Automated ligand fitting by core-fragment fitting and extension into density

Abstract

A procedure for fitting of ligands to electron-density maps by first fitting a core fragment of the ligand to density and then extending the remainder of the ligand into density is presented. The approach was tested by fitting 9327 ligands over a wide range of resolutions (most are in the range 0.8-4.8 A) from the Protein Data Bank (PDB) into (Fo - Fc)exp(i phi(c)) difference density calculated using entries from the PDB without these ligands. The procedure was able to place 58% of these 9327 ligands within 2 A (r.m.s.d.) of the coordinates of the atoms in the original PDB entry for that ligand. The success of the fitting procedure was relatively insensitive to the size of the ligand in the range 10-100 non-H atoms and was only moderately sensitive to resolution, with the percentage of ligands placed near the coordinates of the original PDB entry for fits in the range 58-73% over all resolution ranges tested.

Figure 1

(a) F _o − F _c difference density for NAG-NAG-MAN (PDB entry 1d7d, 1.95 Å; Hallberg et al., 2000 ▶) fitted beginning with the same ligand from a different PDB entry. (b) The same map fitted beginning with ligands from five different PDB entries. (c) R.m.s.d. of fits beginning with NAG-NAG-MAN from 74 different PDB entries to the original ligand in PDB entry 1d7d and correlation coefficient of fitted ligand to the difference density map. (d) Histogram of r.m.s.d. of fits from (c).

Figure 2

Histogram of number of fits with an r.m.s.d. to the original coordinates in the PDB within 1 Å (filled bars) and within 2 Å (entire length of bars including filled and unfilled parts) as a function of the resolution of the maps, considering only ligand–PDB combinations where the original ligand had a correlation with the F _o − F _c map of 0.75 or greater.

Figure 3

Fitting ligands at resolutions from 0.95 to 4.5 Å. (a) Fit of F _o − F _c difference density at 0.95 Å of FAD (PDB entry 1n1p; Lario & Vrielink, 2003 ▶). (b) Fit at 2.2 Å of 8-(2,5-dimethoxybenzyl)-2-fluoro-9-pent-9H-purin-6-ylamine (PDB entry 1uyi; Wright et al., 2004 ▶). (c) Fit at 3 Å of ATP (PDB entry 1nbm; Orriss et al., 1998 ▶). (d) Fit at 4.5 Å of 1-(4-iodobenzoyl)-5-methoxy-2-methyl-indole-3-acetic acid (PDB entry 1pgf; Loll et al., 1996 ▶).

Figure 4

Histogram of number of fits with an r.m.s.d. to the original coordinates in the PDB within within 1 Å (filled bars) and within 2 Å (entire length of bars including filled and unfilled parts) as a function of the number of non-H atoms in the ligand, considering only ligand–PDB combinations where the original ligand had a correlation with the F _o − F _c map of 0.75 or greater. The number of non-H atoms in the ligands considered ranged from 6 to 150.