Distant Homology - Functional Similarity


Our interest is in how nature uses and re-uses the same approaches and to apply this knowledge to research. This case study shows the structural similarity between the ATP binding domains of four proteins that have all been considered as potential drug discovery targets;

  • DNA gyrase B : Novobiocin target.
  • HSP-90 : Oncology
  • Histidine Kinase EnvZ: Antibmicrobial
  • Pyruvate Dehydrogenase Kinase: Hyperglycaemia

For more detailed information see our original Nature publication: Tanaka et al., 1998, 396, 88-92.

Structural Similarity

None of these protein relationships can be identified simple sequence alignment. More advanced profile based methods such as PSI-Blast and GenThreader are required. After structural confirmation of EnvZ, HSP90 and DNA gyraseB a detailed structure based alignment could be made.


The structure based sequence alignment shown below (colours emphasise the structural relationship observed in 3D) is adapted from our original publication. Two key elements of distant relationships are apparent;

  • Low overall sequence identity
  • Clustering of the few residue identities at functionally critical locations.  

Conserved residues are involved with the ATP binding site especially the key DxGxG motif. 

Subsequent to our work being published, other proteins such as Pyruvate Dehydrogenase Kinase for Type 2 diabetes were also found to have the same ATP binding domain, suggesting opportunities to design focused screens rather than needing to start with a conventional HTS approach.

Fragment Based Drug Discovery

The aspartate of the conserved DxGxG motif occurs in publications FBDD by two companies; Vernalis and Astex. The following image shows four fragments from these publications interacting with the Asp.

Vernalis structures are: (a) 2wi1 and (b) 2wi7; Astex structures are: (c) 2xdl and (d) 2xab. 

For more details see our subsequent publication and references therein. LigPlot+: Multiple Ligand-Protein Interaction Diagrams for Drug Discovery, Roman A. Laskowski and Mark B. Swindells. Journal of Chemical Information and Modelling. 2011, 51, 2778–2786