Recently I posted about trying to identify the correct structure of Ginkgolide B and the need for curation of ChemSpider entries. David Barden from the RSC commented on my post:

“Antony – I am an organic chemist working on the RSC journal in which the published structure of ginkgolide B appeared, and am pretty sure that it is correct, having been written by a regular author of ours familiar with the literature on the ginkgolides. I think the problem might lie with the representation (and/or conversion to InChI) of the structures – even in the one structure you indicated as having “full stereochemistry”, it seemed to me that 3 stereocenters were undefined, from a visual inspection of the structure. Apart from these stereocenters, the structure and InChI (generated myself) otherwise seem identical, so I’m not sure why the last part of the string in the ChemSpider entry is “20+” rather than “20-”. The difficulty of visually comparing structures from different sources (rotation, reflection, etc), especially for complex molecules like this, would make the task of validation much more difficult.”

I have redrawn the structure of Ginkgolide to echo that shown in the RSC journal and it is shown below alongside a cropped image from the article:


I’m_pretty sure I have the structure correct. The InChIString is:


and the InChIKey is:


In the previous post I searched on Ginkgolide B as an identifier to see how many Ginkgolide B’s there are. There are 6 as shown here.

I searched on the entire InChIkey and found no hits. This means that the structure is NOT on ChemSpider.

I then searched on the CONNECTIONs captured within the InChIKey and represented by: SQOJOAFXDQDRGF . I received 18 hits in total varying in completeness in terms of incomplete stereochemistry and DIFFERENT but fully assigned stereochemistry. I searched the entire InChIKey on Google (SQOJOAFXDQDRGF-MMQTXUMRBS) but received no hits. Just to check I then searched the InChIString shown above on Google. Surprisingly, I DID get a hit! It was for this structure. I was puzzled and a comparison of the strings showed a difference in ONE section of the string, the stereo layer.

Searched on Google: /t6-,7+,8-,9+,10+,11+,15+,17+,18+,19-,20-/m1/s1

Found by Google: /t6-,7​+,8-,9+,10​+,11+,15+,​17+,18+,19​-,20+/m1/s​1

See the difference? ONE stereocenter… 20- versus 20+ . Thank goodness we are moving to InChIKeys rather than InChIStrings since the majority of people would likely miss the detail. I did the first time! So, based on all of my searches the structure of Ginkgolide B as represented in the article published by the RSC is NOT in the ChemSpider database. I agree with David Barden when he comments “The difficulty of visually comparing structures from different sources (rotation, reflection, etc), especially for complex molecules like this, would make the task of validation much more difficult.” It is very complex and time-consuming and the hope is that comparison of InChIKeys, specifically the second part of the key, will help catch the differences in a more facile manner.

The question, unfortunately, remains. What IS the correct structure of Ginkgolide B? For now I have assumed that the one in the RSC article is correct and have added the structure to the database using the normal deposition process and have associated with the RSC article and the blog discussions on ChemSpider. If it turns out it is not correct then I will leave the structure, the connection to the article but remove the identifier Ginkgolide B.


Stumble it!

One Response to “More on Ginkgolide B”

  1. ChemSpider Blog » Blog Archive » A Request for a Crowdsourced Investigation of Digitonin says:

    [...] we have undertaken some fairly demanding curation activities. For example, Vancomycin and Ginkgolide B. Now we are in the middle of trying to resolve the structure of Digitonin. There are 25 (!) [...]

Leave a Reply