The crystal structure of dw-0254 in complex with PDE6D

Structure

x-ray diffraction · 1 distinct chain · 15% helix, 57% strand (DSSP).

Ligands and binding sites

• O7W · ~{N}-[(4-ethylphenyl)methyl]-3-[5-[2-(1~{H}-indol-3-yl)ethyl]-1,3,4-oxadiazol-2-yl]-~{N}-methyl-propanamide · ligand · chains B
• NI · Nickel (II) ion · metal · chains B
• GOL · Glycerol · additive · chains B
• EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · chains B

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Compared structures

• 7PAD · The crystal structure of DW-0254 in complex with PDE6D · the same entry in another collection · chain B against B, TM-score 1.00
• O43924 · AlphaFold monomer V2.0 prediction for retinal rod rhodopsin-sensitive cgmp 3',5'-cyclic… · a predicted model of the same protein · chain B against A, TM-score 0.97

Analyse

• Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
• Every structure of UniProt O43924
• Elsewhere: RCSB PDB 7PAD · PDBe 7PAD · UniProt O43924