Human PRPF4B bound to benzothiophene inhibitor 224

Structure

x-ray diffraction · 4 distinct chains · 41% helix, 18% strand (DSSP).

Ligands and binding sites

• OCJ · 4-(5-{[(3-aminophenyl)methyl]carbamoyl}thiophen-2-yl)-1-benzothiophene-2-carboxamide · ligand · 4 copies · chains A, B, D, C
• PO4 · Phosphate ion · ion · 8 copies · chains A, B, C, D
• EDO · 1,2-ethanediol · additive · 8 copies · chains A, B, C, D

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

Pockets

12 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.

Interfaces

5 interfaces between chains.

• B–D · 686 Ų buried · 7 hydrogen bonds · protein-protein
• B–C · 647 Ų buried · 8 hydrogen bonds · protein-protein
• A–B · 343 Ų buried · 2 hydrogen bonds · protein-protein
• A–C · 74 Ų buried · 1 hydrogen bond · protein-protein
• A–D · 32 Ų buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 modified (phosphorylation).

Compared structures

• 6PJJ · Human PRPF4B bound to benzothiophene inhibitor 224 · the same entry in another collection · chain D against D, TM-score 1.00
• Q13523 · AlphaFold monomer V2.0 prediction for SERINE/THREONINE-protein kinase PRP4 homolog… · a predicted model of the same protein · chain A 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 Q13523
• Elsewhere: RCSB PDB 6PJJ · PDBe 6PJJ · UniProt Q13523