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Record Information

Version

5.0

Status

Detected but not Quantified

Creation Date

2012-09-11 22:02:29 UTC

Update Date

2022-09-22 18:34:26 UTC

HMDB ID

HMDB0036861

Secondary Accession Numbers

HMDB36861

Metabolite Identification

Common Name

Ginkgolide B

Description

Ginkgolide B, also known as BN52021 or gingko lactone, 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. Based on a literature review a significant number of articles have been published on Ginkgolide B.

Structure

MOL 3D MOL SDF 3D SDF PDB 3D PDB SMILES InChI


  Mrv0541 09111222022D          

 30 35  0  0  0  0            999 V2000
   -2.2744   -0.8637    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6066   -1.3507    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9374   -0.8637    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1942   -0.0786    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0192   -0.0786    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1124   -0.8637    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1401   -0.0786    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5305    0.4043    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0623   -1.1189    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5063    0.5905    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8037    0.4043    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5416    1.1865    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2849    1.1865    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3911   -0.8637    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2093   -0.8637    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4618   -0.0786    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6274    0.4043    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8743    1.1865    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2093    1.6640    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8037   -0.1394    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1869    0.8182    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1869    1.6461    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6595    1.4501    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4552    0.4043    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.2620   -0.2911    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0623   -0.0786    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8470   -0.8761    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2620   -1.1189    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1013   -1.6640    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4080    0.7216    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  5  1  0  0  0  0
  1  9  2  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  3  6  1  0  0  0  0
  4  5  1  0  0  0  0
  4  8  1  0  0  0  0
  4 30  1  0  0  0  0
  5 10  1  0  0  0  0
  6  7  1  0  0  0  0
  6 29  1  0  0  0  0
  7  8  1  0  0  0  0
  7 11  1  0  0  0  0
  7 14  1  0  0  0  0
  8 13  1  0  0  0  0
  8 21  1  0  0  0  0
 11 12  1  0  0  0  0
 11 16  1  0  0  0  0
 11 17  1  0  0  0  0
 12 13  1  0  0  0  0
 12 19  1  0  0  0  0
 14 15  1  0  0  0  0
 14 20  1  0  0  0  0
 15 16  1  0  0  0  0
 16 25  1  0  0  0  0
 17 18  1  0  0  0  0
 17 24  1  0  0  0  0
 18 19  1  0  0  0  0
 18 23  2  0  0  0  0
 20 21  1  0  0  0  0
 21 22  2  0  0  0  0
 25 26  1  0  0  0  0
 25 27  1  0  0  0  0
 25 28  1  0  0  0  0
M  END

HMDB0036861
     RDKit          3D
Ginkgolide B
 54 59  0  0  0  0  0  0  0  0999 V2000
   -3.2418   -1.4061    1.7778 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5471   -0.3695    0.7820 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8614   -0.9019   -0.5947 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9938   -2.1168   -0.9098 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9564    0.2531   -1.3588 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7886    1.0083   -0.9905 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5654    0.3458   -1.6330 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3556    0.9404   -2.8953 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4855    0.6189   -0.6868 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0868    1.9798   -0.7305 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4544    1.8242   -0.1352 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7971    0.3212   -0.2493 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8525    0.0778    0.7024 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4304   -1.3216    0.8113 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6881    0.5687    2.1090 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0518    0.9020    0.1540 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5818   -0.3991   -0.4914 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1650   -1.2143    0.4888 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5408   -2.3556    0.6357 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8548   -2.6872   -0.7070 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1298   -3.8491   -1.1709 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8171   -1.4395   -1.5287 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0473   -1.4931   -2.6270 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6449   -0.4093    1.4127 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1831    0.6278    0.6787 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7800    1.9203    1.2927 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6459    2.0974    2.5178 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6235    2.7559    0.2222 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6307    0.7161    0.5005 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1778    1.8946    1.0952 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5666   -1.0460    2.5719 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8445   -2.3598    1.3164 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1628   -1.7578    2.3115 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5643    0.0513    1.0805 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8683    2.0597   -1.2355 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8607   -0.6906   -1.7308 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8891    0.3816   -3.5438 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0965    2.4542   -1.7281 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4973    2.0545    0.9494 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2091    2.4631   -0.6084 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3295    0.3347   -1.2710 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5158   -1.8374   -0.1626 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.5293   -1.2514    1.1316 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0043   -1.9212    1.6297 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3553    0.0055    2.8271 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0459    1.6176    2.1777 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6470    0.5962    2.4797 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.9642    0.5472    0.6773 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2012    0.6846   -0.9168 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9271    1.9624    0.3930 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0931   -1.5611   -0.1017 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8878   -1.3576   -1.9152 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0024   -2.4353   -2.9522 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0448    2.1164    0.6988 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 18  1  0
 18 19  1  0
 19 20  1  0
 20 21  2  0
 20 22  1  0
 22 23  1  0
 18 24  1  0
 24 25  1  0
 25 26  1  0
 26 27  2  0
 26 28  1  0
 25 29  1  0
 29 30  1  0
 29  2  1  0
 29  6  1  0
 17  9  1  0
 25  9  1  0
 28 10  1  0
 22 17  1  0
  1 31  1  0
  1 32  1  0
  1 33  1  0
  2 34  1  0
  6 35  1  0
  7 36  1  0
  8 37  1  0
 10 38  1  0
 11 39  1  0
 11 40  1  0
 12 41  1  0
 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
 18 51  1  0
 22 52  1  0
 23 53  1  0
 30 54  1  0
M  END


  Mrv0541 09111222022D          

 30 35  0  0  0  0            999 V2000
   -2.2744   -0.8637    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6066   -1.3507    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9374   -0.8637    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1942   -0.0786    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0192   -0.0786    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1124   -0.8637    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1401   -0.0786    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5305    0.4043    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0623   -1.1189    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5063    0.5905    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8037    0.4043    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5416    1.1865    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2849    1.1865    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3911   -0.8637    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2093   -0.8637    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4618   -0.0786    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6274    0.4043    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8743    1.1865    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2093    1.6640    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8037   -0.1394    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1869    0.8182    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1869    1.6461    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6595    1.4501    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4552    0.4043    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.2620   -0.2911    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0623   -0.0786    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8470   -0.8761    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2620   -1.1189    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1013   -1.6640    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4080    0.7216    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  5  1  0  0  0  0
  1  9  2  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  3  6  1  0  0  0  0
  4  5  1  0  0  0  0
  4  8  1  0  0  0  0
  4 30  1  0  0  0  0
  5 10  1  0  0  0  0
  6  7  1  0  0  0  0
  6 29  1  0  0  0  0
  7  8  1  0  0  0  0
  7 11  1  0  0  0  0
  7 14  1  0  0  0  0
  8 13  1  0  0  0  0
  8 21  1  0  0  0  0
 11 12  1  0  0  0  0
 11 16  1  0  0  0  0
 11 17  1  0  0  0  0
 12 13  1  0  0  0  0
 12 19  1  0  0  0  0
 14 15  1  0  0  0  0
 14 20  1  0  0  0  0
 15 16  1  0  0  0  0
 16 25  1  0  0  0  0
 17 18  1  0  0  0  0
 17 24  1  0  0  0  0
 18 19  1  0  0  0  0
 18 23  2  0  0  0  0
 20 21  1  0  0  0  0
 21 22  2  0  0  0  0
 25 26  1  0  0  0  0
 25 27  1  0  0  0  0
 25 28  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0036861

> <DATABASE_NAME>
hmdb

> <SMILES>
CC1C(=O)OC2C(O)C34C5CC(C(C)(C)C)C33C(O)C(=O)OC3OC4(C(=O)O5)C12O

> <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

> <INCHI_KEY>
SQOJOAFXDQDRGF-UHFFFAOYSA-N

> <FORMULA>
C20H24O10

> <MOLECULAR_WEIGHT>
424.3986

> <EXACT_MASS>
424.136946988

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_AVERAGE_POLARIZABILITY>
39.06608332714507

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
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

> <ALOGPS_LOGP>
0.49

> <JCHEM_LOGP>
-0.5822125509999996

> <ALOGPS_LOGS>
-1.91

> <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>
91.38200000000002

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
5.21e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
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

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0036861
     RDKit          3D
Ginkgolide B
 54 59  0  0  0  0  0  0  0  0999 V2000
   -3.2418   -1.4061    1.7778 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5471   -0.3695    0.7820 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8614   -0.9019   -0.5947 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9938   -2.1168   -0.9098 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9564    0.2531   -1.3588 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7886    1.0083   -0.9905 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5654    0.3458   -1.6330 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3556    0.9404   -2.8953 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4855    0.6189   -0.6868 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0868    1.9798   -0.7305 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4544    1.8242   -0.1352 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7971    0.3212   -0.2493 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8525    0.0778    0.7024 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4304   -1.3216    0.8113 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6881    0.5687    2.1090 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0518    0.9020    0.1540 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5818   -0.3991   -0.4914 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1650   -1.2143    0.4888 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5408   -2.3556    0.6357 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8548   -2.6872   -0.7070 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1298   -3.8491   -1.1709 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8171   -1.4395   -1.5287 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0473   -1.4931   -2.6270 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6449   -0.4093    1.4127 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1831    0.6278    0.6787 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7800    1.9203    1.2927 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6459    2.0974    2.5178 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6235    2.7559    0.2222 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6307    0.7161    0.5005 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1778    1.8946    1.0952 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5666   -1.0460    2.5719 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8445   -2.3598    1.3164 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1628   -1.7578    2.3115 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5643    0.0513    1.0805 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8683    2.0597   -1.2355 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8607   -0.6906   -1.7308 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8891    0.3816   -3.5438 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0965    2.4542   -1.7281 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4973    2.0545    0.9494 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2091    2.4631   -0.6084 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3295    0.3347   -1.2710 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5158   -1.8374   -0.1626 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.5293   -1.2514    1.1316 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0043   -1.9212    1.6297 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3553    0.0055    2.8271 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0459    1.6176    2.1777 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6470    0.5962    2.4797 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.9642    0.5472    0.6773 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2012    0.6846   -0.9168 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9271    1.9624    0.3930 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0931   -1.5611   -0.1017 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8878   -1.3576   -1.9152 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0024   -2.4353   -2.9522 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0448    2.1164    0.6988 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 18  1  0
 18 19  1  0
 19 20  1  0
 20 21  2  0
 20 22  1  0
 22 23  1  0
 18 24  1  0
 24 25  1  0
 25 26  1  0
 26 27  2  0
 26 28  1  0
 25 29  1  0
 29 30  1  0
 29  2  1  0
 29  6  1  0
 17  9  1  0
 25  9  1  0
 28 10  1  0
 22 17  1  0
  1 31  1  0
  1 32  1  0
  1 33  1  0
  2 34  1  0
  6 35  1  0
  7 36  1  0
  8 37  1  0
 10 38  1  0
 11 39  1  0
 11 40  1  0
 12 41  1  0
 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
 18 51  1  0
 22 52  1  0
 23 53  1  0
 30 54  1  0
M  END

HEADER    PROTEIN                                 11-SEP-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   11-SEP-12         0                                  
HETATM    1  C   UNK     0      -4.246  -1.612   0.000  0.00  0.00           C+0
HETATM    2  O   UNK     0      -2.999  -2.521   0.000  0.00  0.00           O+0
HETATM    3  C   UNK     0      -1.750  -1.612   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -2.229  -0.147   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -3.769  -0.147   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -0.210  -1.612   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       0.262  -0.147   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -0.990   0.755   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0      -5.716  -2.089   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0      -4.678   1.102   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       1.500   0.755   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       1.011   2.215   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0      -0.532   2.215   0.000  0.00  0.00           O+0
HETATM   14  C   UNK     0       0.730  -1.612   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       2.257  -1.612   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       2.729  -0.147   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       3.038   0.755   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       3.499   2.215   0.000  0.00  0.00           C+0
HETATM   19  O   UNK     0       2.257   3.106   0.000  0.00  0.00           O+0
HETATM   20  O   UNK     0       1.500  -0.260   0.000  0.00  0.00           O+0
HETATM   21  C   UNK     0       0.349   1.527   0.000  0.00  0.00           C+0
HETATM   22  O   UNK     0       0.349   3.073   0.000  0.00  0.00           O+0
HETATM   23  O   UNK     0       4.964   2.707   0.000  0.00  0.00           O+0
HETATM   24  O   UNK     0       4.583   0.755   0.000  0.00  0.00           O+0
HETATM   25  C   UNK     0       4.222  -0.543   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       5.716  -0.147   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0       5.314  -1.635   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0       4.222  -2.089   0.000  0.00  0.00           C+0
HETATM   29  O   UNK     0       0.189  -3.106   0.000  0.00  0.00           O+0
HETATM   30  O   UNK     0      -2.628   1.347   0.000  0.00  0.00           O+0
CONECT    1    2    5    9                                                  
CONECT    2    1    3                                                       
CONECT    3    2    4    6                                                  
CONECT    4    3    5    8   30                                             
CONECT    5    1    4   10                                                  
CONECT    6    3    7   29                                                  
CONECT    7    6    8   11   14                                             
CONECT    8    4    7   13   21                                             
CONECT    9    1                                                            
CONECT   10    5                                                            
CONECT   11    7   12   16   17                                             
CONECT   12   11   13   19                                                  
CONECT   13    8   12                                                       
CONECT   14    7   15   20                                                  
CONECT   15   14   16                                                       
CONECT   16   11   15   25                                                  
CONECT   17   11   18   24                                                  
CONECT   18   17   19   23                                                  
CONECT   19   12   18                                                       
CONECT   20   14   21                                                       
CONECT   21    8   20   22                                                  
CONECT   22   21                                                            
CONECT   23   18                                                            
CONECT   24   17                                                            
CONECT   25   16   26   27   28                                             
CONECT   26   25                                                            
CONECT   27   25                                                            
CONECT   28   25                                                            
CONECT   29    6                                                            
CONECT   30    4                                                            
MASTER        0    0    0    0    0    0    0    0   30    0   70    0
END

COMPND    HMDB0036861
HETATM    1  C1  UNL     1      -3.242  -1.406   1.778  1.00  0.00           C  
HETATM    2  C2  UNL     1      -3.547  -0.370   0.782  1.00  0.00           C  
HETATM    3  C3  UNL     1      -3.861  -0.902  -0.595  1.00  0.00           C  
HETATM    4  O1  UNL     1      -3.994  -2.117  -0.910  1.00  0.00           O  
HETATM    5  O2  UNL     1      -3.956   0.253  -1.359  1.00  0.00           O  
HETATM    6  C4  UNL     1      -2.789   1.008  -0.991  1.00  0.00           C  
HETATM    7  C5  UNL     1      -1.565   0.346  -1.633  1.00  0.00           C  
HETATM    8  O3  UNL     1      -1.356   0.940  -2.895  1.00  0.00           O  
HETATM    9  C6  UNL     1      -0.486   0.619  -0.687  1.00  0.00           C  
HETATM   10  C7  UNL     1       0.087   1.980  -0.731  1.00  0.00           C  
HETATM   11  C8  UNL     1       1.454   1.824  -0.135  1.00  0.00           C  
HETATM   12  C9  UNL     1       1.797   0.321  -0.249  1.00  0.00           C  
HETATM   13  C10 UNL     1       2.852   0.078   0.702  1.00  0.00           C  
HETATM   14  C11 UNL     1       3.430  -1.322   0.811  1.00  0.00           C  
HETATM   15  C12 UNL     1       2.688   0.569   2.109  1.00  0.00           C  
HETATM   16  C13 UNL     1       4.052   0.902   0.154  1.00  0.00           C  
HETATM   17  C14 UNL     1       0.582  -0.399  -0.491  1.00  0.00           C  
HETATM   18  C15 UNL     1      -0.165  -1.214   0.489  1.00  0.00           C  
HETATM   19  O4  UNL     1       0.541  -2.356   0.636  1.00  0.00           O  
HETATM   20  C16 UNL     1       0.855  -2.687  -0.707  1.00  0.00           C  
HETATM   21  O5  UNL     1       1.130  -3.849  -1.171  1.00  0.00           O  
HETATM   22  C17 UNL     1       0.817  -1.439  -1.529  1.00  0.00           C  
HETATM   23  O6  UNL     1       0.047  -1.493  -2.627  1.00  0.00           O  
HETATM   24  O7  UNL     1      -0.645  -0.409   1.413  1.00  0.00           O  
HETATM   25  C18 UNL     1      -1.183   0.628   0.679  1.00  0.00           C  
HETATM   26  C19 UNL     1      -0.780   1.920   1.293  1.00  0.00           C  
HETATM   27  O8  UNL     1      -0.646   2.097   2.518  1.00  0.00           O  
HETATM   28  O9  UNL     1      -0.624   2.756   0.222  1.00  0.00           O  
HETATM   29  C20 UNL     1      -2.631   0.716   0.501  1.00  0.00           C  
HETATM   30  O10 UNL     1      -3.178   1.895   1.095  1.00  0.00           O  
HETATM   31  H1  UNL     1      -2.567  -1.046   2.572  1.00  0.00           H  
HETATM   32  H2  UNL     1      -2.845  -2.360   1.316  1.00  0.00           H  
HETATM   33  H3  UNL     1      -4.163  -1.758   2.312  1.00  0.00           H  
HETATM   34  H4  UNL     1      -4.564   0.051   1.081  1.00  0.00           H  
HETATM   35  H5  UNL     1      -2.868   2.060  -1.236  1.00  0.00           H  
HETATM   36  H6  UNL     1      -1.861  -0.691  -1.731  1.00  0.00           H  
HETATM   37  H7  UNL     1      -1.889   0.382  -3.544  1.00  0.00           H  
HETATM   38  H8  UNL     1       0.096   2.454  -1.728  1.00  0.00           H  
HETATM   39  H9  UNL     1       1.497   2.054   0.949  1.00  0.00           H  
HETATM   40  H10 UNL     1       2.209   2.463  -0.608  1.00  0.00           H  
HETATM   41  H11 UNL     1       2.329   0.335  -1.271  1.00  0.00           H  
HETATM   42  H12 UNL     1       3.516  -1.837  -0.163  1.00  0.00           H  
HETATM   43  H13 UNL     1       4.529  -1.251   1.132  1.00  0.00           H  
HETATM   44  H14 UNL     1       3.004  -1.921   1.630  1.00  0.00           H  
HETATM   45  H15 UNL     1       3.355   0.006   2.827  1.00  0.00           H  
HETATM   46  H16 UNL     1       3.046   1.618   2.178  1.00  0.00           H  
HETATM   47  H17 UNL     1       1.647   0.596   2.480  1.00  0.00           H  
HETATM   48  H18 UNL     1       4.964   0.547   0.677  1.00  0.00           H  
HETATM   49  H19 UNL     1       4.201   0.685  -0.917  1.00  0.00           H  
HETATM   50  H20 UNL     1       3.927   1.962   0.393  1.00  0.00           H  
HETATM   51  H21 UNL     1      -1.093  -1.561  -0.102  1.00  0.00           H  
HETATM   52  H22 UNL     1       1.888  -1.358  -1.915  1.00  0.00           H  
HETATM   53  H23 UNL     1      -0.002  -2.435  -2.952  1.00  0.00           H  
HETATM   54  H24 UNL     1      -4.045   2.116   0.699  1.00  0.00           H  
CONECT    1    2   31   32   33
CONECT    2    3   29   34
CONECT    3    4    4    5
CONECT    5    6
CONECT    6    7   29   35
CONECT    7    8    9   36
CONECT    8   37
CONECT    9   10   17   25
CONECT   10   11   28   38
CONECT   11   12   39   40
CONECT   12   13   17   41
CONECT   13   14   15   16
CONECT   14   42   43   44
CONECT   15   45   46   47
CONECT   16   48   49   50
CONECT   17   18   22
CONECT   18   19   24   51
CONECT   19   20
CONECT   20   21   21   22
CONECT   22   23   52
CONECT   23   53
CONECT   24   25
CONECT   25   26   29
CONECT   26   27   27   28
CONECT   29   30
CONECT   30   54
END

HMDB0036861
     RDKit          3D
Ginkgolide B
 54 59  0  0  0  0  0  0  0  0999 V2000
   -3.2418   -1.4061    1.7778 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5471   -0.3695    0.7820 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8614   -0.9019   -0.5947 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9938   -2.1168   -0.9098 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9564    0.2531   -1.3588 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7886    1.0083   -0.9905 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5654    0.3458   -1.6330 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3556    0.9404   -2.8953 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4855    0.6189   -0.6868 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0868    1.9798   -0.7305 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4544    1.8242   -0.1352 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7971    0.3212   -0.2493 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8525    0.0778    0.7024 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4304   -1.3216    0.8113 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6881    0.5687    2.1090 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0518    0.9020    0.1540 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5818   -0.3991   -0.4914 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1650   -1.2143    0.4888 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5408   -2.3556    0.6357 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8548   -2.6872   -0.7070 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1298   -3.8491   -1.1709 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8171   -1.4395   -1.5287 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0473   -1.4931   -2.6270 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6449   -0.4093    1.4127 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1831    0.6278    0.6787 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7800    1.9203    1.2927 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6459    2.0974    2.5178 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6235    2.7559    0.2222 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6307    0.7161    0.5005 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1778    1.8946    1.0952 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5666   -1.0460    2.5719 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8445   -2.3598    1.3164 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1628   -1.7578    2.3115 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5643    0.0513    1.0805 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8683    2.0597   -1.2355 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8607   -0.6906   -1.7308 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8891    0.3816   -3.5438 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0965    2.4542   -1.7281 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4973    2.0545    0.9494 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2091    2.4631   -0.6084 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3295    0.3347   -1.2710 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5158   -1.8374   -0.1626 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.5293   -1.2514    1.1316 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0043   -1.9212    1.6297 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3553    0.0055    2.8271 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0459    1.6176    2.1777 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6470    0.5962    2.4797 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.9642    0.5472    0.6773 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2012    0.6846   -0.9168 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9271    1.9624    0.3930 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0931   -1.5611   -0.1017 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8878   -1.3576   -1.9152 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0024   -2.4353   -2.9522 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0448    2.1164    0.6988 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 18  1  0
 18 19  1  0
 19 20  1  0
 20 21  2  0
 20 22  1  0
 22 23  1  0
 18 24  1  0
 24 25  1  0
 25 26  1  0
 26 27  2  0
 26 28  1  0
 25 29  1  0
 29 30  1  0
 29  2  1  0
 29  6  1  0
 17  9  1  0
 25  9  1  0
 28 10  1  0
 22 17  1  0
  1 31  1  0
  1 32  1  0
  1 33  1  0
  2 34  1  0
  6 35  1  0
  7 36  1  0
  8 37  1  0
 10 38  1  0
 11 39  1  0
 11 40  1  0
 12 41  1  0
 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
 18 51  1  0
 22 52  1  0
 23 53  1  0
 30 54  1  0
M  END

View in JSmol View NMR Assignments View Stereo Labels

Synonyms

Value	Source
1-Hydroxy-(1beta)-ginkgolide a	HMDB
BN52021	HMDB
Gingko lactone	HMDB
Ginkolide b	HMDB
Ginkgolide b, (1beta)-isomer	HMDB
Ginkgolide b	MeSH

Chemical Formula

C₂₀H₂₄O₁₀

Average Molecular Weight

424.3986

Monoisotopic Molecular Weight

424.136946988

IUPAC Name

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

Traditional Name

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

CAS Registry Number

15291-77-7

SMILES

CC1C(=O)OC2C(O)C34C5CC(C(C)(C)C)C33C(O)C(=O)OC3OC4(C(=O)O5)C12O

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

InChI Key

SQOJOAFXDQDRGF-UHFFFAOYSA-N

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
Cyclic alcohol
Tetrahydrofuran
Tertiary alcohol
Carboxylic acid ester
Lactone
Secondary alcohol
Organoheterocyclic compound
Oxacycle
Acetal
Carboxylic acid derivative
Polyol
Alcohol
Hydrocarbon derivative
Organic oxide
Organic oxygen compound
Carbonyl group
Organooxygen compound
Aliphatic heteropolycyclic compound

Molecular Framework

Aliphatic heteropolycyclic compounds

External Descriptors

Not Available

Ontology

Physiological effect

Organoleptic effect

Taste

Bitter

Disposition

Biological location

Cellular substructure

Source

Exogenous

Exogenous (HMDB: HMDB0036861)

Food

Herb and spice

Other seed

Ginkgo nuts (FooDB: FOOD00367)

Fat and oil

Fats and oils (FooDB: FOOD00864)

Endogenous

Endogenous (HMDB: HMDB0036861)

Process

Not Available

Role

Not Available

Physical Properties

State

Solid

Experimental Molecular Properties

Property	Value	Reference
Melting Point	280 °C	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	Not Available	Not Available
LogP	Not Available	Not Available

Experimental Chromatographic Properties

Not Available

Predicted Molecular Properties

Property	Value	Source
Water Solubility	5.21 g/L	ALOGPS
logP	0.49	ALOGPS
logP	-0.58	ChemAxon
logS	-1.9	ALOGPS
pKa (Strongest Acidic)	11.71	ChemAxon
pKa (Strongest Basic)	-3.5	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	91.38 m³·mol⁻¹	ChemAxon
Polarizability	39.07 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

Predicted Chromatographic Properties

Predicted Collision Cross Sections

Predictor	Adduct Type	CCS Value (Å²)	Reference
DarkChem	[M+H]+	196.873	31661259
DarkChem	[M-H]-	186.435	31661259
DeepCCS	[M-2H]-	232.538	30932474
DeepCCS	[M+Na]+	207.877	30932474
AllCCS	[M+H]+	191.3	32859911
AllCCS	[M+H-H2O]+	189.1	32859911
AllCCS	[M+NH4]+	193.3	32859911
AllCCS	[M+Na]+	193.9	32859911
AllCCS	[M-H]-	199.7	32859911
AllCCS	[M+Na-2H]-	199.7	32859911
AllCCS	[M+HCOO]-	199.9	32859911

Predicted Retention Times

Underivatized

Chromatographic Method	Retention Time	Reference
Measured using a Waters Acquity ultraperformance liquid chromatography (UPLC) ethylene-bridged hybrid (BEH) C18 column (100 mm × 2.1 mm; 1.7 μmparticle diameter). Predicted by Afia on May 17, 2022. Predicted by Afia on May 17, 2022.	5.12 minutes	32390414
Predicted by Siyang on May 30, 2022	12.8705 minutes	33406817
Predicted by Siyang using ReTip algorithm on June 8, 2022	2.18 minutes	32390414
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid	2342.3 seconds	40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid	203.1 seconds	40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid	125.1 seconds	40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid	152.3 seconds	40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	84.1 seconds	40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid	548.0 seconds	40023050
BfG_NTS_RP1 =Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) with Water:ACN and 0.1% Formic Acid	668.7 seconds	40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)	75.1 seconds	40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid	872.9 seconds	40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid	420.1 seconds	40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid	1650.7 seconds	40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	314.7 seconds	40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	320.6 seconds	40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate	304.1 seconds	40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA	115.8 seconds	40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water	74.2 seconds	40023050

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
Ginkgolide B	CC1C(=O)OC2C(O)C34C5CC(C(C)(C)C)C33C(O)C(=O)OC3OC4(C(=O)O5)C12O	4117.2	Standard polar	33892256
Ginkgolide B	CC1C(=O)OC2C(O)C34C5CC(C(C)(C)C)C33C(O)C(=O)OC3OC4(C(=O)O5)C12O	2731.9	Standard non polar	33892256
Ginkgolide B	CC1C(=O)OC2C(O)C34C5CC(C(C)(C)C)C33C(O)C(=O)OC3OC4(C(=O)O5)C12O	3256.5	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
Ginkgolide B,1TMS,isomer #1	CC1C(=O)OC2C(O[Si](C)(C)C)C34C5CC(C(C)(C)C)C36C(OC(=O)C6O)OC4(C(=O)O5)C12O	3249.3	Semi standard non polar	33892256
Ginkgolide B,1TMS,isomer #2	CC1C(=O)OC2C(O)C34C5CC(C(C)(C)C)C36C(OC(=O)C6O[Si](C)(C)C)OC4(C(=O)O5)C12O	3276.8	Semi standard non polar	33892256
Ginkgolide B,1TMS,isomer #3	CC1C(=O)OC2C(O)C34C5CC(C(C)(C)C)C36C(OC(=O)C6O)OC4(C(=O)O5)C12O[Si](C)(C)C	3286.8	Semi standard non polar	33892256
Ginkgolide B,2TMS,isomer #1	CC1C(=O)OC2C(O[Si](C)(C)C)C34C5CC(C(C)(C)C)C36C(OC(=O)C6O[Si](C)(C)C)OC4(C(=O)O5)C12O	3214.6	Semi standard non polar	33892256
Ginkgolide B,2TMS,isomer #2	CC1C(=O)OC2C(O[Si](C)(C)C)C34C5CC(C(C)(C)C)C36C(OC(=O)C6O)OC4(C(=O)O5)C12O[Si](C)(C)C	3218.4	Semi standard non polar	33892256
Ginkgolide B,2TMS,isomer #3	CC1C(=O)OC2C(O)C34C5CC(C(C)(C)C)C36C(OC(=O)C6O[Si](C)(C)C)OC4(C(=O)O5)C12O[Si](C)(C)C	3250.3	Semi standard non polar	33892256
Ginkgolide B,3TMS,isomer #1	CC1C(=O)OC2C(O[Si](C)(C)C)C34C5CC(C(C)(C)C)C36C(OC(=O)C6O[Si](C)(C)C)OC4(C(=O)O5)C12O[Si](C)(C)C	3167.5	Semi standard non polar	33892256
Ginkgolide B,1TBDMS,isomer #1	CC1C(=O)OC2C(O[Si](C)(C)C(C)(C)C)C34C5CC(C(C)(C)C)C36C(OC(=O)C6O)OC4(C(=O)O5)C12O	3494.9	Semi standard non polar	33892256
Ginkgolide B,1TBDMS,isomer #2	CC1C(=O)OC2C(O)C34C5CC(C(C)(C)C)C36C(OC(=O)C6O[Si](C)(C)C(C)(C)C)OC4(C(=O)O5)C12O	3515.2	Semi standard non polar	33892256
Ginkgolide B,1TBDMS,isomer #3	CC1C(=O)OC2C(O)C34C5CC(C(C)(C)C)C36C(OC(=O)C6O)OC4(C(=O)O5)C12O[Si](C)(C)C(C)(C)C	3520.4	Semi standard non polar	33892256
Ginkgolide B,2TBDMS,isomer #1	CC1C(=O)OC2C(O[Si](C)(C)C(C)(C)C)C34C5CC(C(C)(C)C)C36C(OC(=O)C6O[Si](C)(C)C(C)(C)C)OC4(C(=O)O5)C12O	3692.6	Semi standard non polar	33892256
Ginkgolide B,2TBDMS,isomer #2	CC1C(=O)OC2C(O[Si](C)(C)C(C)(C)C)C34C5CC(C(C)(C)C)C36C(OC(=O)C6O)OC4(C(=O)O5)C12O[Si](C)(C)C(C)(C)C	3695.6	Semi standard non polar	33892256
Ginkgolide B,2TBDMS,isomer #3	CC1C(=O)OC2C(O)C34C5CC(C(C)(C)C)C36C(OC(=O)C6O[Si](C)(C)C(C)(C)C)OC4(C(=O)O5)C12O[Si](C)(C)C(C)(C)C	3716.8	Semi standard non polar	33892256
Ginkgolide B,3TBDMS,isomer #1	CC1C(=O)OC2C(O[Si](C)(C)C(C)(C)C)C34C5CC(C(C)(C)C)C36C(OC(=O)C6O[Si](C)(C)C(C)(C)C)OC4(C(=O)O5)C12O[Si](C)(C)C(C)(C)C	3891.1	Semi standard non polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted GC-MS	Predicted GC-MS Spectrum - Ginkgolide B GC-MS (Non-derivatized) - 70eV, Positive	splash10-0563-6309100000-5d8db9a6c653286f45e8	2017-09-01	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Ginkgolide B GC-MS (3 TMS) - 70eV, Positive	splash10-056s-6100293000-ba69172eefbf4842d07e	2017-10-06	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Ginkgolide B GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum

MS/MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Experimental LC-MS/MS	LC-MS/MS Spectrum - Ginkgolide B DI-ESI-qTof , Negative-QTOF	splash10-014i-0009000100-79b8f41db04961920091	2017-09-14	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Ginkgolide B LC-ESI-qTof , Positive-QTOF	splash10-0002-0000900200-8a80deff2715f73fb266	2017-09-14	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Ginkgolide B LC-ESI-QTOF , negative-QTOF	splash10-014i-0009300000-2d1be2b7f4a303dbc532	2017-09-14	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Ginkgolide B LC-ESI-QTOF , negative-QTOF	splash10-014i-0019000000-7e7586a158572b62df99	2017-09-14	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Ginkgolide B LC-ESI-QTOF , negative-QTOF	splash10-004i-0930000000-b50474afac91ca4d0eaa	2017-09-14	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Ginkgolide B , positive-QTOF	splash10-0002-0000900200-8a80deff2715f73fb266	2017-09-14	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Ginkgolide B 6V, Positive-QTOF	splash10-03fr-3910000000-53a6fd3834d255b5e86e	2021-09-20	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Ginkgolide B 6V, Positive-QTOF	splash10-03fr-2910000000-100f0c4006fa857f3d34	2021-09-20	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Ginkgolide B 40V, Negative-QTOF	splash10-004i-0920000000-e7c84af18881fafe1a2d	2021-09-20	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Ginkgolide B 6V, Positive-QTOF	splash10-01b9-0009500000-88dd08d0daa203cf069b	2021-09-20	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Ginkgolide B 6V, Positive-QTOF	splash10-03fs-3910000000-2e6c217b4ef8d6bd2b4c	2021-09-20	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Ginkgolide B 6V, Positive-QTOF	splash10-014i-0309200000-d48c0963d3422e70390d	2021-09-20	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Ginkgolide B 6V, Positive-QTOF	splash10-014i-0309200000-ad7a1024245c3341db4f	2021-09-20	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Ginkgolide B 10V, Negative-QTOF	splash10-014i-0009300000-83413f12ea47ac7ee86f	2021-09-20	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Ginkgolide B 6V, Positive-QTOF	splash10-014i-0209200000-4fad3201746e7206b156	2021-09-20	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Ginkgolide B 6V, Positive-QTOF	splash10-01b9-0009500000-6c4251a9ce278d0f7bac	2021-09-20	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Ginkgolide B 20V, Negative-QTOF	splash10-014i-0019000000-ce93d1194e474d1a5f75	2021-09-20	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Ginkgolide B 6V, Positive-QTOF	splash10-01t9-0910000000-8202fa7dd51883f69a49	2021-09-20	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Ginkgolide B 6V, Positive-QTOF	splash10-01t9-0910000000-5629f53b37c85be8a155	2021-09-20	HMDB team, MONA	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Ginkgolide B 10V, Positive-QTOF	splash10-004i-0003900000-17c76d71f92768eb8b42	2015-04-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Ginkgolide B 20V, Positive-QTOF	splash10-004i-2029500000-f667542ec482ee74195c	2015-04-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Ginkgolide B 40V, Positive-QTOF	splash10-0a5i-5009200000-a198da55d2ed6f6148f3	2015-04-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Ginkgolide B 10V, Negative-QTOF	splash10-00fr-0006900000-efb50da734af1163102e	2015-04-25	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Ginkgolide B 20V, Negative-QTOF	splash10-00fr-1009600000-55a47b898b9ca3aff650	2015-04-25	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Ginkgolide B 40V, Negative-QTOF	splash10-0a5i-1019000000-ce72b770cd3c51f2d411	2015-04-25	Wishart Lab	View Spectrum

NMR Spectra

Spectrum Type	Description	Deposition Date	Source	View
Predicted 1D NMR	¹³C NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum

Biological Properties

Cellular Locations

Cytoplasm
Extracellular
Membrane

Biospecimen Locations

Blood
Urine

Tissue Locations

Not Available

Pathways

Not Available

Name	SMPDB/PathBank	KEGG

Normal Concentrations

Not Available

Abnormal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Blood	Expected but not Quantified	Not Quantified	Not Specified	Not Specified	Cancer patients undergoing total body irradiation	31424920	details
Urine	Detected but not Quantified	Not Quantified	Not Specified	Not Specified	Cancer patients undergoing total body irradiation	31424920	details

Associated Disorders and Diseases

Disease References

None

Associated OMIM IDs

None

External Links

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

KNApSAcK ID

Chemspider ID

KEGG Compound ID

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Ginkgolide

METLIN ID

Not Available

PubChem Compound

65243

PDB ID

Not Available

ChEBI ID

Not Available

Food Biomarker Ontology

Not Available

VMH ID

Not Available

MarkerDB ID

Not Available

Good Scents ID

rw1395201

References

Synthesis Reference

Not Available

Material Safety Data Sheet (MSDS)

Not Available

General References

Simons K, Toomre D: Lipid rafts and signal transduction. Nat Rev Mol Cell Biol. 2000 Oct;1(1):31-9. [PubMed:11413487 ]
Watson AD: Thematic review series: systems biology approaches to metabolic and cardiovascular disorders. Lipidomics: a global approach to lipid analysis in biological systems. J Lipid Res. 2006 Oct;47(10):2101-11. Epub 2006 Aug 10. [PubMed:16902246 ]
Sethi JK, Vidal-Puig AJ: Thematic review series: adipocyte biology. Adipose tissue function and plasticity orchestrate nutritional adaptation. J Lipid Res. 2007 Jun;48(6):1253-62. Epub 2007 Mar 20. [PubMed:17374880 ]
Lingwood D, Simons K: Lipid rafts as a membrane-organizing principle. Science. 2010 Jan 1;327(5961):46-50. doi: 10.1126/science.1174621. [PubMed:20044567 ]
(). Yannai, Shmuel. (2004) Dictionary of food compounds with CD-ROM: Additives, flavors, and ingredients. Boca Raton: Chapman & Hall/CRC.. .
Gunstone, Frank D., John L. Harwood, and Albert J. Dijkstra (2007). The lipid handbook with CD-ROM. CRC Press.

Showing metabocard for Ginkgolide B (HMDB0036861)

MOL for HMDB0036861 (Ginkgolide B)

3D MOL for HMDB0036861 (Ginkgolide B)

3D SDF for HMDB0036861 (Ginkgolide B)

3D-SDF for HMDB0036861 (Ginkgolide B)

PDB for HMDB0036861 (Ginkgolide B)

3D PDB for HMDB0036861 (Ginkgolide B)

SMILES for HMDB0036861 (Ginkgolide B)

INCHI for HMDB0036861 (Ginkgolide B)

Structure for HMDB0036861 (Ginkgolide B)

3D Structure for HMDB0036861 (Ginkgolide B)

Predicted Collision Cross Sections

Predicted Retention Times

Underivatized

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra

NMR Spectra