ZINC-22 rearrangement of May-24

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A few things have happened recently, which we describe below.

Enamine Macrocycles

  • We have released a new layer /zinc-22w/, Enamine macrocycles. These are based on a private library of about 150K from Enamine as follows:
  • 104,060 H19 to H39.
  • 45,985 H40 to H49
  • 654 H50-H54

We have built to H39. Next time (summer) we will build to H49.

The 104,060 expand to 144,978K with steroisomers. That's dockable today in /zinc-22w/ To be clear, this number double-counts protonation states with different charges, thus if there is an imidazole and there is one protonated and one unprotonated, it counts as two. So maybe 140K really.

More ZINC-22 3D structures for docking

  • For background information about layers, see ZINC22:Layers.
  • We have begun to release a new layer, /zinc-22y/.
  • This is an incremental update.
  • We took all the molecules in 2D registered in ZINC to H24 and ask how many of these are _not_ available in 3D ready to dock formats.
  • We found about 4 billion such molecules, just up to H24.
  • /zinc-22y/ is available to H19 as of May 23, 2024. We expect to get up to H24 fully updated by summer. Then we will turn to H25-29.

Molecule counts in 2D tranche browser

  • We have updated 2D molecule counts in ZINC-22.
  • Thus the 2D browser is now a correct summary of what we have loaded.
  • ZINC-22 2D is now about 50% bigger. Old count was around 37B. Now around 55B.

Smallworld and Arthor databases

There are now five servers of each, thus: sw (public, no pw), swp (private, pw, but available), swcc (chemistry commons), swbb (building blocks) and one more that is private to UCSF. For Arthor it is the same thing: arthor, arthorp, arthorcc, arthorbb and a UCSF only one.

3D tranche updates to follow

  • We have been building and updating 3D tranches for about a year, and are now starting to push them to public servers.

This will happen over the coming weeks and we will announce when it is done.

Cartblanche22.docking.org

  • There have been a lot of bug fixes in Cartblanche22.docking.org. It is much more reliable now than earlier versions. If you had trouble with it, please try again.

Freshly updated SDI files

  • new SDI files in /zinc-22x/sets/ as of 2024-05-20
  • also available on Wynton.
  • will be on AWS by June 1, 2024.
/wynton/group/bks/sets/ and
/nfs/exd/zinc-22x/sets/

They contain lists of ZINC-22 tranches organized by charge-HAC-name.suffix where

  • charge: N=neutral, M= -1, O= +1 and so on.
  • HAC is H04 to H39
  • name is lead-like (HAC 17-25), frag-like (HAC 04-16), also big, greasy-leads, big-greasy
  • suffix is txt (our lab), wyn (wynton) and s3 (AWS)

/zinc-22c/ zwitterions

  • Recently updated to H19.
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