3SDK | pdb_00003sdk

Structure of yeast 20S open-gate proteasome with Compound 34

PDB DOI: https://doi.org/10.2210/pdb3SDK/pdb

Classification: HYDROLASE/HYDROLASE INHIBITOR
Organism(s): Saccharomyces cerevisiae S288C
Mutation(s): No

Deposited: 2011-06-09 Released: 2012-06-13
Deposition Author(s): Sintchak, M.D.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free:
0.259 (Depositor), 0.251 (DCC)
R-Value Work:
0.223 (Depositor), 0.219 (DCC)
R-Value Observed:
0.224 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

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.

(2010) Bioorg Med Chem Lett 20: 6581-6586

PubMed: 20875739 Search on PubMed
DOI: https://doi.org/10.1016/j.bmcl.2010.09.032
Primary Citation Related Structures:
3OEU, 3OEV, 3SDI, 3SDK

PubMed Abstract:
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.

Organizational Affiliation

Millennium Pharmaceuticals Inc., 40 Landsdowne St., Cambridge, MA 02139, United States.

Macromolecule Content

Total Structure Weight: 707.74 kDa
Atom Count: 49,255
Modeled Residue Count: 6,315
Deposited Residue Count: 6,382
Unique protein chains: 14

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome component Y7	A, O	250	Saccharomyces cerevisiae S288C	Mutation(s): 0 EC: 3.4.25.1
UniProt
Find proteins for P23639 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P23639 Go to UniProtKB: P23639
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P23639
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome component Y13	B, P	235	Saccharomyces cerevisiae S288C	Mutation(s): 0 EC: 3.4.25.1
UniProt
Find proteins for P23638 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P23638 Go to UniProtKB: P23638
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P23638
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome component PRE6	C, Q	241	Saccharomyces cerevisiae S288C	Mutation(s): 0 EC: 3.4.25.1
UniProt
Find proteins for P40303 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P40303 Go to UniProtKB: P40303
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P40303
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome component PUP2	D, R	260	Saccharomyces cerevisiae S288C	Mutation(s): 0 EC: 3.4.25.1
UniProt
Find proteins for P32379 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P32379 Go to UniProtKB: P32379
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P32379
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Reference Sequence

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| 3D Structure

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome component PRE5	E, S	233	Saccharomyces cerevisiae S288C	Mutation(s): 0 EC: 3.4.25.1
UniProt
Find proteins for P40302 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P40302 Go to UniProtKB: P40302
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P40302
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Reference Sequence

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| 3D Structure

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome component C1	F, T	242	Saccharomyces cerevisiae S288C	Mutation(s): 0 EC: 3.4.25.1
UniProt
Find proteins for P21242 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P21242 Go to UniProtKB: P21242
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P21242
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Reference Sequence

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| 3D Structure

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome component C7-alpha	G, U	243	Saccharomyces cerevisiae S288C	Mutation(s): 0 EC: 3.4.25.1
UniProt
Find proteins for P21243 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P21243 Go to UniProtKB: P21243
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P21243
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Reference Sequence

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| 3D Structure

Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome component PUP1	H, V	222	Saccharomyces cerevisiae S288C	Mutation(s): 0 EC: 3.4.25.1
UniProt
Find proteins for P25043 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P25043 Go to UniProtKB: P25043
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P25043
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Reference Sequence

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| 3D Structure

Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome component PUP3	I, W	204	Saccharomyces cerevisiae S288C	Mutation(s): 0 EC: 3.4.25.1
UniProt
Find proteins for P25451 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P25451 Go to UniProtKB: P25451
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P25451
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Reference Sequence

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| 3D Structure

Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome component C11	J, X	198	Saccharomyces cerevisiae S288C	Mutation(s): 0 EC: 3.4.25.1
UniProt
Find proteins for P22141 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P22141 Go to UniProtKB: P22141
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P22141
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Reference Sequence

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| 3D Structure

Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome component PRE2	K, Y	212	Saccharomyces cerevisiae S288C	Mutation(s): 0 EC: 3.4.25.1
UniProt
Find proteins for P30656 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P30656 Go to UniProtKB: P30656
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P30656
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Reference Sequence

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| 3D Structure

Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome component C5	L, Z	222	Saccharomyces cerevisiae S288C	Mutation(s): 0 EC: 3.4.25.1
UniProt
Find proteins for P23724 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P23724 Go to UniProtKB: P23724
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P23724
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Reference Sequence

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| 3D Structure

Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome component PRE4	AA [auth 1], M	233	Saccharomyces cerevisiae S288C	Mutation(s): 0 EC: 3.4.25.1
UniProt
Find proteins for P30657 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P30657 Go to UniProtKB: P30657
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P30657
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Reference Sequence

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| 3D Structure

Entity ID: 14
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome component PRE3	BA [auth 2], N	196	Saccharomyces cerevisiae S288C	Mutation(s): 0 EC: 3.4.25.1
UniProt
Find proteins for P38624 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P38624 Go to UniProtKB: P38624
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P38624
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
P3N Query on P3N Download:Ideal Coordinates CCD File SDF format, chain JA [auth K] SDF format, chain OA [auth Y] MOL2 format, chain JA [auth K] MOL2 format, chain OA [auth Y] mmCIF format, chain JA [auth K] mmCIF format, chain OA [auth Y]	JA [auth K], OA [auth Y]	N-[(2S)-3-(3-tert-butyl-1,2,4-oxadiazol-5-yl)-1-({(2S)-1-[(4-methylbenzyl)amino]-1-oxo-4-phenylbutan-2-yl}amino)-1-oxopropan-2-yl]-5-methyl-1,2-oxazole-3-carboxamide C₃₂ H₃₈ N₆ O₅ OHMJOYZRJHYMAE-DQEYMECFSA-N		Interactions Focus chain JA [auth K] Focus chain OA [auth Y] Interactions & Density Focus chain JA [auth K] Focus chain OA [auth Y]
MES Query on MES Download:Ideal Coordinates CCD File SDF format, chain KA [auth K] SDF format, chain PA [auth Y] MOL2 format, chain KA [auth K] MOL2 format, chain PA [auth Y] mmCIF format, chain KA [auth K] mmCIF format, chain PA [auth Y]	KA [auth K], PA [auth Y]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C₆ H₁₃ N O₄ S SXGZJKUKBWWHRA-UHFFFAOYSA-N		Interactions Focus chain KA [auth K] Focus chain PA [auth Y] Interactions & Density Focus chain KA [auth K] Focus chain PA [auth Y]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain CA [auth F] SDF format, chain DA [auth F] SDF format, chain EA [auth G] SDF format, chain FA [auth H] SDF format, chain GA [auth I] SDF format, chain HA [auth I] SDF format, chain IA [auth K] SDF format, chain LA [auth L] SDF format, chain MA [auth L] SDF format, chain NA [auth N] MOL2 format, chain CA [auth F] MOL2 format, chain DA [auth F] MOL2 format, chain EA [auth G] MOL2 format, chain FA [auth H] MOL2 format, chain GA [auth I] MOL2 format, chain HA [auth I] MOL2 format, chain IA [auth K] MOL2 format, chain LA [auth L] MOL2 format, chain MA [auth L] MOL2 format, chain NA [auth N] mmCIF format, chain CA [auth F] mmCIF format, chain DA [auth F] mmCIF format, chain EA [auth G] mmCIF format, chain FA [auth H] mmCIF format, chain GA [auth I] mmCIF format, chain HA [auth I] mmCIF format, chain IA [auth K] mmCIF format, chain LA [auth L] mmCIF format, chain MA [auth L] mmCIF format, chain NA [auth N]	CA [auth F] DA [auth F] EA [auth G] FA [auth H] GA [auth I] CA [auth F], DA [auth F], EA [auth G], FA [auth H], GA [auth I], HA [auth I], IA [auth K], LA [auth L], MA [auth L], NA [auth N]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain CA [auth F] Focus chain DA [auth F] Focus chain EA [auth G] Focus chain FA [auth H] Focus chain GA [auth I] Focus chain HA [auth I] Focus chain IA [auth K] Focus chain LA [auth L] Focus chain MA [auth L] Focus chain NA [auth N] Interactions & Density Focus chain CA [auth F] Focus chain DA [auth F] Focus chain EA [auth G] Focus chain FA [auth H] Focus chain GA [auth I] Focus chain HA [auth I] Focus chain IA [auth K] Focus chain LA [auth L] Focus chain MA [auth L] Focus chain NA [auth N]

Biologically Interesting Molecules (External Reference)

1 Unique

Entity ID: 16
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_001075 (P3N) Query on PRD_001075	JA [auth K], OA [auth Y]	N-[(2S)-3-(3-TERT-BUTYL-1,2,4-OXADIAZOL-5-YL)-1-({(2S)-1-[(4-METHYLBENZYL)AMINO]-1-OXO-4-PHENYLBUTAN-2-YL}AMINO)-1-OXOPROPAN-2-YL]-5-METHYL-1,2-OXAZOLE-3-CARBOXAMIDE	Peptide-like / Inhibitor		Interactions Focus chain JA [auth K] Focus chain OA [auth Y] Interactions & Density Focus chain JA [auth K] Focus chain OA [auth Y]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free: 0.259 (Depositor), 0.251 (DCC)
R-Value Work: 0.223 (Depositor), 0.219 (DCC)
R-Value Observed: 0.224 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 136.121	α = 90
b = 299.404	β = 112.92
c = 146.236	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2012-06-13

Deposition Author(s):

Sintchak, M.D.

Revision History (Full details and data files)

Version 1.0: 2012-06-13
Type: Initial release
Version 1.1: 2012-12-12
Changes: Other
Version 1.2: 2013-04-03
Changes: Non-polymer description
Version 1.3: 2017-11-08
Changes: Refinement description
Version 1.4: 2023-09-13
Changes: Data collection, Database references, Derived calculations, Refinement description

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.

3SDK | pdb_00003sdk

Structure of yeast 20S open-gate proteasome with Compound 34

Literature

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.

Biological Assembly 1

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Entity ID: 2

UniProt

Entity Groups

Sequence Annotations

Entity ID: 3

UniProt

Entity Groups

Sequence Annotations

Entity ID: 4

UniProt

Entity Groups

Sequence Annotations

Entity ID: 5

UniProt

Entity Groups

Sequence Annotations

Entity ID: 6

UniProt

Entity Groups

Sequence Annotations

Entity ID: 7

UniProt

Entity Groups

Sequence Annotations

Entity ID: 8

UniProt

Entity Groups

Sequence Annotations

Entity ID: 9

UniProt

Entity Groups

Sequence Annotations

Entity ID: 10

UniProt

Entity Groups

Sequence Annotations

Entity ID: 11

UniProt

Entity Groups

Sequence Annotations

Entity ID: 12

UniProt

Entity Groups

Sequence Annotations

Entity ID: 13

UniProt

Entity Groups

Sequence Annotations

Entity ID: 14

UniProt

Entity Groups

Sequence Annotations

Small Molecules

Biologically Interesting Molecules (External Reference)

Experimental Data & Validation

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Entry History

Deposition Data

Revision History (Full details and data files)