How to use TUGDB

About TUGDB

TUGDB contains all compounds synthesized and tested in the Ulven group (TUG) through the years. All compounds are well-characterized and registered with consecutive TUG numbers. Compounds are organized in projects (often associated with targets), some are in several projects, and current group members have access to compounds in their projects and can submit new compounds to these.

Searching TUGDB

Enter tugdb.dk in the URL field of your browser. This takes you to the search page (you may have to log in).

Structure search: You can search for both substructure and exact structure using SMILES. You can type SMILES directly, mark the structure in ChemDraw and copy the SMILES (on Mac: Cmd+Opt+C) and paste it into the SMILES filed, or you can open the Structure Editor, draw the structure, and press Transfer SMILES.

You can also search for TUG-number, Name (will search for the substring in both common name and systematic name) , Common name, Systematic name, CAS nr, Project, Chemist and Batch reference. All fields search by substring (e.g. "-" in CAS nr returns all compounds with CAR numbers). If you fill in several fields, they are searched with AND logic. If you search for a chemist name, all compounds (in your projects) that the chemists has synthesized will appear, but the name of the chemist that synthesized the first batch will appear in the table under Chemist/Supplier.

If you got less hits than expected, you may have forgotten entries in some fields - press Reset and search again.

When you press Search, all hits are displayed in the table below. You can select the number of hits per page (or all hits on one page) and navigate between pages. Clicking on the table headings (except Structure) will sort the results according to the heading. Click again to switch between ascending and descending.

Browsing compound details

Clicking a TUG number in your hit list will open the details page for the compound in a new tab. If you know the TUG number of the compound you're looking for (e.g. TUG-891), a shortcut is to just write tugdb.dk/891 in the URL field.

The structures of the main compound series are displayed consistently ot facilitate SAR comparison. Below is the common name, if any, and the date first registered.

The Projects field shows which projects the compound is part of. By clicking the project name, you get to the project page with all compounds and persons registered in the project.

Click the Calculated properties field to see average molecular weight (if a salt, with and without counter ions), exact molecular weights for [M]+ and [M+H]+, calculated log P, and topological polar surface area (TPSA).

Click the Compound identifiers to see systematic name (if registered), SMILES (two versions for the same compound), International Chemical Identifiers (InChI and InChIKey). Click on Download MOL file to do that. If you have set download to a speicifc location and ChemDraw as the standard program for opening .mol fiiles, you just click on the downloaded file, and you have the structure in the same conformation as in the database in two click. If you don't like the style (you won't), click File > Apply Document Settings from > ACS Document 1996 in ChemDraw.

Batches

All batches registered for the compund are shown in the table at the bottom of the page. Above the table is a button for registering new batches - see below.

Batch Ref is unique identifier for each batch. For all compounds synthesized in the group, the number consists of the initial of the chemist that synthesized the batch, lab journal number (if organized by lab journals), a dash, and the reaction numbers. The number can be used to quickly identify the reaction in the lab journals, as well as NMR, HPLC, data etc. For commercial compounds, other unique identifiers are used.

Chemist shows who made the compound, Project shows which project the batch was intended for, and Date shows when the batch was registered.

Amount shows the amount originally registered for the compound, corresponding to the amount remaining after the first shipment was weighed out.

The Update remaining button should we used if the remaining amount of the batch is weighed at a later point. The updated amount and the date this was added will then be shown in the Amount column together with the original amount.

In stock shows the amount of the batch in stock calculated from the Original amount or the Updated amount if this exists subtracted by all amounts shipped on dates after the registration of the Original or Updated amounst (presuming that the remaining amount was determined after the shipment on the same date was weighed out).

HPLC purity shows the purity determined for the batch at the time of registration. If the purity of the batch is analyzed later, this should be added to Notes (button for this is currently missing - please write to admin - tu@sund.ku.dk - to add notes for approved batches).

Notes shows anything worth noting about the specific batch - for things to note after approval of a batch, please write to admin - tu@sund.ku.dk (a button for updating Notes is planned).

Click Show shipments to see all shipments registered for this batch. This will show the lab shipped to and, if registered, a slash and the receiving person, as well as the Amount and the Date of shipment. (Click Add Shipment to register a new shipment of the batch - see below.)

Below the table, you can click Show All Shipments to see the list of all shipments for the compound ordered by shipment date. In this table, any comments associated with the individual shipments can also be viewed.

Submitting new compounds/batches

To submit a new compound or batch, press Submit New Cpd/Batch. If you submit a new batch for an existing compound, fill in the TUG ID field (e.g. "TUG-891" or just "891"). This will make the SMILES field grey out. Alternatively, fill in the SMILES filed (e.g. mark the structure in ChemDraw and copy SMILES (on Mac: Cmd+Opt+C) and paste into the field). This will make the TUG ID field grey out. The database will check if the structure already exists. If so, the compound will be registered as a new batch under this TUG numbers. If you enter a new stereoisomer or salt of an existing compound, the compound will get a new TUG number.

Fill out the Common name filed if the compound has one (usually only relevant for commercial compounds), Systematic name determined by ChemDraw, any compound-specific comments (rarely necessary - could be e.g. that the compound is the enantiomer of a previous TUG number). These three fields are optional. This information is associated with the compound, not the batch. NB: If you enter a new Common name, Systematic name or Compound comment for an old compound, the old values will be overwritten (this will probably be changed in the future). Therefore, please leave these fields empty for old compounds unless they need to be corrected.

Fill out the Batch Ref. For synthetic compounds, the batch ref should be the lab journal reference on the form NN-123 (initials of the chemist and experiment/reaction number) or NN1-123 (initials, lab journal number and experiment/reaction number). The Batch Ref should be the same as used in all NMR, LCMS, HPLC, HRMS, etc. for this batch. This field is mandatory and the batch reference has to be unique. If the Batch Ref already exists in the database, you will get an error message. Correct the Batch Ref and press Submit again. If you submit two compounds from the same experiment/reaction, e.g. enantiomers or diastereomer isolated from the same reaction, add a dash and a number, e.g. NN-123-1 and NN-123-2. To ensure that we only have existing compounds in the datagase, new compounds cannot be registered without also registering a compound batch.

Select the Project that the compound/batch should be tested in. Generally, the Project name is the same as the receptor that the compound will be tested on. The Project field is mandatory.

Then enter the Batch amount after the shipment has been weighed out, i.e. the remaining amount in stock. Then select the unit (mg, g, μL or mL). If you enter μL or mL, a field appears where you enter the stock solution (typically "10 mM in DMSO"). Finally, you can add Batch notes (e.g. details about purity if different purity is observed at different HPLC UV wavelengths or in the NMR)

Often, a small sample is dried quickly and sent for testing while the remaining amount is left on vacuum to dry for a couple of days. To facilitate registration in these cases, the TBD tick box is provided to allow registration of the batch amount in stock later. (Please remember this! A function is planned that will spam the submitting chemist until this value is registered.)

When you press Submit, you will get reminders if mandatory fields are missing. If the submission is successful, you will be taken to the compound page. Please check that everything is as expected. Check especially that the structure is correct. If the structure is wrong or other compound-associated information (Common name, Systematic name, Compound comment or Project) is wrong or missing, you can press Edit compound and make editions until the compound is approved by admin. If any batch-associated information (Project, Batch amount, unit, Batch solution, HPLC purity or Batch notes) is wrong or missing, press Edit at the batch and make corrections.

The person logged in will automatically be registered as the Chemist. If the batch was registered by another person, please write to admin (tu@sund.ku.dk), who will correct this.

If the Batch ref is wrong, you need to write to admin (tu@sund.ku.dk), who will correct this. If the batch was registered at the wrong compound, you need to write to admin (tu@sund.ku.dk), who will delete the batch, so that the correct submission can be done.

Submitting new batches for existing compounds

New batches for existing compounds can be submitted as described above, but a more convenient way is to go to the compound page (https://tugdb.dk/1234) and press the Add New Batch button above the batch table. A form will appear where you can enter the same batch info as described above.

Registering shipments

Any time a sample is sent for testing anywhere, it should be registered as a shipment. To register a shipment for a batch, press Add shipment at the right end of the relevant batch entry in the batch table. Fill in the shipped amount, the lab here it will be tested ("TUG" if in our own lab - in this case the person that will test the compound should always be added), the person if a specific person is receiving the shipment in the test lab, and the Project (usually the receptor the compound will be tested on). If there are special things to note about the shipment, this can be added in Shipment comments. The person logged in will automatically be registered as Shipped by.