6E5B

Human Immunoproteasome 20S particle in complex with compound 1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.77 Å
  • R-Value Free: 0.291 
  • R-Value Work: 0.248 
  • R-Value Observed: 0.248 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Design and Evaluation of Highly Selective Human Immunoproteasome Inhibitors Reveal a Compensatory Process That Preserves Immune Cell Viability.

Ladi, E.Everett, C.Stivala, C.E.Daniels, B.E.Durk, M.R.Harris, S.F.Huestis, M.P.Purkey, H.E.Staben, S.T.Augustin, M.Blaesse, M.Steinbacher, S.Eidenschenk, C.Pappu, R.Siu, M.

(2019) J Med Chem 62: 7032-7041

  • DOI: https://doi.org/10.1021/acs.jmedchem.9b00509
  • Primary Citation of Related Structures:  
    6E5B

  • PubMed Abstract: 

    The pan-proteasome inhibitor bortezomib demonstrated clinical efficacy in off-label trials of Systemic Lupus Erythematosus. One potential mechanism of this clinical benefit is from the depletion of pathogenic immune cells (plasmablasts and plasmacytoid dendritic cells). However, bortezomib is cytotoxic against nonimmune cells, which limits its use for autoimmune diseases. An attractive alternative is to selectively inhibit the immune cell-specific immunoproteasome to deplete pathogenic immune cells and spare nonhematopoietic cells. Here, we disclose the development of highly subunit-selective immunoproteasome inhibitors using insights obtained from the first bona fide human immunoproteasome cocrystal structures. Evaluation of these inhibitors revealed that immunoproteasome-specific inhibition does not lead to immune cell death as anticipated and that targeting viability requires inhibition of both immuno- and constitutive proteasomes. CRISPR/Cas9-mediated knockout experiments confirmed upregulation of the constitutive proteasome upon disruption of the immunoproteasome, protecting cells from death. Thus, immunoproteasome inhibition alone is not a suitable approach to deplete immune cells.


  • Organizational Affiliation

    Proteros Biostructures GmbH , Bunsenstrasse 7a , Planegg-Martinsried 82152 , Germany.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-2
A, O
234Homo sapiensMutation(s): 0 
EC: 3.4.25.1
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PHAROS:  P25787
GTEx:  ENSG00000106588 
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UniProt GroupP25787
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-4
B, P
261Homo sapiensMutation(s): 0 
EC: 3.4.25.1
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GTEx:  ENSG00000041357 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-7
C, Q
248Homo sapiensMutation(s): 0 
EC: 3.4.25.1
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GTEx:  ENSG00000101182 
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UniProt GroupO14818
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-5
D, R
241Homo sapiensMutation(s): 0 
EC: 3.4.25.1
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GTEx:  ENSG00000143106 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-1
E, S
263Homo sapiensMutation(s): 0 
EC: 3.4.25.1
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GTEx:  ENSG00000129084 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-3
F, T
255Homo sapiensMutation(s): 0 
EC: 3.4.25.1
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GTEx:  ENSG00000100567 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-6
G, U
246Homo sapiensMutation(s): 0 
EC: 3.4.25.1
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GTEx:  ENSG00000100902 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-10
H, V
273Homo sapiensMutation(s): 0 
EC: 3.4.25.1
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GTEx:  ENSG00000205220 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-3
I, W
205Homo sapiensMutation(s): 0 
EC: 3.4.25.1
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GTEx:  ENSG00000277791 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-2
J, X
201Homo sapiensMutation(s): 0 
EC: 3.4.25.1
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GTEx:  ENSG00000126067 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-8
K, Y
276Homo sapiensMutation(s): 0 
EC: 3.4.25.1
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GTEx:  ENSG00000204264 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-1
L, Z
241Homo sapiensMutation(s): 0 
EC: 3.4.25.1
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GTEx:  ENSG00000008018 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-4AA [auth a],
M
264Homo sapiensMutation(s): 0 
EC: 3.4.25.1
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GTEx:  ENSG00000159377 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-9BA [auth b],
N
219Homo sapiensMutation(s): 0 
EC: 3.4.25.1
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GTEx:  ENSG00000240065 
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Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HUJ (Subject of Investigation/LOI)
Query on HUJ

Download Ideal Coordinates CCD File 
HA [auth K],
MA [auth N],
QA [auth Y],
TA [auth b]
[(1R)-3-methyl-1-[[1-[2-[(2,3,4-trimethoxyphenyl)carbonylamino]ethyl]-1,2,3-triazol-4-yl]carbonylamino]butyl]-tris(oxidanyl)boron
C20 H31 B N5 O8
BKCQATOXENTEDK-INIZCTEOSA-N
SCN
Query on SCN

Download Ideal Coordinates CCD File 
CA [auth E],
JA [auth L],
RA [auth Z]
THIOCYANATE ION
C N S
ZMZDMBWJUHKJPS-UHFFFAOYSA-M
NA
Query on NA

Download Ideal Coordinates CCD File 
DA [auth G]
EA [auth H]
FA [auth I]
GA [auth I]
IA [auth K]
DA [auth G],
EA [auth H],
FA [auth I],
GA [auth I],
IA [auth K],
KA [auth L],
LA [auth L],
NA [auth N],
OA [auth U],
PA [auth W],
SA [auth Z],
UA [auth b]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.77 Å
  • R-Value Free: 0.291 
  • R-Value Work: 0.248 
  • R-Value Observed: 0.248 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 118.573α = 90
b = 203.142β = 106.82
c = 161.487γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
REFMACphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-09-11
    Type: Initial release
  • Version 1.1: 2024-10-23
    Changes: Advisory, Data collection, Database references, Derived calculations, Structure summary