Three cluster representatives for the molecules listed in Table 1. The molecules are annotated according to the interactions that they make with the protein in the top-scoring PDB entry for the cluster. Atoms making hydrogen bonds to protein are depicted with spokes radiating from them, while hydrophobic interactions have a grey circle around them (none in this example). The colour of the spokes corresponds to the similarity of the residue to which the hydrogen bond is made and the corresponding residue in the query protein (which in this case is thymidylate synthase from S. aureus; UniProt ID P65248): red for identical residue type, orange for similar and dark grey for different. The images are provided in the results section for every query with PDB hits. The molecules and the PDB entries from which the data come are (a) P1-(5′-adenosyl)-P5-(5′-thymidyl)pentaphosphate (PDB entry 4tmk), (b) thymidine 5′-diphosphate (PDB entry 3hjn) and (c) 4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid (PDB entry 2pir).