Hi!
Im trying to download lead-like clean commercially available molecules ready for docking with the following properties, xlogp.max = 3.5, molwt.max = 350, rotbond.max = 7, HBD.max = 5, HBA.max = 10, purchasability = purchasable. In the page size box I put down ALL to download and did it in mol2 format.
The mol2 file however only contains about 7.000 molecules and should be quite larger than that. What am I doing wrong? Or is it that I dont have access to the whole database?
Best regards, Ivana
same thing for me
I have a very similar problem! I think it's a bug! I've posted a new thread for my particular problem...
more about HBD and HBA constraints
Hi -
I expect that logP of 3.5 is going to get all the HBD>5 and HBA>10 compounds, and that adding those constraints makes no change to the subset. Do you want them because of Lipinsky 1997? Recall those are needed with mwt 500 and logP of 5. Here, you've already cut off 150 Da and 1.5 logs in lipophilicity, so I don't think they're needed.
Thus just use the pre-made subset.
John
here is how
Here is something close:
1. subsets -> properties (http://zinc.docking.org/browse/subsets/)
2. click on clean-leads http://zinc.docking.org/subsets/clean-leads
3. click on unix download, mol2 under quick links http://zinc.docking.org/db/bysubset/11/usual.mol2.csh
csh usual.mol2.csh
Your protocol includes fragments, which you can get by repeating the above with clean-frags.
You have different values for HBA and HBD. If you must have those values, then I suggest downloading "clean drugs" and filtering what remains yourself.
Good docking