Crystal structure of the catalytic domain of human JARID1B in complex with 3D fragment (3R)-1-[(3-phenyl-1,2,4-oxadiazol-5-yl) METHYL]PYRROLIDIN-3-ol (N10057A) (ligand modelled based on pandda event MAP, sgc - diamond I04-1 fragment screening)

Structure

x-ray diffraction · 1 distinct chain · 38% helix, 21% strand (DSSP).

Ligands and binding sites

• P6B · (3S)-1-[(3-phenyl-1,2,4-oxadiazol-5-yl)methyl]pyrrolidin-3-ol · ligand · chains A
• ZN · Zinc ion · metal · 2 copies · chains A
• MN · Manganese (II) ion · metal · chains A
• CL · Chloride ion · ion · chains A
• PO4 · Phosphate ion · ion · chains A
• EDO · 1,2-ethanediol · additive · 10 copies · chains A
• DMS · Dimethyl sulfoxide · additive · 3 copies · chains A

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

Pockets

6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Compared structures

• 5FZ4 · Crystal structure of the catalytic domain of human JARID1B in complex with 3D fragment… · the same entry in another collection · chain A against A, TM-score 1.00
• Q9UGL1 · AlphaFold monomer V2.0 prediction for lysine-specific demethylase 5B (Q9UGL1) · a predicted model of the same protein · chain A against A, TM-score 0.96

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 Q9UGL1
• Elsewhere: RCSB PDB 5FZ4 · PDBe 5FZ4 · UniProt Q9UGL1