8RHJ

Yeast 20S proteasome in complex with a macrocyclic oxindole epoxyketone (compound 5)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.05 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.177 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


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Literature

Macrocyclic Oxindole Peptide Epoxyketones-A Comparative Study of Macrocyclic Inhibitors of the 20S Proteasome.

Gotz, M.G.Godwin, K.Price, R.Dorn, R.Merrill-Steskal, G.Klemmer, W.Hansen, H.Produturi, G.Rocha, M.Palmer, M.Molacek, L.Strater, Z.Groll, M.

(2024) ACS Med Chem Lett 15: 533-539

  • DOI: https://doi.org/10.1021/acsmedchemlett.4c00017
  • Primary Citation of Related Structures:  
    8RHJ, 8RHK, 8RHL

  • PubMed Abstract: 

    Peptide macrocycles have recently gained attention as protease inhibitors due to their metabolic stability and specificity. However, the development of peptide macrocycles with improved binding potency has so far been challenging. Here we present macrocyclic peptides derived from the clinically applied proteasome inhibitor carfilzomib with an oxindole group that mimics the natural product TMC-95A. Fluorescence kinetic activity assays reveal a high potency of the oxindole group (IC 50 = 0.19 μM) compared with agents lacking this motif. X-ray structures of the ligands with the β5-subunit of the yeast 20S proteasome illustrate that the installed macrocycle forces strong hydrogen bonding of the oxindole group with β5-Gly23NH. Thus, the binding of our designed oxindole epoxyketones is entropically and enthalpically favored in contrast to more flexible proteasome inhibitors such as carfilzomib.


  • Organizational Affiliation

    Department of Chemistry, Whitman College, Walla Walla, Washington 99362, United States.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-2
A, O
250Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-3
B, P
258Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-4
C, Q
254Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-5
D, R
260Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-6
E, S
234Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Probable proteasome subunit alpha type-7
F, T
288Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-1
G, U
252Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-2
H, V
232Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.4.25.1
UniProt
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-3
I, W
205Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-4
J, X
198Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-5
K, Y
212Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.4.25.1
UniProt
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-6
L, Z
222Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-7AA [auth a],
M
246Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-1BA [auth b],
N
196Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.4.25.1
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Macrocyclic oxindole epoxyketone5synthetic constructMutation(s): 0 
Sequence Annotations
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Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download Ideal Coordinates CCD File 
JA [auth G],
NA [auth U]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG
Query on MG

Download Ideal Coordinates CCD File 
IA [auth G]
KA [auth I]
LA [auth K]
MA [auth N]
OA [auth V]
IA [auth G],
KA [auth I],
LA [auth K],
MA [auth N],
OA [auth V],
PA [auth X],
QA [auth Y],
RA [auth Z]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  2 Unique
IDChains TypeFormula2D DiagramParent
A1H45
Query on A1H45
CA [auth g]
DA [auth e]
EA [auth i]
FA [auth f]
GA [auth h]
CA [auth g],
DA [auth e],
EA [auth i],
FA [auth f],
GA [auth h],
HA [auth j]
L-PEPTIDE LINKINGC11 H12 N2 O4TRP
PPN
Query on PPN
CA [auth g]
DA [auth e]
EA [auth i]
FA [auth f]
GA [auth h]
CA [auth g],
DA [auth e],
EA [auth i],
FA [auth f],
GA [auth h],
HA [auth j]
L-PEPTIDE LINKINGC9 H10 N2 O4PHE
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.05 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.177 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 135.69α = 90
b = 302.01β = 113.18
c = 144.24γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)GermanyGR 1861/10-3

Revision History  (Full details and data files)

  • Version 1.0: 2024-05-01
    Type: Initial release