Comparison of crystal and docked binding poses of ligand 30 (BAZ2B)
Binding mode of compound 30 (see reference publication below) in BAZ2B. The crystal (PDB code 5ORB) and docking binding poses are essentially identical with the main difference found in the methoxybenzene tail, which contacts an adjacent protein chain of a crystal symmetric unit and is affected by significant anisotropy (bottom part). Six bromodomain-family conserved water molecules are visible with added hydrogens. In addition, a part of an adjacent chain in a crystal symmetric unit is present as chain Z (cf hereafter).
If you apply the commands hereafter, the crystal ligand will be colored in green, the docked ligand in pink, and a neighboring protein chain (from another crystal unit cell) in blue. A ring of van der Waals contacts between the aforementioned chain and the crystal ligand will be highlighted, which possibly bias the position of the methoxybenzene tail of the ligand. Simply copy the following script into the corresponding box and hit "Apply":
ZOOM IN ; ZOOM IN ;
select chain=A ; trace ;
select chain=A ; wireframe off ;
select within(group, within(6, hetero)) ; wireframe on ;
select altloc=A and hetero ; wireframe 0.2 ;
select altloc=A and carbon and hetero ; color green ;
select [LIG]1972:B.*%B ; wireframe 0.2 ;
select [LIG]1972:B.*%B and carbon ; color pink ;
select chain=Z and carbon ; color blue ;
contact {chain=Z} {hetero} plane 175% ;
center {hetero} ;
See Figure 2 panel C of paper for discussion.