Recently David Bradley blogged on Spinneret about the application of coherent anti-Stokes Raman scattering microscopy to evaluate a new approach to the controlled released of the drug Taxol. I’m sure all chemists have heard of Taxol at this point? It’s got a great history and that is discussed on many other places so I’m not going to belabor that. What Taxol is, for the purpose of this rant, is a nice structure…lots of stereochemistry and not simple to draw (there are certainly worse of course.) The structure is shown below.

Structure of Taxol

While thinking through the concept of providing a central resource for Natural Product chemists to deposit and access information of value to their community I started looking at Taxol as an example of the type of complexity we’d be dealing with in terms of structural complexity during the deposition process. My question was how well would it be dealt with already…

So, I did a few searches….

I searched the InChI generated from the structure shown above in Google. I received three hits on this search including

1) Goodman’s Group in Cambridge – check out the page..uses Jmol and is a good example of how nice this tool is. Click and rotate the molecule! JMol will show up on ChemSpider soon.

2) A link into Drugbank

I also used PubChem, Emolecules and ChemSpider to provide me links into their various data sources. The search was simple..I searched on the compound name of Taxol in each system since I was trying to emulate a search that a user would do…search for the compound by name and identify the “correct structure”. Some interesting results…

1) PubChem: 37 hits total with the top 4 being “Taxol” hits rather than Taxol analogs. The structures are shown below.

Taxol on PubChem

Consistent masses…of the four, three have the same mass one doesn’t. The FIRST in the list matches what we believe is the correct structure for Taxol based on matching the InChIs with that of the structure above.

2) Emolecules : I received two results…sometimes 7 hits, sometimes 4…including the issue observed in PubChem of one Taxol not having the correct mass. I cannot find InChI codes on Emolecules (though they might be there) so cannot confirm which is the right Taxol or even whether it is on there. Since a lot of the data includes PubChem deposition I believe it will be there but I searched on the two PubChem links for CID 36314 (the first structure in the PubChem image above) and could not find that link (here or here). Again…I think it’s there but don’t know where.

3) ChemSpider : 4 hits obtained, one with the Mw issue shown in Emolecules and PubChem and the correct Taxol being record ID 390039. The first record is the correct Taxol as evidenced by the InChI match as well as the link back to PubChem 36314 as shown below.

ChemSPider to PubCHem link

Confused yet??? Here’s what it means …the data quality of Taxol across many databases is in question. Online resources, including our own (!) abound with errors and while there are ongoing discussions about scraping data from this source and that using robots are appropriate in technology WHO is going to ensure quality? We would like to hold ChemSpider up as a quality resource of course…as would our other colleagues at PubChem, Emolecules and a majority of data source providers. I’ve just shown…there are issues.

We ARE curating our data…thankfully the chemistry community is helping. Together we have a chance to make a difference.

Last night we received a comment from a curator stating “This structure is not correct for bis(3-ethylhexyl) phthalate. Also, on a somewhat related note, I couldn’t find an entry for bis(2-ethylhexyl) phthalate, which, in terms of chemical production, is probably the most abundant of all phthalates.” for record 556873. How RIGHT he is. A lot of us have the same problem! See here

Issues like this can be caught with name to structure conversion algorithms and comparisons but the work must be done…until then, manual curation of the database is necessary. Thanks to those helping!

Stumble it!

6 Responses to “Will the Correct Structure of Taxol PLEASE STAND UP!!!!”

  1. David Bradley says:

    Hey Tony, glad that latest Spinneret item was so inspirational, there does seem to be a whole lot of pent up confusion in Taxol, especially as the authors of the original CARS research use only its generic name, paclitaxel, and searching with that term in itself seems to be something of a minefield.


  2. ChemSpider Blog » Blog Archive » Does ChemSpider Unashamedly Exploit the PubChem Resource? says:

    [...] and there will be an abundance of data to return to PubChem. See the recent discussions about Taxol and Thimerasol as examples. There’s a lot more where those came [...]

  3. ChemSpider Blog » Blog Archive » Will the Correct Structure of Taxol Please Stand Up. Part 2. says:

    [...] Â covered the issue of taxol a few weeks ago: Today Taxol came up again on a post by Peter Murray-Rust. First of all a couple of comments re the [...]

  4. ChemSpider Blog » Blog Archive » Will the Correct Structure of Taxol Please Stand Up. Part 3. says:

    [...] is part 3 (1,2) in the mission to correctly identify the structure of Taxol. I’ve gone on the mission to [...]

  5. Unilever Centre for Molecular Informatics, Cambridge - petermr’s blog » Blog Archive » Comments on comments and agents and eyeballs says:

    [...] 3:55 pm ePeter, I’ve given many examples of the issue of Data Quality on the blog. Some links are: [...]

  6. ChemSpider Blog » Blog Archive » STOP COUNTING the Number of Chemical Entities in Public Compound Databases and There are Ghosts in the Closet says:

    [...] to communicate the issue. I’ll try again but I reference you to previous posts about Taxol (1,2,3), Vancomycin (4) and Ginkgolide B (5,6). I suggest you read these earlier posts but will try [...]

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