CDD Vault Update (August 2023)

Atropisomer Registration in CDD Vault

CDD Chemistry now provides a unique, efficient, and robust way of registering atropisomers. Distinct atropisomers can be drawn and registered into CDD Vault as separate Molecules with unique IDs.

Here are the rules for successfully representing an atropisomer:

1. molecule must have coordinates
2. atropisomer bond must be a single bond
3. each atom of that bond must be sp2 hybridized
4. each atom of that bond must have 1 or 2 neighboring single, double or aromatic bonds where at least one neighboring bond is a single bond drawn using either "wedged" (up) or "hashed" (down) bond type
1. Neighboring bonds on the same end atom must be opposed, one wedged and the other hashed.
2. Bonds appearing on opposite sides of the atropisomer bond must be consistent, both wedges or hashes.
3. If two wedged/hashed bonds are on the same side of the atropisomer bond, one must be a wedge and the other a hash.

Helpful Hints:

• Atropisomers can include enhanced stereochemistry groups (Or, And, Absolute), which are indicated by marking one or both of the atropisomer bond's atoms.
• If 3D coordinates are available (and 2D coordinates are not), the atropisomer bond is recognized only if one of the neighbor bonds is wedged/hashed (up/down). The wedge/hash information is ignored except for signaling the presence of the atropisomer. The actual configuration is determined by the 3D coordinates.
• Explicit atropisomers drawn as queries are ignored in substructure (SSS) and similarity searching.
• The structures drawn below are unique atropisomer examples handled by CDD Vault.

Streamlining API Slurps

Additional parameters have been added to the POST Slurps API call to resolve Ambiguous and Suspicious events and ignore errors that occur during an import.

Specify how Ambiguous events, if any, are handled:

none - Ambiguous events are not resolved and the autoreject parameter is used to determine the behavior

reject - automatically rejects all Ambiguous events

new_molecule - automatically creates new parent-level Molecules (used when tautomers are detected or an enhanced stereo OR label exists)

new_batch - automatically creates new Batches of existing Molecules (used when tautomers are detected or an enhanced stereo OR label exists)

Specify how Suspicious events, if any, are handled:

none - Suspicious events will not be resolved and the autoreject parameter is used to determine the behavior

reject - automatically rejects all Suspicious events

accept - automatically accepts all Suspicious events 

Option to ignore errors and commit your file:

true - all errors will be ignored

false - errors will not be ignored and the autoreject parameter is used to determine the behavior

When using the API to post multiple files, the use of these parameters can help ensure all files are processed appropriately and without manual intervention.

This blog is authored by members of the CDD Vault community. CDD Vault is a hosted drug discovery informatics platform that securely manages both private and external biological and chemical data. It provides core functionality including chemical registration, data visualization, inventory, and electronic lab notebook capabilities.