3SDK image
Deposition Date 2011-06-09
Release Date 2012-06-13
Last Version Date 2023-09-13
Entry Detail
PDB ID:
3SDK
Keywords:
HYDROLASE/HYDROLASE INHIBITOR
Title:
Structure of yeast 20S open-gate proteasome with Compound 34
Biological Source:
Source Organism:
Saccharomyces cerevisiae (Taxon ID: 559292)
Method Details:
Experimental Method:
X-RAY DIFFRACTION
Resolution:
2.70 Å
R-Value Free:
0.25
R-Value Work:
0.22
R-Value Observed:
0.22
Space Group:
P 1 21 1
3SDK validation report
Macromolecular Entities
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Proteasome component Y7
Gene (Uniprot):PRE8
Chain IDs:A, O
Chain Length:250
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
UniProt ID:P23639 Pfam ID:PF10584, PF00227
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Proteasome component Y13
Gene (Uniprot):PRE9
Chain IDs:B, P
Chain Length:235
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
UniProt ID:P23638 Pfam ID:PF10584, PF00227
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Proteasome component PRE6
Gene (Uniprot):PRE6
Chain IDs:C, Q
Chain Length:241
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
UniProt ID:P40303 Pfam ID:PF10584, PF00227
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Proteasome component PUP2
Gene (Uniprot):PUP2
Chain IDs:D, R
Chain Length:260
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
UniProt ID:P32379 Pfam ID:PF10584, PF00227
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Proteasome component PRE5
Gene (Uniprot):PRE5
Chain IDs:E, S
Chain Length:233
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
UniProt ID:P40302 Pfam ID:PF10584, PF00227
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Proteasome component C1
Gene (Uniprot):PRE10
Chain IDs:F, T
Chain Length:242
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
UniProt ID:P21242 Pfam ID:PF10584, PF00227
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Proteasome component C7-alpha
Gene (Uniprot):SCL1
Chain IDs:G, U
Chain Length:243
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
UniProt ID:P21243 Pfam ID:PF10584, PF00227 EC:3.4.25.1
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Proteasome component PUP1
Gene (Uniprot):PUP1
Chain IDs:H, V
Chain Length:222
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
UniProt ID:P25043 Pfam ID:PF00227, PF12465
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Proteasome component PUP3
Gene (Uniprot):PUP3
Chain IDs:I, W
Chain Length:204
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
UniProt ID:P25451 Pfam ID:PF00227
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Proteasome component C11
Gene (Uniprot):PRE1
Chain IDs:J, X
Chain Length:198
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
UniProt ID:P22141 Pfam ID:PF00227
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Proteasome component PRE2
Gene (Uniprot):PRE2
Chain IDs:K, Y
Chain Length:212
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
UniProt ID:P30656 Pfam ID:PF00227
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Proteasome component C5
Gene (Uniprot):PRE7
Chain IDs:L, Z
Chain Length:222
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
UniProt ID:P23724 Pfam ID:PF00227
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Proteasome component PRE4
Gene (Uniprot):PRE4
Chain IDs:M, AA (auth: 1)
Chain Length:233
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
UniProt ID:P30657 Pfam ID:PF00227
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Proteasome component PRE3
Gene (Uniprot):PRE3
Chain IDs:N, BA (auth: 2)
Chain Length:196
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
UniProt ID:P38624 Pfam ID:PF00227 EC:3.4.25.1
Ligand Molecules
MES
MG
P3N
Peptide-like Molecules
PRD_001075
Primary Citation
Optimization of a series of dipeptides with a P3 threonine residue as non-covalent inhibitors of the chymotrypsin-like activity of the human 20S proteasome.
Bioorg.Med.Chem.Lett. 20 6581 6586 (2010)
PMID: 20875739 DOI: 10.1016/j.bmcl.2010.09.032

Abstact

Starting from a tripeptide screening hit, a series of dipeptide inhibitors of the proteasome with Thr as the P3 residue has been optimized with the aid of crystal structures in complex with the β-5/6 active site of y20S. Derivative 25, (β5 IC(50)=7.4 nM) inhibits only the chymotryptic activity of the proteasome, shows cellular activity against targets in the UPS, and inhibits proliferation.

Legend

Protein

Chemical

Disease

Primary Citation of related structures
3MG4
3MG6
3MG7
3MG8
3OEU
3OEV
3SDI