Compare HSP90 ligand binding

Tom Goddard
December 11, 2017

How to look at bound ligands to HSP90 and compare the binding in two structures.

Compare structure determined by class (f20) to similar PDB structures 2xdk and 4lwf which also have ligands with 2 rings joined by a bond. (Chimera 1.12 session.) Found these structures by searching HSP90 bound structures (found 70) and visually inspecting ligand report.

Open f20_refine_8-coot-0.pdb
Command "color orange ligand & C"
menu Tools / Structure Analysis / FindHBond
menu Select / Structure / ligand
check Only find H-bonds with at least one end selected
RCSB PDB Advanced search
HSP90 in title and "bound" in title,
70 hits,
Reports: ligands
Commands:
open 2xdk
matchmaker #0 #1
select #1 & ligand
hbond sel cross intermodel false retain true
Commands:
open 4lwf
matchmaker #0 #2
select #2 & ligand
hbond sel cross intermodel false retain true
Show model #0 and #1 (Model Panel)
~ribbon #1
Movie made in ChimeraX showing 70 bound structures.