NP-MRD: Showing NP-Card for Loganin (NP0051775)

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Record Information

Version

2.0

Created at

2022-04-27 23:00:51 UTC

Updated at

2022-04-27 23:00:51 UTC

NP-MRD ID

NP0051775

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Loganin

Description

Loganin, also known as loganoside, belongs to the class of organic compounds known as iridoid o-glycosides. These are iridoid monoterpenes containing a glycosyl (usually a pyranosyl) moiety linked to the iridoid skeleton. Thus, loganin is considered to be an isoprenoid lipid molecule. Loganin is found in Adina racemosa, Apis cerana, Arabidopsis thaliana, Avicennia marina, Calycophyllum spruceanum , Catharanthus roseus , Centaurium erythraea , Cephalanthus occidentalis, Cerbera manghas, Cinchona calisaya, Coelospermum balansanum, Cornus controversa , Cornus officinalis , Desfontainia spinosa, Diplopanax stachyanthus, Dipsacus asper, Dipsacus asperoides , Dipsacus inermis, Dipsacus laciniatus, Tabernaemontana divaricata, Eucnide bartonioides, Fouquieria columnaris, Gentiana depressa, Gentiana loureirii, Gentiana pedicellata, Gentiana pyrenaica, Gentiana straminea , Gentiana verna, Guettarda platypoda, Hydrangea macrophylla, Jasminum grandiflorum , Jasminum nervosum, Jasminum hemsleyi Yamamoto, Jasminum officinale , Phlomoides rotata, Lippia graveolens , Lippia origanoides, Loasa acerifolia, Loasa tricolor, Lonicera angustifolia, Lonicera caerulea, Lonicera japonica Thunb. , Lonicera periclymenum, Lonicera quinquelocularis, Menyanthes trifoliata , Neonauclea sessilifolia , Nyctanthes arbor-tristis L. , Ophiorrhiza kuroiwae, Ophiorrhiza liukiuensis, Osmanthus austrocaledonicus (Vieill.) Knobl., Patrinia villosa, Penstemon barbatus, Penstemon serrulatus, Picconia excelsa, Picconia excelsa (Aiton) DC., Pileostegia viburnoides var. glabrescens, Pterocephalus perennis, Rauvolfia grandiflora, Rauvolfia serpentina, Rehmannia glutinosa , Scabiosa japonica, Scaevola floribunda, Scaevola montana, Sertia mussotii, Simira rubescens, Sinoadina Racemosa, Strychnos axillaris, Strychnos ignatii , Strychnos lucida, Strychnos nux-vomica, Strychnos nux-vomica , Strychnos spinosa , Timonius timon and Weigela coraeensis. Loganin was first documented in 2009 (PMID: 19666019). Loganin is a very hydrophobic molecule, practically insoluble (in water), and relatively neutral (PMID: 22931211) (PMID: 25778782) (PMID: 26231452) (PMID: 26287995) (PMID: 26407655) (PMID: 26591537).

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv0541 09041214192D          

 37 39  0  0  0  0            999 V2000
    1.5249   -1.0396    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9934    3.3000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7798    1.0799    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7079   -3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9934    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7798   -0.2549    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.5645    0.8250    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.2789    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2949    0.4125    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    4.7079   -2.8875    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.5645    0.0000    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    5.4223   -2.4750    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    5.4223   -1.6500    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    4.7079   -1.2375    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.2789    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2789   -0.4125    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.9934   -1.6500    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    5.4223   -4.1250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.4699    0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.1368   -2.8875    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.1368   -1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.7079   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.5645    2.4750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.9934    2.4750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.9934    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.9934   -2.4750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.2789   -1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9650   -0.3840    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4782    1.6455    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
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    5.5203   -3.0308    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7640   -0.8005    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.7045   -3.2502    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.1368   -2.0625    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.4223   -0.8250    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
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    3.9934   -0.8250    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  6  1  1  1  0  0  0
  7  3  1  0  0  0  0
  8  5  2  0  0  0  0
  8  7  1  0  0  0  0
  9  3  1  0  0  0  0
  9  6  1  0  0  0  0
 10  4  1  1  0  0  0
 11  6  1  0  0  0  0
 11  7  1  0  0  0  0
 12 10  1  0  0  0  0
 13 12  1  0  0  0  0
 14 13  1  0  0  0  0
 15  8  1  0  0  0  0
 16 11  1  0  0  0  0
 17 14  1  0  0  0  0
 18  4  1  0  0  0  0
  9 19  1  1  0  0  0
 12 20  1  6  0  0  0
 13 21  1  1  0  0  0
 14 22  1  6  0  0  0
 23 15  2  0  0  0  0
 24  2  1  0  0  0  0
 24 15  1  0  0  0  0
 25  5  1  0  0  0  0
 25 16  1  0  0  0  0
 26 10  1  0  0  0  0
 26 17  1  0  0  0  0
 16 27  1  1  0  0  0
 17 27  1  1  0  0  0
  6 28  1  6  0  0  0
  7 29  1  1  0  0  0
  9 30  1  6  0  0  0
 10 31  1  6  0  0  0
 11 32  1  1  0  0  0
 12 33  1  1  0  0  0
 13 34  1  6  0  0  0
 14 35  1  1  0  0  0
 16 36  1  6  0  0  0
 17 37  1  6  0  0  0
M  END

     RDKit          3D

 53 55  0  0  0  0  0  0  0  0999 V2000
    6.6698    0.8846    0.9238 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3277    0.8006    0.4763 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.2969    1.2397    1.3176 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6049    1.6978    2.4532 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8961    1.1899    0.9393 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9964    1.6285    1.8022 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6663    1.5690    1.4119 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.2667    0.4026    0.6907 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.0703    0.6347    0.3382 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9431   -0.2507    0.9691 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.6289   -1.0581    0.0751 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8920   -0.6260   -0.2263 C   0  0  2  0  0  0  0  0  0  0  0  0
   -4.2722   -1.2658   -1.5579 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5299   -0.9065   -1.9722 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9391    0.8809   -0.3075 C   0  0  1  0  0  0  0  0  0  0  0  0
   -5.1394    1.3704   -0.7510 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7511    1.3900    1.1252 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.3224    2.6925    1.0875 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8737    0.4704    1.9195 C   0  0  1  0  0  0  0  0  0  0  0  0
   -3.5982   -0.4767    2.6186 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1470    0.1106   -0.4708 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.5370    0.6525   -0.3931 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.4802   -0.4821   -0.7180 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5769   -1.4692   -1.4242 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.3408   -0.9660   -2.7036 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3237   -1.4121   -0.5766 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.1488   -2.0497   -1.2833 C   0  0  0  0  0  0  0  0  0  0  0  0
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    6.6803    1.1106    2.0104 H   0  0  0  0  0  0  0  0  0  0  0  0
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    2.3106    2.0199    2.7827 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2806   -0.4505    1.3981 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3179   -0.9204    1.5979 H   0  0  0  0  0  0  0  0  0  0  0  0
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   -4.3014   -2.3735   -1.3485 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4883   -1.1293   -2.3135 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.2496   -1.4646   -1.5652 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0719    1.1899   -0.9380 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0845    1.9791   -1.5151 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7643    1.3678    1.5892 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4028    2.7395    0.6943 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2308    1.0074    2.6484 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1961   -1.3809    2.5651 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6355    0.4048   -1.4276 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6504    1.4144   -1.2040 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8193   -0.9645    0.2119 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.3131   -0.1490   -1.3764 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0163   -2.4896   -1.4456 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2096   -0.6750   -3.1123 H   0  0  0  0  0  0  0  0  0  0  0  0
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   -0.3948   -2.6907   -0.5850 H   0  0  0  0  0  0  0  0  0  0  0  0
 24 25  1  0
 24 23  1  0
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 22  5  1  0
  5  6  2  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  9 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  1  0
 13 14  1  0
 12 15  1  0
 15 16  1  0
 15 17  1  0
 17 18  1  0
 17 19  1  0
 19 20  1  0
  8 21  1  0
 21 26  1  0
 26 27  1  0
  5  3  1  0
  3  4  2  0
  3  2  1  0
  2  1  1  0
 26 24  1  0
 21 22  1  0
 19 10  1  0
 24 48  1  6
 25 49  1  0
 23 46  1  0
 23 47  1  0
 22 45  1  6
  6 31  1  0
  8 32  1  1
 10 33  1  1
 12 34  1  1
 13 35  1  0
 13 36  1  0
 14 37  1  0
 15 38  1  6
 16 39  1  0
 17 40  1  1
 18 41  1  0
 19 42  1  1
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 21 44  1  6
 26 50  1  1
 27 51  1  0
 27 52  1  0
 27 53  1  0
  1 28  1  0
  1 29  1  0
  1 30  1  0
M  END


  Mrv0541 09041214192D          

 37 39  0  0  0  0            999 V2000
    1.5249   -1.0396    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9934    3.3000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7798    1.0799    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7079   -3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9934    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7798   -0.2549    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.5645    0.8250    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.2789    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2949    0.4125    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    4.7079   -2.8875    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.5645    0.0000    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    5.4223   -2.4750    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    5.4223   -1.6500    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    4.7079   -1.2375    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.2789    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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    3.9934   -1.6500    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    5.4223   -4.1250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.4699    0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.1368   -2.8875    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
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    4.7079   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.5645    2.4750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.9934    2.4750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.9934    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
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    3.2789   -1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9650   -0.3840    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4782    1.6455    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9204    1.1476    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.5203   -3.0308    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7640   -0.8005    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.7045   -3.2502    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.1368   -2.0625    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.4223   -0.8250    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9968   -1.1877    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9934   -0.8250    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  6  1  1  1  0  0  0
  7  3  1  0  0  0  0
  8  5  2  0  0  0  0
  8  7  1  0  0  0  0
  9  3  1  0  0  0  0
  9  6  1  0  0  0  0
 10  4  1  1  0  0  0
 11  6  1  0  0  0  0
 11  7  1  0  0  0  0
 12 10  1  0  0  0  0
 13 12  1  0  0  0  0
 14 13  1  0  0  0  0
 15  8  1  0  0  0  0
 16 11  1  0  0  0  0
 17 14  1  0  0  0  0
 18  4  1  0  0  0  0
  9 19  1  1  0  0  0
 12 20  1  6  0  0  0
 13 21  1  1  0  0  0
 14 22  1  6  0  0  0
 23 15  2  0  0  0  0
 24  2  1  0  0  0  0
 24 15  1  0  0  0  0
 25  5  1  0  0  0  0
 25 16  1  0  0  0  0
 26 10  1  0  0  0  0
 26 17  1  0  0  0  0
 16 27  1  1  0  0  0
 17 27  1  1  0  0  0
  6 28  1  6  0  0  0
  7 29  1  1  0  0  0
  9 30  1  6  0  0  0
 10 31  1  6  0  0  0
 11 32  1  1  0  0  0
 12 33  1  1  0  0  0
 13 34  1  6  0  0  0
 14 35  1  1  0  0  0
 16 36  1  6  0  0  0
 17 37  1  6  0  0  0
M  END
> <DATABASE_ID>
NP0051775

> <DATABASE_NAME>
NP-MRD

> <SMILES>
[H][C@]1(O)C[C@]2([H])C(=CO[C@@]([H])(O[C@]3([H])O[C@]([H])(CO)[C@@]([H])(O)[C@]([H])(O)[C@@]3([H])O)[C@]2([H])[C@@]1([H])C)C(=O)OC

> <INCHI_IDENTIFIER>
InChI=1S/C17H26O10/c1-6-9(19)3-7-8(15(23)24-2)5-25-16(11(6)7)27-17-14(22)13(21)12(20)10(4-18)26-17/h5-7,9-14,16-22H,3-4H2,1-2H3/t6-,7+,9-,10+,11+,12+,13-,14+,16-,17-/m0/s1

> <INCHI_KEY>
AMBQHHVBBHTQBF-UOUCRYGSSA-N

> <FORMULA>
C17H26O10

> <MOLECULAR_WEIGHT>
390.3823

> <EXACT_MASS>
390.152597052

> <JCHEM_ACCEPTOR_COUNT>
9

> <JCHEM_AVERAGE_POLARIZABILITY>
38.23258568219819

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
methyl (1S,4aS,6S,7R,7aS)-6-hydroxy-7-methyl-1-{[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-1H,4aH,5H,6H,7H,7aH-cyclopenta[c]pyran-4-carboxylate

> <ALOGPS_LOGP>
-1.50

> <JCHEM_LOGP>
-1.8371454643333336

> <ALOGPS_LOGS>
-1.17

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
13.191381843920968

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.206190359688502

> <JCHEM_PKA_STRONGEST_BASIC>
-2.8340463100910975

> <JCHEM_POLAR_SURFACE_AREA>
155.14

> <JCHEM_REFRACTIVITY>
87.4744

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.66e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
loganin

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 04-SEP-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   04-SEP-12         0                                  
HETATM    1  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   19  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   20  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   21  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   22  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   23  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   24  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   25  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   26  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   27  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   28  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
HETATM   29  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
HETATM   30  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
HETATM   31  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
HETATM   32  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
HETATM   33  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
HETATM   34  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
HETATM   35  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
HETATM   36  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
HETATM   37  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
CONECT    1    6                                                            
CONECT    2   24                                                            
CONECT    3    7    9                                                       
CONECT    4   10   18                                                       
CONECT    5    8   25                                                       
CONECT    6    1    9   11   28                                             
CONECT    7    3    8   11   29                                             
CONECT    8    5    7   15                                                  
CONECT    9    3    6   19   30                                             
CONECT   10    4   12   26   31                                             
CONECT   11    6    7   16   32                                             
CONECT   12   10   13   20   33                                             
CONECT   13   12   14   21   34                                             
CONECT   14   13   17   22   35                                             
CONECT   15    8   23   24                                                  
CONECT   16   11   25   27   36                                             
CONECT   17   14   26   27   37                                             
CONECT   18    4                                                            
CONECT   19    9                                                            
CONECT   20   12                                                            
CONECT   21   13                                                            
CONECT   22   14                                                            
CONECT   23   15                                                            
CONECT   24    2   15                                                       
CONECT   25    5   16                                                       
CONECT   26   10   17                                                       
CONECT   27   16   17                                                       
CONECT   28    6                                                            
CONECT   29    7                                                            
CONECT   30    9                                                            
CONECT   31   10                                                            
CONECT   32   11                                                            
CONECT   33   12                                                            
CONECT   34   13                                                            
CONECT   35   14                                                            
CONECT   36   16                                                            
CONECT   37   17                                                            
MASTER        0    0    0    0    0    0    0    0   37    0   78    0
END

View in JSmol

Synonyms

Value	Source
1-(beta-D-Glucopyranosyloxy)-1,4a,5,6,7,7a-hexahydro-6-hydroxy-7-methylcyclopenta[c]pyran-4-carboxylic acid methyl ester	ChEBI
Loganoside	ChEBI
1-(b-D-Glucopyranosyloxy)-1,4a,5,6,7,7a-hexahydro-6-hydroxy-7-methylcyclopenta[c]pyran-4-carboxylate methyl ester	Generator
1-(b-D-Glucopyranosyloxy)-1,4a,5,6,7,7a-hexahydro-6-hydroxy-7-methylcyclopenta[c]pyran-4-carboxylic acid methyl ester	Generator
1-(beta-D-Glucopyranosyloxy)-1,4a,5,6,7,7a-hexahydro-6-hydroxy-7-methylcyclopenta[c]pyran-4-carboxylate methyl ester	Generator
1-(Β-D-glucopyranosyloxy)-1,4a,5,6,7,7a-hexahydro-6-hydroxy-7-methylcyclopenta[c]pyran-4-carboxylate methyl ester	Generator
1-(Β-D-glucopyranosyloxy)-1,4a,5,6,7,7a-hexahydro-6-hydroxy-7-methylcyclopenta[c]pyran-4-carboxylic acid methyl ester	Generator
7-Deoxyloganin	MeSH

Chemical Formula

C₁₇H₂₆O₁₀

Average Mass

390.3823 Da

Monoisotopic Mass

390.15260 Da

IUPAC Name

methyl (1S,4aS,6S,7R,7aS)-6-hydroxy-7-methyl-1-{[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-1H,4aH,5H,6H,7H,7aH-cyclopenta[c]pyran-4-carboxylate

Traditional Name

loganin

CAS Registry Number

Not Available

SMILES

[H][C@]1(O)C[C@]2([H])C(=CO[C@@]([H])(O[C@]3([H])O[C@]([H])(CO)[C@@]([H])(O)[C@]([H])(O)[C@@]3([H])O)[C@]2([H])[C@@]1([H])C)C(=O)OC

InChI Identifier

InChI=1S/C17H26O10/c1-6-9(19)3-7-8(15(23)24-2)5-25-16(11(6)7)27-17-14(22)13(21)12(20)10(4-18)26-17/h5-7,9-14,16-22H,3-4H2,1-2H3/t6-,7+,9-,10+,11+,12+,13-,14+,16-,17-/m0/s1

InChI Key

AMBQHHVBBHTQBF-UOUCRYGSSA-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, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, 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
Adina racemosa	Plant	KNApSAcK
Apis cerana	LOTUS Database	35616633
Arabidopsis thaliana	LOTUS Database	35616633
Avicennia marina	LOTUS Database	35616633
Calycophyllum spruceanum	Plant	KNApSAcK
Catharanthus roseus	Plant	KNApSAcK
Centaurium erythraea	Plant	KNApSAcK
Cephalanthus occidentalis	LOTUS Database	35616633
Cerbera manghas	LOTUS Database	35616633
Cinchona calisaya	LOTUS Database	35616633
Coelospermum balansanum	LOTUS Database	35616633
Cornus controversa	Plant	KNApSAcK
Cornus officinalis	Plant	KNApSAcK
Desfontainia spinosa	LOTUS Database	35616633
Diplopanax stachyanthus	LOTUS Database	35616633
Dipsacus asper	Plant	KNApSAcK
Dipsacus asperoides	Plant	KNApSAcK
Dipsacus inermis	LOTUS Database	35616633
Dipsacus laciniatus	LOTUS Database	35616633
Ervatamia coronaria	LOTUS Database	35616633
Eucnide bartonioides	LOTUS Database	35616633
Fouquieria columnaris	LOTUS Database	35616633
Gentiana depressa	LOTUS Database	35616633
Gentiana loureirii	Plant	KNApSAcK
Gentiana pedicellata	Plant	KNApSAcK
Gentiana pyrenaica	LOTUS Database	35616633
Gentiana straminea	Plant	KNApSAcK
Gentiana verna	LOTUS Database	35616633
Guettarda platypoda	LOTUS Database	35616633
Hydrangea macrophylla	LOTUS Database	35616633
Jasminum grandiflorum	Plant	KNApSAcK
Jasminum hemsleyi	LOTUS Database	35616633
Jasminum hemsleyi Yamamoto	Plant	KNApSAcK
Jasminum officinale	Plant	KNApSAcK
Lamiophlomis rotata	LOTUS Database	35616633
Lippia graveolens	Plant	KNApSAcK
Lippia origanoides	LOTUS Database	35616633
Loasa acerifolia	LOTUS Database	35616633
Loasa tricolor	LOTUS Database	35616633
Lonicera angustifolia	LOTUS Database	35616633
Lonicera caerulea	LOTUS Database	35616633
Lonicera japonica	Plant	KNApSAcK
Lonicera periclymenum	LOTUS Database	35616633
Lonicera quinquelocularis	Plant	KNApSAcK
Menyanthes trifoliata	Plant	KNApSAcK
Neonauclea sessilifolia	Plant	KNApSAcK
Nyctanthes arbor-tristis	Plant	KNApSAcK
Ophiorrhiza kuroiwai	LOTUS Database	35616633
Ophiorrhiza liukiuensis	Plant	KNApSAcK
Osmanthus austrocaledonicus (Vieill.) Knobl.	Plant	KNApSAcK
Patrinia villosa	Plant	KNApSAcK
Penstemon barbatus	LOTUS Database	35616633
Penstemon serrulatus	LOTUS Database	35616633
Picconia excelsa	LOTUS Database	35616633
Picconia excelsa (Aiton) DC.	Plant	KNApSAcK
Pileostegia viburnoides var. glabrescens	Plant	KNApSAcK
Pterocephalus perennis	LOTUS Database	35616633
Rauvolfia grandiflora	LOTUS Database	35616633
Rauvolfia serpentina	LOTUS Database	35616633
Rehmannia glutinosa	Plant	KNApSAcK
Scabiosa japonica	Plant	KNApSAcK
Scaevola floribunda	LOTUS Database	35616633
Scaevola montana	LOTUS Database	35616633
Sertia mussotii	-	KNApSAcK
Simira rubescens	LOTUS Database	35616633
Sinoadina racemosa	Plant	KNApSAcK
Strychnos axillaris	Plant	KNApSAcK
Strychnos ignatii	Plant	KNApSAcK
Strychnos lucida	Plant	KNApSAcK
Strychnos nux-vomica	LOTUS Database	35616633
Strychnos nux-vomica L.	Plant	KNApSAcK
Strychnos spinosa	Plant	KNApSAcK
Timonius timon	LOTUS Database	35616633
Weigela coraeensis	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as iridoid o-glycosides. These are iridoid monoterpenes containing a glycosyl (usually a pyranosyl) moiety linked to the iridoid skeleton.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Prenol lipids

Sub Class

Terpene glycosides

Direct Parent

Iridoid O-glycosides

Alternative Parents

Substituents

Iridoid o-glycoside
Hexose monosaccharide
Glycosyl compound
Iridoid-skeleton
O-glycosyl compound
Bicyclic monoterpenoid
Monoterpenoid
Monosaccharide
Oxane
Cyclic alcohol
Vinylogous ester
Alpha,beta-unsaturated carboxylic ester
Enoate ester
Methyl ester
Carboxylic acid ester
Secondary alcohol
Organoheterocyclic compound
Monocarboxylic acid or derivatives
Oxacycle
Acetal
Carboxylic acid derivative
Polyol
Organooxygen compound
Alcohol
Hydrocarbon derivative
Organic oxide
Organic oxygen compound
Primary alcohol
Carbonyl group
Aliphatic heteropolycyclic compound

Molecular Framework

Aliphatic heteropolycyclic compounds

External Descriptors

beta-D-glucoside (CHEBI:15771 )
monosaccharide derivative (CHEBI:15771 )
methyl ester (CHEBI:15771 )
enoate ester (CHEBI:15771 )
iridoid monoterpenoid (CHEBI:15771 )
cyclopentapyran (CHEBI:15771 )
Iridoid, 10-alkyliridoid and secoiridoid monoterpenoids (C01433 )
Iridoids (C01433 )
Iridoid, 10-alkyliridoid and secoiridoid monoterpenoids (LMPR0102070001 )

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	-1.5	ALOGPS
logP	-1.8	ChemAxon
logS	-1.2	ALOGPS
pKa (Strongest Acidic)	12.21	ChemAxon
pKa (Strongest Basic)	-2.8	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	9	ChemAxon
Hydrogen Donor Count	5	ChemAxon
Polar Surface Area	155.14 Å²	ChemAxon
Rotatable Bond Count	5	ChemAxon
Refractivity	87.47 m³·mol⁻¹	ChemAxon
Polarizability	38.23 Å³	ChemAxon
Number of Rings	3	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

External Links

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

FDB030984

KNApSAcK ID

C00003088

Chemspider ID

Not Available

KEGG Compound ID

C01433

BioCyc ID

LOGANIN

BiGG ID

Not Available

Wikipedia Link

Loganin

METLIN ID

Not Available

PubChem Compound

87691

PDB ID

Not Available

ChEBI ID

15771

Good Scents ID

Not Available

References

General References

Kwon SH, Kim HC, Lee SY, Jang CG: Loganin improves learning and memory impairments induced by scopolamine in mice. Eur J Pharmacol. 2009 Oct 1;619(1-3):44-9. doi: 10.1016/j.ejphar.2009.06.062. Epub 2009 Aug 7. [PubMed:19666019 ]
Youn K, Jeong WS, Jun M: beta-Secretase (BACE1) inhibitory property of loganin isolated from Corni fructus. Nat Prod Res. 2013;27(16):1471-4. doi: 10.1080/14786419.2012.718774. Epub 2012 Aug 29. [PubMed:22931211 ]
Kim H, Youn K, Ahn MR, Kim OY, Jeong WS, Ho CT, Jun M: Neuroprotective effect of loganin against Abeta25-35-induced injury via the NF-kappaB-dependent signaling pathway in PC12 cells. Food Funct. 2015 Apr;6(4):1108-16. doi: 10.1039/c5fo00055f. [PubMed:25778782 ]
Zhao M, Qian D, Shang EX, Jiang S, Guo J, Liu P, Su SL, Duan JA, Du L, Tao J: Comparative pharmacokinetics of the main compounds of Shanzhuyu extract after oral administration in normal and chronic kidney disease rats. J Ethnopharmacol. 2015 Sep 15;173:280-6. doi: 10.1016/j.jep.2015.07.037. Epub 2015 Jul 29. [PubMed:26231452 ]
Tsai WH, Wu CH, Cheng CH, Chien CT: Ba-Wei-Di-Huang-Wan through its active ingredient loganin counteracts substance P-enhanced NF-kappaB/ICAM-1 signaling in rats with bladder hyperactivity. Neurourol Urodyn. 2016 Sep;35(7):771-9. doi: 10.1002/nau.22816. Epub 2015 Aug 19. [PubMed:26287995 ]
Kim MJ, Bae GS, Jo IJ, Choi SB, Kim DG, Shin JY, Lee SK, Kim MJ, Shin S, Song HJ, Park SJ: Loganin protects against pancreatitis by inhibiting NF-kappaB activation. Eur J Pharmacol. 2015 Oct 15;765:541-50. doi: 10.1016/j.ejphar.2015.09.019. Epub 2015 Sep 25. [PubMed:26407655 ]
Liu XD, Huang P, Lu YH, Ma M, Zhou RB, Yuan LX, Peng XJ: [Pharmacokinetics of loganin, ferulic acid and stilbene glucoside in Bushen Tongluo formula in vivo]. Zhongguo Zhong Yao Za Zhi. 2015 Jun;40(12):2428-34. [PubMed:26591537 ]
He K, Song S, Zou Z, Feng M, Wang D, Wang Y, Li X, Ye X: The Hypoglycemic and Synergistic Effect of Loganin, Morroniside, and Ursolic Acid Isolated from the Fruits of Cornus officinalis. Phytother Res. 2016 Feb;30(2):283-91. doi: 10.1002/ptr.5529. Epub 2015 Dec 1. [PubMed:26619955 ]
Zhao M, Tao J, Qian D, Liu P, Shang EX, Jiang S, Guo J, Su SL, Duan JA, Du L: Simultaneous determination of loganin, morroniside, catalpol and acteoside in normal and chronic kidney disease rat plasma by UPLC-MS for investigating the pharmacokinetics of Rehmannia glutinosa and Cornus officinalis Sieb drug pair extract. J Chromatogr B Analyt Technol Biomed Life Sci. 2016 Jan 15;1009-1010:122-9. doi: 10.1016/j.jchromb.2015.12.020. Epub 2015 Dec 14. [PubMed:26720701 ]
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Showing NP-Card for Loganin (NP0051775)

MOL for NP0051775 (Loganin)

3D MOL for NP0051775 (Loganin)

3D SDF for NP0051775 (Loganin)

3D-SDF for NP0051775 (Loganin)

PDB for NP0051775 (Loganin)

3D PDB for NP0051775 (Loganin)

SMILES for NP0051775 (Loganin)

INCHI for NP0051775 (Loganin)

Structure for NP0051775 (Loganin)

3D Structure for NP0051775 (Loganin)