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Figure 2
Automatic ligand fitting in CCP4. The SMILES string corresponding to 3-aminobenzamide is pasted into the `Make Ligand' task interface in CCP4i2 (a). Upon running the job, AceDRG is used to generate ligand restraints and RDKit is used to generate an initial conformer and a two-dimensional representation of the ligand (b). The `Manual Model Building' task is then executed to open Coot. (c) displays the model (sticks) and 2mFoDFc density map (blue) corresponding to a structure solved with data extending to 2 Å resolution (PDB entry 3kcz; Karlberg et al., 2010BB24) after manually removing the ligands. The maps are shown using Coot's default contour levels. Automatic ligand fitting is performed, using 3-aminobenzamide as the target. The focal region corresponds to the top-ranked blob identified in the masked map (orange). The ligand coordinates are nominally positioned onto the centre of the blob (d). The ligand is then optimally oriented and rigid-body refined into the masked density (e). In this case, manual intervention would be required in order to ensure favourable hydrogen bonds are satisfied: this issue is further addressed in §[link]6 and Fig. 7[link]. Multiple blobs are found in the map and ligands are fitted into them; the third-highest ranked ligand is automatically fitted into a blob that actually corresponds to a glycerol molecule (f).

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ISSN: 2059-7983
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