NP-MRD: Showing NP-Card for (3r,6r,8s,9r,10s,12s,13r,16s,17s)-8-tert-butyl-6,9,12-trihydroxy-16-methyl-2,4,14,19-tetraoxahexacyclo[8.7.2.0¹,¹¹.0³,⁷.0⁷,¹¹.0¹³,¹⁷]nonadecane-5,15,18-trione (NP0158217)

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Record Information

Version

2.0

Created at

2022-09-02 15:46:10 UTC

Updated at

2022-09-02 15:46:10 UTC

NP-MRD ID

NP0158217

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(3r,6r,8s,9r,10s,12s,13r,16s,17s)-8-tert-butyl-6,9,12-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

GinkgolideM 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. (3r,6r,8s,9r,10s,12s,13r,16s,17s)-8-tert-butyl-6,9,12-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. Based on a literature review very few articles have been published on GinkgolideM.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309022217462D          

 30 35  0  0  1  0            999 V2000
    1.3347    1.5271    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6713    0.5717    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.5777   -0.0127    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8829   -0.5741    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.3068   -0.3987    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8993    0.1755    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.5363    0.9163    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.1445    1.4264    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9726    1.6242    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.4275    0.9102    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    5.2340    0.6982    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.2895   -0.1290    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.1576   -0.1995    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.5176   -0.4225    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.5081   -1.2273    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.9269    0.1954    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5911   -0.6186    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.0492   -1.4958    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7750   -2.1284    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3967   -2.1092    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0489   -1.4701    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7483   -0.6665    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.9603   -1.2224    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4014    0.1370    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.8033    0.9211    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.2873    1.6732    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2684    2.5445    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.1980    0.5961    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2198    0.5683    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.1976    0.9355    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  1  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
  7  6  1  6  0  0  0
  2  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
 10  9  1  6  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  2  0  0  0  0
 12 14  1  0  0  0  0
 14 15  1  6  0  0  0
 14 16  1  0  0  0  0
 10 16  1  0  0  0  0
 16 17  1  0  0  0  0
 17 18  1  6  0  0  0
 18 19  1  0  0  0  0
 18 20  1  0  0  0  0
 18 21  1  0  0  0  0
 17 22  1  0  0  0  0
 22 23  1  1  0  0  0
 22 24  1  0  0  0  0
 24 25  1  1  0  0  0
 25 26  1  0  0  0  0
  8 26  1  0  0  0  0
 26 27  2  0  0  0  0
 24 28  1  0  0  0  0
  8 28  1  0  0  0  0
 16 28  1  0  0  0  0
 28 29  1  0  0  0  0
  6 29  1  0  0  0  0
 29 30  1  1  0  0  0
M  END

     RDKit          3D

 54 59  0  0  0  0  0  0  0  0999 V2000
    5.1874   -0.0024   -0.6715 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8561    0.5032   -0.0985 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.0601    0.5667    1.3725 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5097    1.5816    1.9687 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.6632   -0.6671    1.8654 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.5651   -1.1011    1.1233 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.8333   -0.5629   -0.2781 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.5402   -0.1226   -0.8488 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.3753    1.2181   -1.0281 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0405    1.5293   -0.9494 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.0939    2.7977   -0.3919 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3146    2.7049    0.9531 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0330    3.5019    1.8844 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0082    1.3785    1.1435 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.7875    0.8970    2.4073 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6096    0.5308    0.0219 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.6265   -0.2946   -0.6445 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.0611    0.0274   -0.5174 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4519    1.3900   -1.0207 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7497   -0.9640   -1.4909 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6994   -0.1979    0.8058 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4162   -1.7148   -0.1582 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.8292   -2.6346   -1.1213 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0915   -1.7898   -0.0693 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.5472   -2.1026   -1.3951 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.0674   -0.9511   -1.9758 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1306   -0.6596   -3.1978 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5179   -0.4152    0.2449 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.3020   -0.2948    1.4723 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.7593    0.9824    1.7508 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.9961    0.7183   -0.4175 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.4218   -0.9179   -0.0532 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.1161   -0.2437   -1.7312 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5860    1.4782   -0.5330 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3859   -2.1712    1.1378 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2431   -1.4380   -0.8517 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3973    1.4282   -1.9599 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0967    1.6544    1.0763 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3252    1.4420    3.0411 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3829   -0.3242   -1.7436 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0717    1.9449   -0.2550 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6003    2.0497   -1.2365 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0841    1.3804   -1.9328 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7204   -0.5064   -1.8373 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0324   -1.8746   -0.9456 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1322   -1.1491   -2.3696 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0284   -0.4803    1.6248 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4875   -1.0112    0.7994 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2851    0.6958    1.1775 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8172   -1.9126    0.8293 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8587   -3.5202   -0.6729 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4349   -2.5666    0.6422 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8318   -0.8047    2.3096 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9389    0.9944    2.7454 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  7  1  0
  7  6  1  0
  6  5  1  0
  5  3  1  0
  3  4  2  0
  6 29  1  0
 29 30  1  0
 29 28  1  0
 28 24  1  0
 24 25  1  0
 25 26  1  0
 26 27  2  0
 26  8  1  0
  8  9  1  6
  9 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  2  0
 12 14  1  0
 14 15  1  0
 14 16  1  0
 16 17  1  0
 17 22  1  0
 22 23  1  0
 17 18  1  0
 18 19  1  0
 18 20  1  0
 18 21  1  0
  3  2  1  0
 28  8  1  6
 16 10  1  0
  8  7  1  0
 16 28  1  1
 22 24  1  0
  1 31  1  0
  1 32  1  0
  1 33  1  0
  2 34  1  6
  7 36  1  6
  6 35  1  6
 29 53  1  1
 30 54  1  0
 24 52  1  1
 10 37  1  6
 14 38  1  6
 15 39  1  0
 17 40  1  6
 22 50  1  1
 23 51  1  0
 19 41  1  0
 19 42  1  0
 19 43  1  0
 20 44  1  0
 20 45  1  0
 20 46  1  0
 21 47  1  0
 21 48  1  0
 21 49  1  0
M  END


  Mrv1652309022217462D          

 30 35  0  0  1  0            999 V2000
    1.3347    1.5271    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6713    0.5717    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.5777   -0.0127    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8829   -0.5741    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.3068   -0.3987    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8993    0.1755    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.5363    0.9163    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.1445    1.4264    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9726    1.6242    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.4275    0.9102    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    5.2340    0.6982    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.2895   -0.1290    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.1576   -0.1995    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.5176   -0.4225    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.5081   -1.2273    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.9269    0.1954    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5911   -0.6186    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.0492   -1.4958    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7750   -2.1284    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3967   -2.1092    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0489   -1.4701    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7483   -0.6665    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.9603   -1.2224    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4014    0.1370    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.8033    0.9211    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.2873    1.6732    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2684    2.5445    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.1980    0.5961    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2198    0.5683    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.1976    0.9355    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  1  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
  7  6  1  6  0  0  0
  2  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
 10  9  1  6  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  2  0  0  0  0
 12 14  1  0  0  0  0
 14 15  1  6  0  0  0
 14 16  1  0  0  0  0
 10 16  1  0  0  0  0
 16 17  1  0  0  0  0
 17 18  1  6  0  0  0
 18 19  1  0  0  0  0
 18 20  1  0  0  0  0
 18 21  1  0  0  0  0
 17 22  1  0  0  0  0
 22 23  1  1  0  0  0
 22 24  1  0  0  0  0
 24 25  1  1  0  0  0
 25 26  1  0  0  0  0
  8 26  1  0  0  0  0
 26 27  2  0  0  0  0
 24 28  1  0  0  0  0
  8 28  1  0  0  0  0
 16 28  1  0  0  0  0
 28 29  1  0  0  0  0
  6 29  1  0  0  0  0
 29 30  1  1  0  0  0
M  END
> <DATABASE_ID>
NP0158217

> <DATABASE_NAME>
NP-MRD

> <SMILES>
C[C@H]1[C@H]2[C@@H](OC1=O)[C@@H](O)C13[C@@H]4OC(=O)C21O[C@@H]1OC(=O)[C@H](O)C31[C@@H]([C@H]4O)C(C)(C)C

> <INCHI_IDENTIFIER>
InChI=1S/C20H24O10/c1-5-6-8(27-13(5)24)10(22)19-12-7(21)9(17(2,3)4)18(19)11(23)14(25)29-16(18)30-20(6,19)15(26)28-12/h5-12,16,21-23H,1-4H3/t5-,6-,7+,8+,9-,10+,11-,12+,16-,18?,19?,20?/m0/s1

> <INCHI_KEY>
KDKROYXEHCYLJQ-ULHXRYPXSA-N

> <FORMULA>
C20H24O10

> <MOLECULAR_WEIGHT>
424.402

> <EXACT_MASS>
424.136946973

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_ATOM_COUNT>
54

> <JCHEM_AVERAGE_POLARIZABILITY>
39.006117916770734

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(3R,6R,8S,9R,10S,12S,13R,16S,17S)-8-tert-butyl-6,9,12-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

> <ALOGPS_LOGP>
0.60

> <JCHEM_LOGP>
-0.923982046000001

> <ALOGPS_LOGS>
-1.73

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
6

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
13.356226311772904

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.046694404213882

> <JCHEM_PKA_STRONGEST_BASIC>
-3.3010627504948387

> <JCHEM_POLAR_SURFACE_AREA>
148.82

> <JCHEM_REFRACTIVITY>
91.57859999999998

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
7.96e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(3R,6R,8S,9R,10S,12S,13R,16S,17S)-8-tert-butyl-6,9,12-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                                 02-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   02-SEP-22         0                                  
HETATM    1  C   UNK     0       2.492   2.851   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       3.120   1.067   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       2.945  -0.024   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0       1.648  -1.072   0.000  0.00  0.00           O+0
HETATM    5  O   UNK     0       4.306  -0.744   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0       5.412   0.328   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       4.734   1.710   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       5.870   2.663   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0       7.416   3.032   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0       8.265   1.699   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0       9.770   1.303   0.000  0.00  0.00           O+0
HETATM   12  C   UNK     0       9.874  -0.241   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0      11.494  -0.372   0.000  0.00  0.00           O+0
HETATM   14  C   UNK     0       8.433  -0.789   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0       8.415  -2.291   0.000  0.00  0.00           O+0
HETATM   16  C   UNK     0       7.330   0.365   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       6.703  -1.155   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       7.559  -2.792   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       8.913  -3.973   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       6.341  -3.937   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       9.425  -2.744   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       5.130  -1.244   0.000  0.00  0.00           C+0
HETATM   23  O   UNK     0       3.659  -2.282   0.000  0.00  0.00           O+0
HETATM   24  C   UNK     0       4.483   0.256   0.000  0.00  0.00           C+0
HETATM   25  O   UNK     0       3.366   1.719   0.000  0.00  0.00           O+0
HETATM   26  C   UNK     0       4.270   3.123   0.000  0.00  0.00           C+0
HETATM   27  O   UNK     0       4.234   4.750   0.000  0.00  0.00           O+0
HETATM   28  C   UNK     0       5.970   1.113   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0       4.144   1.061   0.000  0.00  0.00           C+0
HETATM   30  O   UNK     0       2.236   1.746   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    7                                                  
CONECT    3    2    4    5                                                  
CONECT    4    3                                                            
CONECT    5    3    6                                                       
CONECT    6    5    7   29                                                  
CONECT    7    6    2    8                                                  
CONECT    8    7    9   26   28                                             
CONECT    9    8   10                                                       
CONECT   10    9   11   16                                                  
CONECT   11   10   12                                                       
CONECT   12   11   13   14                                                  
CONECT   13   12                                                            
CONECT   14   12   15   16                                                  
CONECT   15   14                                                            
CONECT   16   14   10   17   28                                             
CONECT   17   16   18   22                                                  
CONECT   18   17   19   20   21                                             
CONECT   19   18                                                            
CONECT   20   18                                                            
CONECT   21   18                                                            
CONECT   22   17   23   24                                                  
CONECT   23   22                                                            
CONECT   24   22   25   28                                                  
CONECT   25   24   26                                                       
CONECT   26   25    8   27                                                  
CONECT   27   26                                                            
CONECT   28   24    8   16   29                                             
CONECT   29   28    6   30                                                  
CONECT   30   29                                                            
MASTER        0    0    0    0    0    0    0    0   30    0   70    0
END

View in JSmol

Synonyms

Value	Source
Ginkgolide m	MeSH

Chemical Formula

C₂₀H₂₄O₁₀

Average Mass

424.4020 Da

Monoisotopic Mass

424.13695 Da

IUPAC Name

(3R,6R,8S,9R,10S,12S,13R,16S,17S)-8-tert-butyl-6,9,12-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

Traditional Name

(3R,6R,8S,9R,10S,12S,13R,16S,17S)-8-tert-butyl-6,9,12-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

CAS Registry Number

Not Available

SMILES

C[C@H]1[C@H]2[C@@H](OC1=O)[C@@H](O)C13[C@@H]4OC(=O)C21O[C@@H]1OC(=O)[C@H](O)C31[C@@H]([C@H]4O)C(C)(C)C

InChI Identifier

InChI=1S/C20H24O10/c1-5-6-8(27-13(5)24)10(22)19-12-7(21)9(17(2,3)4)18(19)11(23)14(25)29-16(18)30-20(6,19)15(26)28-12/h5-12,16,21-23H,1-4H3/t5-,6-,7+,8+,9-,10+,11-,12+,16-,18?,19?,20?/m0/s1

InChI Key

KDKROYXEHCYLJQ-ULHXRYPXSA-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
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
logP	0.6	ALOGPS
logP	-0.92	ChemAxon
logS	-1.7	ALOGPS
pKa (Strongest Acidic)	12.05	ChemAxon
pKa (Strongest Basic)	-3.3	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	7	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	148.82 Å²	ChemAxon
Rotatable Bond Count	1	ChemAxon
Refractivity	91.58 m³·mol⁻¹	ChemAxon
Polarizability	39.01 Å³	ChemAxon
Number of Rings	6	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

Not Available

KNApSAcK ID

Not Available

Chemspider ID

57620890

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

138394154

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for (3r,6r,8s,9r,10s,12s,13r,16s,17s)-8-tert-butyl-6,9,12-trihydroxy-16-methyl-2,4,14,19-tetraoxahexacyclo[8.7.2.0¹,¹¹.0³,⁷.0⁷,¹¹.0¹³,¹⁷]nonadecane-5,15,18-trione (NP0158217)

MOL for NP0158217 ((3r,6r,8s,9r,10s,12s,13r,16s,17s)-8-tert-butyl-6,9,12-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 NP0158217 ((3r,6r,8s,9r,10s,12s,13r,16s,17s)-8-tert-butyl-6,9,12-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 NP0158217 ((3r,6r,8s,9r,10s,12s,13r,16s,17s)-8-tert-butyl-6,9,12-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 NP0158217 ((3r,6r,8s,9r,10s,12s,13r,16s,17s)-8-tert-butyl-6,9,12-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 NP0158217 ((3r,6r,8s,9r,10s,12s,13r,16s,17s)-8-tert-butyl-6,9,12-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 NP0158217 ((3r,6r,8s,9r,10s,12s,13r,16s,17s)-8-tert-butyl-6,9,12-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 NP0158217 ((3r,6r,8s,9r,10s,12s,13r,16s,17s)-8-tert-butyl-6,9,12-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 NP0158217 ((3r,6r,8s,9r,10s,12s,13r,16s,17s)-8-tert-butyl-6,9,12-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 NP0158217 ((3r,6r,8s,9r,10s,12s,13r,16s,17s)-8-tert-butyl-6,9,12-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 NP0158217 ((3r,6r,8s,9r,10s,12s,13r,16s,17s)-8-tert-butyl-6,9,12-trihydroxy-16-methyl-2,4,14,19-tetraoxahexacyclo[8.7.2.0¹,¹¹.0³,⁷.0⁷,¹¹.0¹³,¹⁷]nonadecane-5,15,18-trione)