Structure of human ERK1 in complex with SCH772984 revealing a novel inhibitor-induced binding pocket

Structure

x-ray diffraction · 2 distinct chains · 41% helix, 16% strand (DSSP).

Ligands and binding sites

• 38Z · (3R)-1-(2-oxo-2-{4-[4-(pyrimidin-2-yl)phenyl]piperazin-1-yl}ethyl)-N-[3-(pyridin-4-yl)-2H-indazol-5-yl]pyrrolidine-3-carboxamide · ligand · 2 copies · chains A, B
• CL · Chloride ion · ion · 3 copies · chains A, B
• SO4 · Sulfate ion · ion · 2 copies · chains A, B
• EDO · 1,2-ethanediol · additive · 20 copies · chains A, B
• DMS · Dimethyl sulfoxide · additive · 3 copies · chains A, B

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

Pockets

9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Interfaces

1 interface between chains.

• A–B · 1086 Ų buried · 14 hydrogen bonds · protein-protein

Compared structures

• 4QTB · Structure of human ERK1 in complex with SCH772984 revealing a novel inhibitor-induced… · the same entry in another collection · chain A against A, TM-score 1.00
• P27361 · AlphaFold monomer V2.0 prediction for mitogen-activated protein kinase 3 (P27361) · a predicted model of the same protein · chain B against A, TM-score 0.99

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 P27361
• Elsewhere: RCSB PDB 4QTB · PDBe 4QTB · UniProt P27361