PDBsum entry 6hv5

Hydrolase

PDB id: 6hv5

Contents

Protein chains

250 a.a.

244 a.a.

240 a.a.

235 a.a.

231 a.a.

243 a.a.

241 a.a.

226 a.a.

204 a.a.

195 a.a.

212 a.a.

222 a.a.

233 a.a.

196 a.a.

Ligands

GQH ×4

Metals

_CL ×2

_MG ×8

Waters ×248

References listed in PDB file

Key reference

• Title: Structure-Based design of inhibitors selective for human proteasome β2c or β2i subunits.
• Authors: B.T.Xin, E.M.Huber, G.De bruin, W.Heinemeyer, E.Maurits, C.Espinal, Y.Du, M.Janssens, E.S.Weyburne, A.F.Kisselev, B.I.Florea, C.Driessen, G.A.Van der marel, M.Groll, H.S.Overkleeft.
• Ref.: J Med Chem, 2019, 62, 1626-1642. [DOI no: 10.1021/acs.jmedchem.8b01884]
• PubMed id: 30657666

Abstract

Subunit-selective proteasome inhibitors are valuable tools to assess the biological and medicinal relevance of individual proteasome active sites. Whereas the inhibitors for the β1c, β1i, β5c, and β5i subunits exploit the differences in the substrate-binding channels identified by X-ray crystallography, compounds selectively targeting β2c or β2i could not yet be rationally designed because of the high structural similarity of these two subunits. Here, we report the development, chemical synthesis, and biological screening of a compound library that led to the identification of the β2c- and β2i-selective compounds LU-002c (4; IC₅₀ β2c: 8 nM, IC₅₀ β2i/β2c: 40-fold) and LU-002i (5; IC₅₀ β2i: 220 nM, IC₅₀ β2c/β2i: 45-fold), respectively. Co-crystal structures with β2 humanized yeast proteasomes visualize protein-ligand interactions crucial for subunit specificity. Altogether, organic syntheses, activity-based protein profiling, yeast mutagenesis, and structural biology allowed us to decipher significant differences of β2 substrate-binding channels and to complete the set of subunit-selective proteasome inhibitors.