journal menu
![[Figure 4]](gin5003fig4mag.jpg)
|
|
Figure 4
The sildenafil ligand in PDB entry 1udt is improved by refitting. (a) The sildenafil ligand of interest in PDB entry 1udt has a good fit to clear electron density, but the N-methylpiperazine ring was modelled with poor geometry. The piperazine ring (marked with an orange arrow) is not in a chair conformation, resulting in a poor Mogul ring score marked in purple in the Buster-report 2D graphic. Furthermore, the methyl group (highlighted with a blue arrow) is axial to the piperazine ring. (b) Re-refinement of the PDB entry with BUSTER improves the geometry of the piperazine ring so that the Mogul ring score is classified as `good' by Buster-report. However, the methyl group remains trapped in an axial conformation. (c) Refitting sildenafil with the methyl group in an equatorial conformation yields a good fit to the electron density and favourable geometry. The piperazine is clearly protonated and forms a salt bridge with the side chain of a glutamate residue from an adjacent, symmetry-related protein molecule. The ligand's overall fit to electron density, as assessed by RSCC, is as good as that in PDB entry 1udt, but refitting results in less difference density, better ring geometry and better ligand–protein contacts. Figure produced using Coot with the BUSTER 2mFo − DFc map contoured at 1.3 r.m.s.d. shown as a grey mesh and the mFo − DFc difference maps contoured at 3.5 r.m.s.d. shown as red (negative) and green (positive) solid surfaces. |
![[Figure 4]](gin5003fig4.jpg)
 | STRUCTURAL BIOLOGY |
ISSN: 2059-7983
access
