Crystal structure of an engineered construct of phosphatidylinositol 4 kinase III beta with a potent and selective inhibitor in complex with GDP loaded RAB11

Structure

x-ray diffraction · 2 distinct chains · 48% helix, 14% strand (DSSP).

Ligands and binding sites

• GDP · Guanosine-5'-diphosphate · ligand · chains B, E
• 5S8 · ~{N}-[5-[3-[[(4-hydroxyphenyl)amino]-bis(oxidanyl)-$l^{4}-sulfanyl]-4-methoxy-phenyl]-4-methyl-1,3-thiazol-2-yl]cyclopentanecarboxamide · ligand · chains E
• SO4 · Sulfate ion · ion · 2 copies · chains E

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

Pockets

10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Interfaces

1 interface between chains.

• B–E · 597 Ų buried · 4 hydrogen bonds · protein-protein

Compared structures

• 5EUQ · Crystal structure of an engineered construct of phosphatidylinositol 4 kinase III beta… · the same entry in another collection · chain B against B, TM-score 1.00
• O02810 · AlphaFold monomer V2.0 prediction for phosphatidylinositol 4-kinase beta (O02810) · a predicted model of the same protein · chain E against A, TM-score 0.99
• Q9UBF8 · AlphaFold monomer V2.0 prediction for phosphatidylinositol 4-kinase beta (Q9UBF8) · a predicted model of the same protein · chain E against A, TM-score 0.99
• P62491 · AlphaFold monomer V2.0 prediction for RAS-related protein rab-11A (P62491) · 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 P62491
• Every structure of UniProt Q9UBF8
• Every structure of UniProt O02810
• Elsewhere: RCSB PDB 5EUQ · PDBe 5EUQ · UniProt P62491 · UniProt Q9UBF8 · UniProt O02810