6H39 image
Deposition Date 2018-07-17
Release Date 2018-11-07
Last Version Date 2024-01-17
Entry Detail
PDB ID:
6H39
Keywords:
Title:
Yeast 20S proteasome in complex with the peptidic non-covalent binding inhibitor RTS-V5
Biological Source:
Method Details:
Experimental Method:
Resolution:
2.50 Å
R-Value Free:
0.21
R-Value Work:
0.18
R-Value Observed:
0.18
Space Group:
P 1 21 1
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:Proteasome subunit alpha type-2
Gene (Uniprot):PRE8
Chain IDs:A, O
Chain Length:250
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Polymer Type:polypeptide(L)
Molecule:Proteasome subunit alpha type-3
Gene (Uniprot):PRE9
Chain IDs:B, P
Chain Length:196
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Polymer Type:polypeptide(L)
Molecule:Proteasome subunit alpha type-4
Gene (Uniprot):PRE6
Chain IDs:C, Q
Chain Length:254
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Polymer Type:polypeptide(L)
Molecule:Proteasome subunit alpha type-5
Gene (Uniprot):PUP2
Chain IDs:D, R
Chain Length:260
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Polymer Type:polypeptide(L)
Molecule:Proteasome subunit alpha type-6
Gene (Uniprot):PRE5
Chain IDs:E, S
Chain Length:234
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Polymer Type:polypeptide(L)
Molecule:Probable proteasome subunit alpha type-7
Gene (Uniprot):PRE10
Chain IDs:F, T
Chain Length:288
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Polymer Type:polypeptide(L)
Molecule:Proteasome subunit alpha type-1
Gene (Uniprot):SCL1
Chain IDs:G, U
Chain Length:252
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Polymer Type:polypeptide(L)
Molecule:Proteasome subunit beta type-2
Gene (Uniprot):PUP1
Chain IDs:H, V
Chain Length:232
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Polymer Type:polypeptide(L)
Molecule:Proteasome subunit beta type-3
Gene (Uniprot):PUP3
Chain IDs:I, W
Chain Length:205
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Polymer Type:polypeptide(L)
Molecule:Proteasome subunit beta type-4
Gene (Uniprot):PRE1
Chain IDs:J, X
Chain Length:198
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Polymer Type:polypeptide(L)
Molecule:Proteasome subunit beta type-5
Gene (Uniprot):PRE2
Chain IDs:K, Y
Chain Length:212
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Polymer Type:polypeptide(L)
Molecule:Proteasome subunit beta type-6
Gene (Uniprot):PRE7
Chain IDs:L, Z
Chain Length:222
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Polymer Type:polypeptide(L)
Molecule:Proteasome subunit beta type-7
Gene (Uniprot):PRE4
Chain IDs:M, AA (auth: a)
Chain Length:250
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Polymer Type:polypeptide(L)
Molecule:Proteasome subunit beta type-1
Gene (Uniprot):PRE3
Chain IDs:N, BA (auth: b)
Chain Length:196
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Primary Citation
Discovery of the First-in-Class Dual Histone Deacetylase-Proteasome Inhibitor.
J. Med. Chem. 61 10299 10309 (2018)
PMID: 30365892 DOI: 10.1021/acs.jmedchem.8b01487

Abstact

Dual- or multitarget drugs have emerged as a promising alternative to combination therapies. Proteasome inhibitors (PIs) possess synergistic activity with histone deacetylase (HDAC) inhibitors due to the simultaneous blockage of the ubiquitin degradation and aggresome pathways. Here, we present the design, synthesis, binding modes, and anticancer properties of RTS-V5 as the first-in-class dual HDAC-proteasome ligand. The inhibition of both targets was confirmed by biochemical and cellular assays as well as X-ray crystal structures of the 20S proteasome and HDAC6 complexed with RTS-V5. Cytotoxicity assays with leukemia and multiple myeloma cell lines as well as therapy refractory primary patient-derived leukemia cells demonstrated that RTS-V5 possesses potent and selective anticancer activity. Our results will thus guide the structure-based optimization of dual HDAC-proteasome inhibitors for the treatment of hematological malignancies.

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Primary Citation of related structures