Fig. 8: Crystal structure of the PROTAC 4 ternary complex with DCAF1 and WDR5.

a Cartoon representation of the crystal structure showing PROTAC 4 (orange sticks), DCAF1 (purple) and WDR5 (blue). A 2F_o-F_c electron density map contoured at 1.0σ surrounds PROTAC 4. Unlike PROTAC 1-3, PROTAC 4 forms a ternary complex with WDR5 and DCAF1 in which the latter’s long loop (residues 1313–1333) forms a loop-helix-loop structure. b PROTAC 4 (black sticks) is compressed to an effective length of 38.9 Å, similar with those observed for PROTAC 1-3 in their ternary complexes. Surface representation indicates contacts between protein components enabled by PROTAC 4. c Electrostatic/hydrogen bonding (broken black line) and hydrophobic/van der Waals interactions (brown concave lines) occur between the top side of the WDR domains of DCAF1 and WDR5 in the presence of PROTAC 4. d The PROTAC 4 linker is accommodated inside the space formed by DCAF1 and WDR5 by coiling and compacting. A portion of the PROTAC 4 linker close to the WDR5 anchor forms a coiled structure stabilized by an ordered water molecule (red sphere) located below the center of the coil, and interaction with the loop-helix-loop structure formed by residues 1313–1333. Specifically, R1325 of the loop-helix-loop structure of DCAF1 interacts with the coiled structure using hydrogen bonds. The coiled structure fills the space bordered by WDR5 residues D107, Y131, F149, Y191, and Y260. The coiled structure is further stabilized by water-mediated interactions with WDR5 residues and the WDR5 anchor of PROTAC 4 itself. The rest of the PROTAC 4 linker is curved and is also supported by the helix-loop-helix structure of DCAF1. Near the DCAF1 anchor, several water-mediated interactions with DCAF1 residues stabilize the linker conformation. As is also seen in the PROTAC 2 and PROTAC 3 ternary complexes, residue R1225 helps stabilize the linker and the base of the loop-helix-loop structure through direct and water-mediated hydrogen bonding interactions.