydroxyphenyl)-1λ⁴-chromen-1-ylium)

INCHI for NP0242582 (3-{[(2s,3r,4s,5s,6r)-4,5-dihydroxy-6-(hydroxymethyl)-3-{[(2s,3r,4s,5r)-3,4,5-trihydroxyoxan-2-yl]oxy}oxan-2-yl]oxy}-5,7-dihydroxy-2-(3,4,5-trihydroxyphenyl)-1λ⁴-chromen-1-ylium)

Structure for NP0242582 (3-{[(2s,3r,4s,5s,6r)-4,5-dihydroxy-6-(hydroxymethyl)-3-{[(2s,3r,4s,5r)-3,4,5-trihydroxyoxan-2-yl]oxy}oxan-2-yl]oxy}-5,7-dihydroxy-2-(3,4,5-trihydroxyphenyl)-1λ⁴-chromen-1-ylium)

3D Structure for NP0242582 (3-{[(2s,3r,4s,5s,6r)-4,5-dihydroxy-6-(hydroxymethyl)-3-{[(2s,3r,4s,5r)-3,4,5-trihydroxyoxan-2-yl]oxy}oxan-2-yl]oxy}-5,7-dihydroxy-2-(3,4,5-trihydroxyphenyl)-1λ⁴-chromen-1-ylium)