The registration of chemical structures is the default registration setting in CDD Vault. Additional registration types can be enabled. Please contact CDD Support if you would like to register other types of entities.
A molecule can be either a chemical structure (with salt(s) and/or solvents), a structureless record (i.e. a molecule record which is chemical structure is unknown) or a simple mixture of two or more disconnected structural fragments.
A single chemical entity can be registered with salts or solvents, and associated Molecule and Batch information from either the Explore Data tab (Create a new… > Molecule)
or from the Molecules page (+ Create a new molecule).
In the past, structureless chemical entities were commonly used to register molecules where the structure was either unknown, or large, such as antibodies, sequences, proteins, etc. However, with the recent CDD Vault updates it is now possible to register different entities in CDD Vault.
The registration of different types of entities, including biological entities is described in this KB article.
Registering a chemical structure with salts
- Click Launch the Structure Editor or paste the SMILES, MOL file or IUPAC name in the Structure box.
- To add salts:
If the structure you provided contains salts or solvents drawn as part of the chemical structure, click the Strip radio button.
- To add salts:
- To enter salt or solvent information textually (not included in the structure object):
- Click the Stoichiometry radio button.
- Enter the salt ratio then type the salt name. A filtered list of salts will be displayed. Select the appropriate salt. More information about salts can be found here.
- For solvents, enter the solvent ratio and select the solvent from the pick list.
If the salt or solvent you need is not in the list, please contact CDD support to have the salt or solvent added to the list.
If you want to register a pair of pure enantiomers with unknown absolute configuration, please see this article.
Registering a chemical entity without a structure (a structureless or “No-Struct” entity)
- Do not click Launch the Structure Editor and leave Structure box blank.
- Fill in any data you wish to populate in the Molecule and Batch Information section. Note: The Batch Salt will be set to "Unknown Salt".
- Select the desired Project and click the green button Create Molecule.
Registering simple mixtures as structure
Chemical entity mixtures can contain 2 or more structural fragments.
Please note that there is a new CDD Vault configuration which supports the registration of pure mixtures and includes a brand new editor to accurately capture and fully annotate components, amounts, hierarchy and additional properties. More details can be found here.
To register a mixture of disconnected fragments as a chemical structure:
- Click Launch the Structure Editor to draw the mixture or paste the SMILES, MOL file or IUPAC name in the Structure box.
- Click the Stoichiometry radio button (this will prevent CDD Vault from stripping one of the molecules as a salt)
- If salts or solvents to be added, enter Salt and/or Solvent
- If the Salt field is left blank, the Salt will be set to "No Salt, free base or acid".
Your registered mixture will look like this:
Note: If you choose Strip, CDD Vault will try to strip salts and solvents from the structure. If a salt is recognized, a single entity with salt information in the salt batch field will be registered.
If no salts are recognized, an error message is displayed.
Registering a Pure Mixture Entity
Once the multiple registration types is enabled by CDD Support, the Vault Administrator can navigate into Settings -> Vault -> General within each individual Vault to select the Mixtures entity type. If you are a Vault Administrator click here to find out more.
This article describes how to register a mixture entity.