Step 2: building a model based on your chosen template

Figure 17 Choosing your own structural template.

You can also choose your own structural template. Click on ‘Search for templates’. SWISS-MODEL will look for structures in the PDB that have a closely related sequence (Figure 17). Be patient; it can take some time to generate your list of templates. Once you’ve done this, you can align as many of these templates as you like to your target sequence. Here we’ve chosen structures for IRAK4 (2oib.2.A), brassinosteroid insensitive 1-associated receptor kinase 1 (3tl8.2.A) and JAK2 (4bbe.1.A). These three structures align quite closely to each other. Based on this evidence, it might be worth doing some assays to find out whether any known inhibitors of these enzymes also inhibit IRAK2.