ISDA

Entry Detail

PDB ID:

3SDI

Keywords:

Hydrolase/Hydrolase Inhibitor

Title:

Structure of yeast 20S open-gate proteasome with Compound 20

Biological Source:

Source Organism:

Saccharomyces cerevisiae

PDB Version:

Deposition Date:

2011-06-09

Release Date:

2012-06-13

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

2.65 Å

R-Value Free:

0.25

R-Value Work:

0.21

R-Value Observed:

0.21

Space Group:

P 1 21 1

Download Validation Report

Macromolecular Entities

Protein Blast

Polymer Type:polypeptide(L)
Description:Proteasome component Y7
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)
Description:Proteasome component Y13
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)
Description:Proteasome component 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)
Description:Proteasome component 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)
Description:Proteasome component 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)
Description:Proteasome component C1
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)
Description:Proteasome component C7-alpha
Chain IDs:G, U
Chain Length:243
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae

UniProt ID:P21243 Pfam ID:PF10584, PF00227

Protein Blast

Polymer Type:polypeptide(L)
Description:Proteasome component 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)
Description:Proteasome component 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)
Description:Proteasome component C11
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)
Description:Proteasome component 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)
Description:Proteasome component C5
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)
Description:Proteasome component 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)
Description:Proteasome component PRE3
Chain IDs:N, BA (auth: 2)
Chain Length:196
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae

UniProt ID:P38624 Pfam ID:PF00227

Ligand Molecules

3SD

MES

Peptide-like Molecules

PRD_001071

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.

Blackburn, C, Barrett, C, Blank, J.L, Bruzzese, F.J, Bump, N, Dick, L.R, Fleming, P, Garcia, K, Hales, P, Hu, Z, Jones, M, Liu, J.X, Sappal, D.S, Sintchak, M.D, Tsu, C, Gigstad, K.M.Show

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.

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Protein

Chemical

Disease

Primary Citation of related structures