4EU2 image
Deposition Date 2012-04-25
Release Date 2013-05-01
Last Version Date 2024-03-20
Entry Detail
PDB ID:
4EU2
Title:
Crystal structure of 20s proteasome with novel inhibitor K-7174
Biological Source:
Source Organism:
Method Details:
Experimental Method:
Resolution:
2.51 Å
R-Value Free:
0.25
R-Value Work:
0.20
R-Value Observed:
0.20
Space Group:
P 1 21 1
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:Proteasome component C7-alpha
Gene (Uniprot):SCL1
Chain IDs:A, O
Chain Length:241
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Molecule:Proteasome component Y7
Gene (Uniprot):PRE8
Chain IDs:B, P
Chain Length:250
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Molecule:Proteasome component Y13
Gene (Uniprot):PRE9
Chain IDs:C, Q
Chain Length:244
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Molecule:Proteasome component PRE6
Gene (Uniprot):PRE6
Chain IDs:D, R
Chain Length:241
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Molecule:Proteasome component PUP2
Gene (Uniprot):PUP2
Chain IDs:E, S
Chain Length:242
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Molecule:Proteasome component PRE5
Gene (Uniprot):PRE5
Chain IDs:F, T
Chain Length:233
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Molecule:Proteasome component C1
Gene (Uniprot):PRE10
Chain IDs:G, U
Chain Length:244
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Molecule:Proteasome component PRE3
Gene (Uniprot):PRE3
Chain IDs:H, V
Chain Length:196
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Molecule:Proteasome component PUP1
Gene (Uniprot):PUP1
Chain IDs:I, W
Chain Length:222
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Molecule:Proteasome component PUP3
Gene (Uniprot):PUP3
Chain IDs:J, X
Chain Length:204
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Molecule:Proteasome component C11
Gene (Uniprot):PRE1
Chain IDs:K, Y
Chain Length:198
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Molecule:Proteasome component PRE2
Gene (Uniprot):PRE2
Chain IDs:L, Z
Chain Length:212
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Molecule:Proteasome component C5
Gene (Uniprot):PRE7
Chain IDs:M, AA (auth: 1)
Chain Length:222
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Molecule:Proteasome component PRE4
Gene (Uniprot):PRE4
Chain IDs:N, BA (auth: 2)
Chain Length:233
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
Ligand Molecules
Primary Citation
Homopiperazine derivatives as a novel class of proteasome inhibitors with a unique mode of proteasome binding.
Plos One 8 e60649 e60649 (2013)
PMID: 23593271 DOI: 10.1371/journal.pone.0060649

Abstact

The proteasome is a proteolytic machinery that executes the degradation of polyubiquitinated proteins to maintain cellular homeostasis. Proteasome inhibition is a unique and effective way to kill cancer cells because they are sensitive to proteotoxic stress. Indeed, the proteasome inhibitor bortezomib is now indispensable for the treatment of multiple myeloma and other intractable malignancies, but is associated with patient inconvenience due to intravenous injection and emerging drug resistance. To resolve these problems, we attempted to develop orally bioavailable proteasome inhibitors with distinct mechanisms of action and identified homopiperazine derivatives (HPDs) as promising candidates. Biochemical and crystallographic studies revealed that some HPDs inhibit all three catalytic subunits (ß 1, ß 2 and ß 5) of the proteasome by direct binding, whereas bortezomib and other proteasome inhibitors mainly act on the ß5 subunit. Proteasome-inhibitory HPDs exhibited cytotoxic effects on cell lines from various hematological malignancies including myeloma. Furthermore, K-7174, one of the HPDs, was able to inhibit the growth of bortezomib-resistant myeloma cells carrying a ß5-subunit mutation. Finally, K-7174 had additive effects with bortezomib on proteasome inhibition and apoptosis induction in myeloma cells. Taken together, HPDs could be a new class of proteasome inhibitors, which compensate for the weak points of conventional ones and overcome the resistance to bortezomib.

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Primary Citation of related structures