8YPK image
Entry Detail
PDB ID:
8YPK
EMDB ID:
Keywords:
Title:
mouse proteasome 20S subunit in complex with compound 1
Biological Source:
Source Organism:
PDB Version:
Deposition Date:
2024-03-17
Release Date:
2024-07-31
Method Details:
Experimental Method:
Resolution:
2.70 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:Proteasome subunit beta type-6
Chain IDs:A, X (auth: F)
Chain Length:205
Number of Molecules:2
Biological Source:Mus musculus
Polymer Type:polypeptide(L)
Description:Proteasome subunit beta type-7
Chain IDs:Q (auth: B), T (auth: E)
Chain Length:234
Number of Molecules:2
Biological Source:Mus musculus
Polymer Type:polypeptide(L)
Description:Proteasome subunit beta type-5
Chain IDs:G (auth: D), N (auth: C)
Chain Length:205
Number of Molecules:2
Biological Source:Mus musculus
Polymer Type:polypeptide(L)
Description:Proteasome subunit alpha type-5
Chain IDs:M (auth: H), R (auth: M)
Chain Length:241
Number of Molecules:2
Biological Source:Mus musculus
Polymer Type:polypeptide(L)
Description:Proteasome subunit alpha type-3
Chain IDs:H (auth: J), V (auth: Q)
Chain Length:255
Number of Molecules:2
Biological Source:Mus musculus
Polymer Type:polypeptide(L)
Description:Proteasome subunit alpha type-1
Chain IDs:L, U (auth: G)
Chain Length:263
Number of Molecules:2
Biological Source:Mus musculus
Polymer Type:polypeptide(L)
Description:Proteasome subunit alpha type-7
Chain IDs:C (auth: N), P (auth: I)
Chain Length:248
Number of Molecules:2
Biological Source:Mus musculus
Polymer Type:polypeptide(L)
Description:Proteasome subunit alpha type-4
Chain IDs:O, Y (auth: Z)
Chain Length:261
Number of Molecules:2
Biological Source:Mus musculus
Polymer Type:polypeptide(L)
Description:Proteasome subunit alpha type-2
Chain IDs:B (auth: P), K (auth: b)
Chain Length:234
Number of Molecules:2
Biological Source:Mus musculus
Polymer Type:polypeptide(L)
Description:Proteasome subunit alpha type-6
Chain IDs:D (auth: R), I (auth: K)
Chain Length:246
Number of Molecules:2
Biological Source:Mus musculus
Polymer Type:polypeptide(L)
Description:Proteasome subunit beta type-1
Chain IDs:F (auth: S), BA (auth: X)
Chain Length:240
Number of Molecules:2
Biological Source:Mus musculus
Polymer Type:polypeptide(L)
Description:Proteasome subunit beta type-2
Chain IDs:E (auth: T), J (auth: V)
Chain Length:201
Number of Molecules:2
Biological Source:Mus musculus
Polymer Type:polypeptide(L)
Description:Proteasome subunit beta type-4
Chain IDs:S (auth: W), W (auth: a)
Chain Length:205
Number of Molecules:2
Biological Source:Mus musculus
Polymer Type:polypeptide(L)
Description:Proteasome subunit beta type-3
Chain IDs:Z (auth: Y), AA (auth: U)
Chain Length:205
Number of Molecules:2
Biological Source:Mus musculus
Ligand Molecules
Primary Citation
Optimization of alpha-amido boronic acids via cryo-electron microscopy analysis: Discovery of a novel highly selective immunoproteasome subunit LMP7 ( beta 5i)/LMP2 ( beta 1i) dual inhibitor.
Bioorg.Med.Chem. 109 117790 117790 (2024)
PMID: 38906067 DOI: 10.1016/j.bmc.2024.117790

Abstact

The immunoproteasome subunit LMP7 (β5i)/LMP2 (β1i) dual blockade has been reported to suppress B cell differentiation and activation, suggesting that the dual inhibition of LMP7/LMP2 is a promising approach for treating autoimmune diseases. In contrast, the inhibition of the constitutive proteasome subunit β5c correlates with cytotoxicity against non-immune cells. Therefore, LMP7/LMP2 dual inhibitors with high selectivity over β5c may be desirable for treating autoimmune diseases. In this study, we present the optimization and discovery of α-amido boronic acids using cryo-electron microscopy (cryo-EM). The exploitation of structural differences between the proteasome subunits led to the identification of a highly selective LMP7/LMP2 dual inhibitor 19. Molecular dynamics simulation based on cryo-EM structures of the proteasome subunits complexed with 19 explained the inhibitory activity profile. In mice immunized with 4-hydroxy-3-nitrophenylacetyl conjugated to ovalbumin, results indicate that 19 is orally bioavailable and shows promise as potential treatment for autoimmune diseases.

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