9FST | pdb_00009fst

Yeast 20S proteasome with human beta1i (1-51) in complex with epoxyketone inhibitor LU-001i


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 
    0.245 (Depositor), 0.244 (DCC) 
  • R-Value Work: 
    0.205 (Depositor), 0.209 (DCC) 
  • R-Value Observed: 
    0.207 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

Structure-Based Design of Pan-Selective Peptide Epoxyketones for the Three Human Immunoproteasome Active Sites.

Dekker, P.M.Huber, E.M.Maurits, E.Wang, X.Heinemeyer, W.Florea, B.I.Groll, M.Overkleeft, H.S.

(2026) J Med Chem 69: 1247-1263

  • DOI: https://doi.org/10.1021/acs.jmedchem.5c02639
  • Primary Citation Related Structures: 
    9FRW, 9FST, 9FSU, 9FSV, 9FT0, 9FT1

  • PubMed Abstract: 

    The proteasome inhibitors bortezomib, carfilzomib, and ixazomib all act by inhibiting multiple active sites of both constitutive proteasomes and immunoproteasomes. These clinical anticancer drugs are effective, but also display side effects, and evidence is amassing that their toxicity arises from constitutive proteasome inhibition. In this work, we describe the structure-guided discovery of a new class of pan-immunoproteasome-selective inhibitors. We identified the peptide epoxyketone BocPip-Ser ( 8 ), which targets all three human immunoproteasome active sites potently and with excellent selectivity over constitutive proteasome active sites (IC 50 values for i-subunits ≤ 0.92 μM; IC 50 ratio β1c/β1i: 13, β2c/β2i: 14, β5c/β5i: 18; Table 1 and Figure 3). We propose compound 8 (BocPip-Ser), which is of a similar size and general properties as carfilzomib, as a lead compound for the development of improved drugs targeting hematological cancers, and possibly also autoimmune diseases, driven by immunoproteasome but not constitutive proteasome activities.


  • Organizational Affiliation
    • Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands.

Macromolecule Content 

  • Total Structure Weight: 734.43 kDa 
  • Atom Count: 49,773 
  • Modeled Residue Count: 6,327 
  • Deposited Residue Count: 6,610 
  • Unique protein chains: 14

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-2
A, O
250Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-3
B, P
258Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Reference Sequence
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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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Reference Sequence
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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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Reference Sequence
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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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Reference Sequence
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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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Reference Sequence
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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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Reference Sequence
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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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Reference Sequence
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Entity ID: 9
MoleculeChains  Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-3
I, W
205Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Reference Sequence
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Entity ID: 10
MoleculeChains  Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-4
J, X
198Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Reference Sequence
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Entity ID: 11
MoleculeChains  Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-5
K, Y
211Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.4.25.1
UniProt
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Reference Sequence
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Entity ID: 12
MoleculeChains  Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-6
L, Z
222Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Reference Sequence
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Entity ID: 13
MoleculeChains  Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-7AA [auth a],
M
246Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Reference Sequence
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Entity ID: 14
MoleculeChains  Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-9,Proteasome subunit beta type-1BA [auth b],
N
195Homo sapiensSaccharomyces cerevisiae
This entity is chimeric
Mutation(s): 0 
Gene Names: PSMB9LMP2PSMB6iRING12PRE3YJL001WJ1407
EC: 3.4.25.1
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GTEx:  ENSG00000240065 
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Reference Sequence

Small Molecules

Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1IF8
(Subject of Investigation/LOI)

Query on A1IF8



Download:Ideal Coordinates CCD File
GA [auth K],
KA [auth N],
RA [auth Y],
WA [auth b]
azanylidene-[2-[[(2S)-1-[(2S)-2-[[(2S)-1-[[(1S)-2-cyclohexyl-1-[(2R,3S,6R,7S)-3-methanoyl-2,6-dimethyl-6,7-bis(oxidanyl)-1,4-oxazepan-7-yl]ethyl]amino]-1-oxidanylidene-hexan-2-yl]carbamoyl]-4,4-bis(fluoranyl)pyrrolidin-1-yl]-1-oxidanylidene-propan-2-yl]amino]-2-oxidanylidene-ethyl]imino-azanium
C32 H53 F2 N8 O8
RZBRYLLVVLXELI-JBOYJDAMSA-O
MES

Query on MES



Download:Ideal Coordinates CCD File
HA [auth K],
JA [auth M],
SA [auth Y],
VA [auth a]
2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
LA [auth N]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
CL

Query on CL



Download:Ideal Coordinates CCD File
CA [auth G],
EA [auth H],
NA [auth U],
OA [auth V]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG

Query on MG



Download:Ideal Coordinates CCD File
DA [auth G]
FA [auth I]
IA [auth K]
MA [auth N]
PA [auth W]
DA [auth G],
FA [auth I],
IA [auth K],
MA [auth N],
PA [auth W],
QA [auth X],
TA [auth Y],
UA [auth Z]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free:  0.245 (Depositor), 0.244 (DCC) 
  • R-Value Work:  0.205 (Depositor), 0.209 (DCC) 
  • R-Value Observed: 0.207 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 135.37α = 90
b = 300.16β = 112.78
c = 143.97γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing

Structure Validation

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Ligand Structure Quality Assessment 


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: 2024-07-17
    Type: Initial release
  • Version 1.1: 2024-11-13
    Changes: Structure summary
  • Version 1.2: 2026-01-21
    Changes: Database references
  • Version 1.3: 2026-01-28
    Changes: Database references