NP-MRD: Showing NP-Card for (1r,3r,6r,8s,10r,11s,12r,13s,16s,17r)-8-tert-butyl-6,12,17-trihydroxy-16-methyl-2,4,14,19-tetraoxahexacyclo[8.7.2.0¹,¹¹.0³,⁷.0⁷,¹¹.0¹³,¹⁷]nonadecane-5,15,18-trione (NP0187496)

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Record Information

Version

2.0

Created at

2022-09-04 03:40:29 UTC

Updated at

2022-09-04 03:40:29 UTC

NP-MRD ID

NP0187496

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(1r,3r,6r,8s,10r,11s,12r,13s,16s,17r)-8-tert-butyl-6,12,17-trihydroxy-16-methyl-2,4,14,19-tetraoxahexacyclo[8.7.2.0¹,¹¹.0³,⁷.0⁷,¹¹.0¹³,¹⁷]nonadecane-5,15,18-trione

Description

Ginkgolide B belongs to the class of organic compounds known as ginkgolides and bilobalides. These are diterpene lactones with a structure based either on the gingkolide or the bilobalide skeleton. The ginkgolide skeleton is a very rigid structure consisting of hexacyclic C20 trilactone. The cis-fused F/A/D/C ring junction forms an empty semi-ball hole, the D ring contains a cage form tetrahydrofuran ring which occupies the center of the empty hole, and the oxygen atoms of the D,C and F ring and 10-hydroxyl group consist of an analogous crown ether structure. (1r,3r,6r,8s,10r,11s,12r,13s,16s,17r)-8-tert-butyl-6,12,17-trihydroxy-16-methyl-2,4,14,19-tetraoxahexacyclo[8.7.2.0¹,¹¹.0³,⁷.0⁷,¹¹.0¹³,¹⁷]nonadecane-5,15,18-trione is found in Ginkgo biloba. (1r,3r,6r,8s,10r,11s,12r,13s,16s,17r)-8-tert-butyl-6,12,17-trihydroxy-16-methyl-2,4,14,19-tetraoxahexacyclo[8.7.2.0¹,¹¹.0³,⁷.0⁷,¹¹.0¹³,¹⁷]nonadecane-5,15,18-trione was first documented in 2021 (PMID: 34944919). Based on a literature review a significant number of articles have been published on Ginkgolide B (PMID: 35276465) (PMID: 35343157) (PMID: 36044079) (PMID: 36015354) (PMID: 35948139) (PMID: 35922794).

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309042205402D          

 30 35  0  0  1  0            999 V2000
    2.7841   -0.8923    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7352   -0.0688    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.0401    0.3757    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2720    0.0746    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.2481    1.1740    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.0716    1.2230    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.9047    1.6118    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.9028    2.4368    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.6604    1.2634    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.4653    2.0874    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    5.1797    2.5198    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7849    1.9590    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    6.5837    2.1652    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.3825    2.3714    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.7899    1.3664    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.3775    2.9640    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.5121    1.1310    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.5023    0.2626    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    6.2650   -0.0646    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.7999    0.5661    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.6230    0.5097    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.3559    1.2637    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    7.1759    1.1732    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.7375   -0.0679    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.2264    0.5787    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.5871    1.1123    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8368    0.7693    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.6037    2.0409    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.3726    0.4549    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.7059   -0.2998    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  6  0  0  0
  2  3  1  0  0  0  0
  3  4  2  0  0  0  0
  3  5  1  0  0  0  0
  6  5  1  1  0  0  0
  6  7  1  0  0  0  0
  7  8  1  6  0  0  0
  9  7  1  6  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
 13 15  1  0  0  0  0
 13 16  1  0  0  0  0
 12 17  1  0  0  0  0
  9 17  1  0  0  0  0
 17 18  1  0  0  0  0
 18 19  1  1  0  0  0
 19 20  1  0  0  0  0
 20 21  2  0  0  0  0
 20 22  1  0  0  0  0
 17 22  1  0  0  0  0
 22 23  1  1  0  0  0
 18 24  1  0  0  0  0
 25 24  1  6  0  0  0
  9 25  1  0  0  0  0
 25 26  1  0  0  0  0
 26 27  2  0  0  0  0
 26 28  1  0  0  0  0
 10 28  1  6  0  0  0
 25 29  1  0  0  0  0
  2 29  1  0  0  0  0
  6 29  1  0  0  0  0
 29 30  1  6  0  0  0
M  END

     RDKit          2D

 54 59  0  0  0  0  0  0  0  0999 V2000
    2.3907    1.0037    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2760    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3943    1.2135    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6805    2.6860    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0323    0.7500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0323   -0.7500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9140   -1.9635    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0287   -0.9598    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0323   -3.1771    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4589   -2.7135    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3405   -3.9271    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4589   -5.1406    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7579   -5.8906    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0569   -6.6406    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0079   -7.1896    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5079   -4.5915    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0323   -4.6771    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3943   -5.1406    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3943   -6.6406    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0323   -7.1041    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3185   -8.5766    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9140   -5.8906    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0287   -4.8869    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2760   -3.9271    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3943   -2.7135    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0692   -4.1401    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4926   -5.5309    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5692   -4.1401    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3943   -1.2135    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8209   -1.6771    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5054    2.0074    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5228    0.0196    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5304    2.2324    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6764   -0.5374    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
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   -3.1427   -2.8239    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8980    0.5345    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2538   -1.4415    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3246   -2.7950    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7410   -4.4645    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0204   -6.5750    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.3560   -7.3906    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.9597   -5.4426    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4709   -8.0213    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4218   -8.5704    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2058   -8.0924    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5264   -6.9551    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4107   -3.3936    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.8887   -5.1776    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3100   -3.6888    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8209   -5.6041    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7527   -7.1342    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5011   -5.1731    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1453   -0.9729    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  0
  3  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  7  9  1  0
  9 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  1  0
 13 14  1  0
 13 15  1  0
 13 16  1  0
 12 17  1  0
 17 22  1  0
 22 23  1  0
 22 20  1  0
 20 21  2  0
 20 19  1  0
 19 18  1  0
 18 24  1  0
 25 24  1  6
 25 26  1  0
 26 27  2  0
 26 28  1  0
 25 29  1  0
 29 30  1  1
 29  2  1  0
 29  6  1  0
  9 17  1  1
 18 17  1  0
 25  9  1  0
 28 10  1  0
  1 31  1  0
  1 32  1  0
  1 33  1  0
  2 34  1  6
  6 35  1  1
  7 36  1  6
  8 37  1  0
 10 38  1  1
 11 39  1  0
 11 40  1  0
 12 41  1  1
 14 42  1  0
 14 43  1  0
 14 44  1  0
 15 45  1  0
 15 46  1  0
 15 47  1  0
 16 48  1  0
 16 49  1  0
 16 50  1  0
 22 52  1  1
 23 53  1  0
 18 51  1  1
 30 54  1  0
M  END


  Mrv1652309042205402D          

 30 35  0  0  1  0            999 V2000
    2.7841   -0.8923    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7352   -0.0688    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.0401    0.3757    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2720    0.0746    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.2481    1.1740    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.0716    1.2230    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.9047    1.6118    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.9028    2.4368    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.6604    1.2634    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.4653    2.0874    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    5.1797    2.5198    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7849    1.9590    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    6.5837    2.1652    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.3825    2.3714    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.7899    1.3664    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.3775    2.9640    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.5121    1.1310    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.5023    0.2626    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    6.2650   -0.0646    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.7999    0.5661    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.6230    0.5097    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.3559    1.2637    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    7.1759    1.1732    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.7375   -0.0679    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.2264    0.5787    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.5871    1.1123    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8368    0.7693    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.6037    2.0409    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.3726    0.4549    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.7059   -0.2998    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  6  0  0  0
  2  3  1  0  0  0  0
  3  4  2  0  0  0  0
  3  5  1  0  0  0  0
  6  5  1  1  0  0  0
  6  7  1  0  0  0  0
  7  8  1  6  0  0  0
  9  7  1  6  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
 13 15  1  0  0  0  0
 13 16  1  0  0  0  0
 12 17  1  0  0  0  0
  9 17  1  0  0  0  0
 17 18  1  0  0  0  0
 18 19  1  1  0  0  0
 19 20  1  0  0  0  0
 20 21  2  0  0  0  0
 20 22  1  0  0  0  0
 17 22  1  0  0  0  0
 22 23  1  1  0  0  0
 18 24  1  0  0  0  0
 25 24  1  6  0  0  0
  9 25  1  0  0  0  0
 25 26  1  0  0  0  0
 26 27  2  0  0  0  0
 26 28  1  0  0  0  0
 10 28  1  6  0  0  0
 25 29  1  0  0  0  0
  2 29  1  0  0  0  0
  6 29  1  0  0  0  0
 29 30  1  6  0  0  0
M  END
> <DATABASE_ID>
NP0187496

> <DATABASE_NAME>
NP-MRD

> <SMILES>
C[C@@H]1C(=O)O[C@H]2[C@H](O)[C@]34[C@H]5C[C@@H](C(C)(C)C)C33[C@@H](O)C(=O)O[C@H]3O[C@@]4(C(=O)O5)[C@@]12O

> <INCHI_IDENTIFIER>
InChI=1S/C20H24O10/c1-6-12(23)28-11-9(21)18-8-5-7(16(2,3)4)17(18)10(22)13(24)29-15(17)30-20(18,14(25)27-8)19(6,11)26/h6-11,15,21-22,26H,5H2,1-4H3/t6-,7+,8-,9+,10+,11+,15+,17?,18-,19-,20-/m1/s1

> <INCHI_KEY>
SQOJOAFXDQDRGF-AFUSRUNCSA-N

> <FORMULA>
C20H24O10

> <MOLECULAR_WEIGHT>
424.402

> <EXACT_MASS>
424.136946973

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_ATOM_COUNT>
54

> <JCHEM_AVERAGE_POLARIZABILITY>
46.004497891310876

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(1R,3R,6R,8S,10R,11S,12R,13S,16S,17R)-8-tert-butyl-6,12,17-trihydroxy-16-methyl-2,4,14,19-tetraoxahexacyclo[8.7.2.0^{1,11}.0^{3,7}.0^{7,11}.0^{13,17}]nonadecane-5,15,18-trione

> <JCHEM_LOGP>
-0.5822125509999996

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
6

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.305421395496875

> <JCHEM_PKA_STRONGEST_ACIDIC>
11.70994054475649

> <JCHEM_PKA_STRONGEST_BASIC>
-3.4968247045047107

> <JCHEM_POLAR_SURFACE_AREA>
148.82

> <JCHEM_REFRACTIVITY>
91.38199999999998

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(1R,3R,6R,8S,10R,11S,12R,13S,16S,17R)-8-tert-butyl-6,12,17-trihydroxy-16-methyl-2,4,14,19-tetraoxahexacyclo[8.7.2.0^{1,11}.0^{3,7}.0^{7,11}.0^{13,17}]nonadecane-5,15,18-trione

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 04-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   04-SEP-22         0                                  
HETATM    1  C   UNK     0       5.197  -1.666   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       5.106  -0.128   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       3.808   0.701   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0       2.374   0.139   0.000  0.00  0.00           O+0
HETATM    5  O   UNK     0       4.196   2.192   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0       5.734   2.283   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       7.289   3.009   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0       7.285   4.549   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0       8.699   2.358   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       8.335   3.897   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       9.669   4.704   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      10.798   3.657   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      12.290   4.042   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      13.781   4.427   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      12.674   2.551   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      11.905   5.533   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      10.289   2.111   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      10.271   0.490   0.000  0.00  0.00           C+0
HETATM   19  O   UNK     0      11.695  -0.121   0.000  0.00  0.00           O+0
HETATM   20  C   UNK     0      12.693   1.057   0.000  0.00  0.00           C+0
HETATM   21  O   UNK     0      14.230   0.951   0.000  0.00  0.00           O+0
HETATM   22  C   UNK     0      11.864   2.359   0.000  0.00  0.00           C+0
HETATM   23  O   UNK     0      13.395   2.190   0.000  0.00  0.00           O+0
HETATM   24  O   UNK     0       8.843  -0.127   0.000  0.00  0.00           O+0
HETATM   25  C   UNK     0       7.889   1.080   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       6.696   2.076   0.000  0.00  0.00           C+0
HETATM   27  O   UNK     0       5.295   1.436   0.000  0.00  0.00           O+0
HETATM   28  O   UNK     0       6.727   3.810   0.000  0.00  0.00           O+0
HETATM   29  C   UNK     0       6.296   0.849   0.000  0.00  0.00           C+0
HETATM   30  O   UNK     0       6.918  -0.560   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3   29                                                  
CONECT    3    2    4    5                                                  
CONECT    4    3                                                            
CONECT    5    3    6                                                       
CONECT    6    5    7   29                                                  
CONECT    7    6    8    9                                                  
CONECT    8    7                                                            
CONECT    9    7   10   17   25                                             
CONECT   10    9   11   28                                                  
CONECT   11   10   12                                                       
CONECT   12   11   13   17                                                  
CONECT   13   12   14   15   16                                             
CONECT   14   13                                                            
CONECT   15   13                                                            
CONECT   16   13                                                            
CONECT   17   12    9   18   22                                             
CONECT   18   17   19   24                                                  
CONECT   19   18   20                                                       
CONECT   20   19   21   22                                                  
CONECT   21   20                                                            
CONECT   22   20   17   23                                                  
CONECT   23   22                                                            
CONECT   24   18   25                                                       
CONECT   25   24    9   26   29                                             
CONECT   26   25   27   28                                                  
CONECT   27   26                                                            
CONECT   28   26   10                                                       
CONECT   29   25    2    6   30                                             
CONECT   30   29                                                            
MASTER        0    0    0    0    0    0    0    0   30    0   70    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₀H₂₄O₁₀

Average Mass

424.4020 Da

Monoisotopic Mass

424.13695 Da

IUPAC Name

Not Available

Traditional Name

Not Available

CAS Registry Number

Not Available

SMILES

C[C@@H]1C(=O)O[C@H]2[C@H](O)[C@]34[C@H]5C[C@@H](C(C)(C)C)C33[C@@H](O)C(=O)O[C@H]3O[C@@]4(C(=O)O5)[C@@]12O

InChI Identifier

InChI=1S/C20H24O10/c1-6-12(23)28-11-9(21)18-8-5-7(16(2,3)4)17(18)10(22)13(24)29-15(17)30-20(18,14(25)27-8)19(6,11)26/h6-11,15,21-22,26H,5H2,1-4H3/t6-,7+,8-,9+,10+,11+,15+,17?,18-,19-,20-/m1/s1

InChI Key

SQOJOAFXDQDRGF-AFUSRUNCSA-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
Ginkgo biloba	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as ginkgolides and bilobalides. These are diterpene lactones with a structure based either on the gingkolide or the bilobalide skeleton. The ginkgolide skeleton is a very rigid structure consisting of hexacyclic C20 trilactone. The cis-fused F/A/D/C ring junction forms an empty semi-ball hole, the D ring contains a cage form tetrahydrofuran ring which occupies the center of the empty hole, and the oxygen atoms of the D,C and F ring and 10-hydroxyl group consist of an analogous crown ether structure.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Prenol lipids

Sub Class

Terpene lactones

Direct Parent

Ginkgolides and bilobalides

Alternative Parents

Substituents

Ginkgolide-skeleton
Diterpenoid
Tricarboxylic acid or derivatives
Furofuran
Gamma butyrolactone
Tetrahydrofuran
Tertiary alcohol
Cyclic alcohol
Secondary alcohol
Lactone
Carboxylic acid ester
Oxacycle
Organoheterocyclic compound
Polyol
Carboxylic acid derivative
Acetal
Organic oxygen compound
Organic oxide
Hydrocarbon derivative
Organooxygen compound
Carbonyl group
Alcohol
Aliphatic heteropolycyclic compound

Molecular Framework

Aliphatic heteropolycyclic 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

External Links

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

C00035830

Chemspider ID

Not Available

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Ginkgolide

METLIN ID

Not Available

PubChem Compound

138404401

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Liang H, Yuan X, Sun C, Sun Y, Yang M, Feng S, Yao J, Liu Z, Zhang G, Li F: Preparation of a new component group of Ginkgo biloba leaves and investigation of the antihypertensive effects in spontaneously hypertensive rats. Biomed Pharmacother. 2022 May;149:112805. doi: 10.1016/j.biopha.2022.112805. Epub 2022 Mar 8. [PubMed:35276465 ]
He YQ, Zong CH, Wang J, Li Q, Wang J, Wu YJ, Chen Y, Liu XS: [Application of near infrared spectroscopy to predict contents of various lactones in chromatographic process of Ginkgo Folium]. Zhongguo Zhong Yao Za Zhi. 2022 Mar;47(5):1293-1299. doi: 10.19540/j.cnki.cjcmm.20211206.202. [PubMed:35343157 ]
Samandar F, Tehranizadeh ZA, Saberi MR, Chamani J: CB1 as a novel target for Ginkgo biloba's terpene trilactone for controlling chemotherapy-induced peripheral neuropathy (CIPN). J Mol Model. 2022 Aug 31;28(9):283. doi: 10.1007/s00894-022-05284-8. [PubMed:36044079 ]
Wang Q, Ma R, Liu P, Cheng G, Yang Q, Chen X, Wu Z, Yuan D, Chen T: Efficient Sustained-Release Nanoparticle Delivery System Protects Nigral Neurons in a Toxin Model of Parkinson's Disease. Pharmaceutics. 2022 Aug 18;14(8):1731. doi: 10.3390/pharmaceutics14081731. [PubMed:36015354 ]
Zhang J, Cheng J, Yan L, Yu Y, Hao C, Zhao A, Chen S, Liu A: Discovery of unreported ginkgolides of anti-PAF activity using characteristic ion and neutral loss recognition strategy in Ginkgo biloba L. Phytochemistry. 2022 Nov;203:113355. doi: 10.1016/j.phytochem.2022.113355. Epub 2022 Aug 7. [PubMed:35948139 ]
Briskey D, Rao A: A double-blind, randomised cross-over study to evaluate the absorption of a commercially available Ginkgo biloba extract compared to the liposomal extract Ginkgosome. BMC Complement Med Ther. 2022 Aug 3;22(1):206. doi: 10.1186/s12906-022-03679-x. [PubMed:35922794 ]
Luo T, Hao YN, Lin DD, Huang X, Wu AS: Ginkgolide B improved postoperative cognitive dysfunction by inhibiting microgliosis-mediated neuroinflammation in the hippocampus of mice. BMC Anesthesiol. 2022 Jul 18;22(1):229. doi: 10.1186/s12871-022-01750-1. [PubMed:35850641 ]
Cao Y, Yang L, Cheng H: Ginkgolide B Protects Against Ischemic Stroke via Targeting AMPK/PINK1. Front Pharmacol. 2022 Jun 28;13:941094. doi: 10.3389/fphar.2022.941094. eCollection 2022. [PubMed:35837278 ]
Jahan S, Redhu NS, Siddiqui AJ, Iqbal D, Khan J, Banawas S, Alaidarous M, Alshehri B, Mir SA, Adnan M, Pant AB: Nobiletin as a Neuroprotectant against NMDA Receptors: An In Silico Approach. Pharmaceutics. 2022 May 25;14(6):1123. doi: 10.3390/pharmaceutics14061123. [PubMed:35745697 ]
Wang L, Xia K, Han L, Zhang M, Fan J, Song L, Liao A, Wang W, Guo J: Local Administration of Ginkgolide B Using a Hyaluronan-Based Hydrogel Improves Wound Healing in Diabetic Mice. Front Bioeng Biotechnol. 2022 May 25;10:898231. doi: 10.3389/fbioe.2022.898231. eCollection 2022. [PubMed:35694224 ]
Zhang X, Diao X, Li L, Zhang Y, Liao M, Zhang G, Zhang L: Identification of metabolites of Ginkgolide B in vivo and in vitro using ultra-high-performance liquid chromatography-quadrupole time-of-flight mass spectrometry. J Sep Sci. 2022 Jul;45(14):2458-2477. doi: 10.1002/jssc.202101016. Epub 2022 May 18. [PubMed:35543088 ]
Zhu J, Jin Z, Yang L, Zhao C, Hu J, Chen J, Han Y, Yu P, Luo J, Kong L, Zhang C: Ginkgolide B targets and inhibits creatine kinase B to regulate the CCT/TRiC-SK1 axis and exerts pro-angiogenic activity in middle cerebral artery occlusion mice. Pharmacol Res. 2022 Jun;180:106240. doi: 10.1016/j.phrs.2022.106240. Epub 2022 May 2. [PubMed:35513225 ]
Zhao H, Guo Q, Li B, Shi M: The Efficacy and Safety of Ginkgo Terpene Lactone Preparations in the Treatment of Ischemic Stroke: A Systematic Review and Meta-Analysis of Randomized Clinical Trials. Front Pharmacol. 2022 Mar 18;13:821937. doi: 10.3389/fphar.2022.821937. eCollection 2022. [PubMed:35392576 ]
Cai D, Luo Z, Su J, Gan H, Wang Z, Liu X, Li S, Wu J, Chen J, Ma R, Huang M, Zhong G: Exposure-Response Analysis and Mechanism of Ginkgolide B's Neuroprotective Effect in Acute Cerebral Ischemia/Reperfusion Stage in Rat. Biol Pharm Bull. 2022;45(4):409-420. doi: 10.1248/bpb.b21-00781. [PubMed:35370265 ]
Authors unspecified: Statement of Retraction: Hypoxia-induced apoptosis of cardiomyocytes is restricted by ginkgolide B-downregulated microRNA-29. Cell Cycle. 2022 Apr;21(7):757. doi: 10.1080/15384101.2021.2014708. Epub 2022 Feb 22. [PubMed:35191821 ]
Zhu T, Wang L, Wang LP, Wan Q: Therapeutic targets of neuroprotection and neurorestoration in ischemic stroke: Applications for natural compounds from medicinal herbs. Biomed Pharmacother. 2022 Apr;148:112719. doi: 10.1016/j.biopha.2022.112719. Epub 2022 Feb 12. [PubMed:35168073 ]
Shao L, Dong C, Geng D, He Q, Shi Y: Ginkgolide B inactivates the NLRP3 inflammasome by promoting autophagic degradation to improve learning and memory impairment in Alzheimer's disease. Metab Brain Dis. 2022 Feb;37(2):329-341. doi: 10.1007/s11011-021-00886-2. Epub 2022 Jan 20. [PubMed:35050445 ]
Kawasaki K, Kasamatsu A, Ando T, Saito T, Nobuchi T, Nozaki R, Iyoda M, Uzawa K: Ginkgolide B Regulates CDDP Chemoresistance in Oral Cancer via the Platelet-Activating Factor Receptor Pathway. Cancers (Basel). 2021 Dec 15;13(24):6299. doi: 10.3390/cancers13246299. [PubMed:34944919 ]
LOTUS database [Link]

Showing NP-Card for (1r,3r,6r,8s,10r,11s,12r,13s,16s,17r)-8-tert-butyl-6,12,17-trihydroxy-16-methyl-2,4,14,19-tetraoxahexacyclo[8.7.2.0¹,¹¹.0³,⁷.0⁷,¹¹.0¹³,¹⁷]nonadecane-5,15,18-trione (NP0187496)

MOL for NP0187496 ((1r,3r,6r,8s,10r,11s,12r,13s,16s,17r)-8-tert-butyl-6,12,17-trihydroxy-16-methyl-2,4,14,19-tetraoxahexacyclo[8.7.2.0¹,¹¹.0³,⁷.0⁷,¹¹.0¹³,¹⁷]nonadecane-5,15,18-trione)

3D MOL for NP0187496 ((1r,3r,6r,8s,10r,11s,12r,13s,16s,17r)-8-tert-butyl-6,12,17-trihydroxy-16-methyl-2,4,14,19-tetraoxahexacyclo[8.7.2.0¹,¹¹.0³,⁷.0⁷,¹¹.0¹³,¹⁷]nonadecane-5,15,18-trione)

3D SDF for NP0187496 ((1r,3r,6r,8s,10r,11s,12r,13s,16s,17r)-8-tert-butyl-6,12,17-trihydroxy-16-methyl-2,4,14,19-tetraoxahexacyclo[8.7.2.0¹,¹¹.0³,⁷.0⁷,¹¹.0¹³,¹⁷]nonadecane-5,15,18-trione)

3D-SDF for NP0187496 ((1r,3r,6r,8s,10r,11s,12r,13s,16s,17r)-8-tert-butyl-6,12,17-trihydroxy-16-methyl-2,4,14,19-tetraoxahexacyclo[8.7.2.0¹,¹¹.0³,⁷.0⁷,¹¹.0¹³,¹⁷]nonadecane-5,15,18-trione)

PDB for NP0187496 ((1r,3r,6r,8s,10r,11s,12r,13s,16s,17r)-8-tert-butyl-6,12,17-trihydroxy-16-methyl-2,4,14,19-tetraoxahexacyclo[8.7.2.0¹,¹¹.0³,⁷.0⁷,¹¹.0¹³,¹⁷]nonadecane-5,15,18-trione)

3D PDB for NP0187496 ((1r,3r,6r,8s,10r,11s,12r,13s,16s,17r)-8-tert-butyl-6,12,17-trihydroxy-16-methyl-2,4,14,19-tetraoxahexacyclo[8.7.2.0¹,¹¹.0³,⁷.0⁷,¹¹.0¹³,¹⁷]nonadecane-5,15,18-trione)

SMILES for NP0187496 ((1r,3r,6r,8s,10r,11s,12r,13s,16s,17r)-8-tert-butyl-6,12,17-trihydroxy-16-methyl-2,4,14,19-tetraoxahexacyclo[8.7.2.0¹,¹¹.0³,⁷.0⁷,¹¹.0¹³,¹⁷]nonadecane-5,15,18-trione)

INCHI for NP0187496 ((1r,3r,6r,8s,10r,11s,12r,13s,16s,17r)-8-tert-butyl-6,12,17-trihydroxy-16-methyl-2,4,14,19-tetraoxahexacyclo[8.7.2.0¹,¹¹.0³,⁷.0⁷,¹¹.0¹³,¹⁷]nonadecane-5,15,18-trione)

Structure for NP0187496 ((1r,3r,6r,8s,10r,11s,12r,13s,16s,17r)-8-tert-butyl-6,12,17-trihydroxy-16-methyl-2,4,14,19-tetraoxahexacyclo[8.7.2.0¹,¹¹.0³,⁷.0⁷,¹¹.0¹³,¹⁷]nonadecane-5,15,18-trione)

3D Structure for NP0187496 ((1r,3r,6r,8s,10r,11s,12r,13s,16s,17r)-8-tert-butyl-6,12,17-trihydroxy-16-methyl-2,4,14,19-tetraoxahexacyclo[8.7.2.0¹,¹¹.0³,⁷.0⁷,¹¹.0¹³,¹⁷]nonadecane-5,15,18-trione)