The ChEMBL-og

As chemical curator for ChEMBL, I spend a lot of time processing, checking and standardising the compounds in the database. I use various pieces of software for this, but mostly it’s  Pipeline Pilot . For those of you who don’t know, Pipeline Pilot is Accelrys’s graphical scientific workflow authoring application, that allows passing hundreds of thousands of compounds through various components to make sure they meet our standards to be loaded into ChEMBL. However, it’s always incredibly useful to utilise other available software in a complementary manner to see if anything may have been missed, could be done in a different way or just to see what alternative results you can get. One such open source software package is Indigo , created by GGA Software Services . On of the web application developers was passing all of the ChEMBL compounds through the standard Indigo loader, via a Python script, during the course of his work, and found that there were about 9,000 compoun...

Further to my post a few months ago ( To Remove or Not to Remove ) about removing certain problem metal-containing compounds, we have now come up with a plan of what to do. Instead of labeling this curation as ‘removal of inorganics’, or ‘removal of organometallics’, we simply want this to be known as ‘removal of some metal-containing compounds’. The criterion that we used was to exclude a large proportion of compounds that contained a metal, apart from cases where a metal was commonly found as part of a pharmaceutical preparation (e.g. Ranitidine Bismuth Citrate CHEMBL2111286 , Silver Sulfadiazine CHEMBL1382627 , Bacitracin Zinc CHEMBL2096639 ). The reasoning behind the removal of such compounds was that most of these metals are bonded to the rest of the compound components via coordinate bonds. However, due to InChI limitations , there is no way of creating a Standard InChI that retains coordinate bond information. As we use Standard InChI as the ...

During the course of standard compound curation, I come across problem inorganic compounds. An example of these are Cisplatin and Transplatin . These compounds only differ in the orientation of their complex bonds but complex bonds cannot be drawn in a standard molfile without causing InChI issues. At the  moment, they are kept separate by showing standard bonds between the Pt, Cl and NH3 in Cisplatin, but we have removed the bonds altogether for Transplatin. This is not an ideal situation, nor an accurate structural representation. Another example is the compound , below left, and how it should look as a complex, right, from the paper: At the moment, there are approximately 1,800 cases like this, which only accounts for 0.15% of the entire ChEMBL compound set. What we are proposing to do is to remove the structures for these complex compounds and to keep only their names and all of the associated biological data. This would then treat them in a similar way to the a...

For the last three months, I've been busy working my way through a 9000 long (sometimes headache-inducing) set of ChEMBL compound ids. These had been highlighted for curation for the reason that for each ChEMBL_id in the list, there were two or more compound keys from the same paper. This implied that either there were two indistinguishable using InChI representation compounds described in the paper or they were different compounds that had been somehow merged together in the database. Each ChEMBL_id was individually checked against the data in the original paper to see if there were indeed two compound keys for the same structure. The outcome of this check gave rise to one of four cases: The structure(s) was found to be incorrect and was redrawn. The structure was correct for some records but not others, so a new compound was created for those selected records. The structure required the definition of stereochemistry or a salt. The structure was le...