LigandScout

Wolber G, Langer T LigandScout 3-D pharmacophores derived from protein-bound ligands and their use as virtual screening filters. / Chem Inf Model 2005 45 160-9. 

We thank Gerhard Wolber from Inte Ligand GmbH for providing the depiction of (S)-warfarin in P450 2C9, a functionality that will be available in a future release of LigandScout. 

Pharmacophores from Macromolecular Complexes with LigandScout... 

Chemical Feature-based Pharmacophores Used by LigandScout... 

LigandScout should serve as a basis for the comparison of feature locations and properties. Therefore, we needed to design a chemical feature set that is still universal but yet selective enough to reflect all relevant types of ligand-receptor interaction. This set is described in the next section. 

Fig. 6.4 Render styles in LigandScout (a) lines, (b) ball and stick, (c) stick and (d) spacefi 11 i ng/CP K.

LigandScout pharmacophores solely consist of chemical features classified as layers 3 and 4 (Table 6.2). Visualization mainly distinguishes between point and vector features point features (layer 4) are defined as a center with a tolerance this group encompasses hydrophobic, positively ionizable and negatively ioniz-able areas, in addition to excluded volume spheres. Hydrogen donors, acceptors and donor-acceptor pairs belong to the vector features group. 

The information about selected objects is also communicated to other views in LigandScout, such as a 2D depiction and a tree-viewer. In this way, the user can easily identify parts of the molecule in the different views and find additional information about them. 

Inte Ligand. LigandScout. Inte Ligand, GmbH, Maria Enzerdorf, Austria www.inteligand.com. 

Figure 3.1 Thrombin inhibitor SN3401 in complex with Thrombin (PDB entry 2GDE) three hydrogen bond donors (green), one acceptor (red), and one charge transfer feature (blue) are recognized by LigandScout. In order to show more detail of the interaction, only a portion of the structure of SN3401 has been shown.

---