ZINC:Problems

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Problems with individual molecular representations (e.g. broken molecules), questions about the interface, non catastrophic errors should be reported in our Support Forum. Emergencies (e.g. the site is down, no search will work) should be reported to Zinc Support.

This is the ZINC problems page, which describes all the problems specific to ZINC. Other problem pages are available: DOCK Blaster:Problems, DUD:Problems, DOCK:Problems, Problems.

Problem 1

In this paper

http://www.sciencedirect.com/science/article/pii/S0968089609001114?np=y

It is sub nanomolar

http://zinc15.docking.org/genes/ADRA2B/observations/?zinc_id=ZINC000100006770

But the compound in ZINC (and likely ChEMBL) is not the right one

Have not yet written to ChEMBL

Problem 2 - Sept 2016

Incorrect imidazole with =C= traced back to PDB

Wrote to RCSB

They sent it along to EBI

Have not heard back

Problem 3 - Aug 2016

Wrote to biosynth vendor about an error

Not sure if we heard back

Deleted wrong molecule from ZINC

Problem 4 - Sept 29

roglizitizone is not a AGTR1 agonist

http://zinc15.docking.org/substances/ZINC000000968330/

Have not told ChEMBL yet.

Paper is suspicious

http://link.springer.com/article/10.1007%2Fs00044-008-9152-x

Problem 5 - Oct 4

http://zinc15.docking.org/substances/ZINC000112987563/

is a radical. comes from MolPort. Wrote to them on Oct 4.

Problem 6 - Sept 29

Non-exhaustive list of problems we are aware of

  • Molecule duplication
  • Incorrect representation
  • Missing representation
  • Missing catalog
  • Missing molecule
  • Out of date catalogs

broken molecules

C04476765 C05925570 C04914001 C00315585 C02483697 C05477751 C67328881 C21032807 C10809385 C00238298 C20580044 C10809385


  • Probably incorrect enumeration/sampling of stereochemistry both R/S and E/Z
  • incorrect treatment of protonation and tautomerization in some cases
  • search way too slow
  • problem with links to supplier web sites
  • tutorials
  • protocols

More details about problems we are aware of

  • Unreasonable tautomers: We generate some tautomers that we shouldn't. Among the ones we know about is CH3-C=NH -> CH2=C-N.
  • Aggressive protonation: We generate protonated forms that are probably unreasonable for most targets, such as protonated pyridines. This is an active area of research. Please be patient.
  • Truncated Searches: Search results currently limited to 500 (anonymous) or 5000 (logged in). We are working towards a solution (expected Fall 2012).
  • Duplication: We are aware of a thousands of duplicate molecules in ZINC. We continue to work on a robust solution to this problem.


  • duplicates:
http://zinc.docking.org/substance/13952160
http://zinc.docking.org/substance/4798508

There are literally thousands of these. We regret this problem, and will fix it one day. For now, please try to ignore it.