7B12

HUMAN IMMUNOPROTEASOME 20S PARTICLE IN COMPLEX WITH [2-(3-ethylphenyl)-1-[(2S)-3-phenyl-2-[(pyrazin-2-yl)formamido]propanamido]ethyl]boronic acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.43 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.182 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structure-Based Optimization and Discovery of M3258, a Specific Inhibitor of the Immunoproteasome Subunit LMP7 ( beta 5i).

Klein, M.Busch, M.Friese-Hamim, M.Crosignani, S.Fuchss, T.Musil, D.Rohdich, F.Sanderson, M.P.Seenisamy, J.Walter-Bausch, G.Zanelli, U.Hewitt, P.Esdar, C.Schadt, O.

(2021) J Med Chem 64: 10230-10245

  • DOI: https://doi.org/10.1021/acs.jmedchem.1c00604
  • Primary Citation of Related Structures:  
    7B12

  • PubMed Abstract: 

    Proteasomes are broadly expressed key components of the ubiquitin-dependent protein degradation pathway containing catalytically active subunits (β1, β2, and β5). LMP7 (β5i) is a subunit of the immunoproteasome, an inducible isoform that is predominantly expressed in hematopoietic cells. Clinically effective pan-proteasome inhibitors for the treatment of multiple myeloma (MM) nonselectively target LMP7 and other subunits of the constitutive proteasome and immunoproteasome with comparable potency, which can limit the therapeutic applicability of these drugs. Here, we describe the discovery and structure-based hit optimization of novel amido boronic acids, which selectively inhibit LMP7 while sparing all other subunits. The exploitation of structural differences between the proteasome subunits culminated in the identification of the highly potent, exquisitely selective, and orally available LMP7 inhibitor 50 (M3258). Based on the strong antitumor activity observed with M3258 in MM models and a favorable preclinical data package, a phase I clinical trial was initiated in relapsed/refractory MM patients.


  • Organizational Affiliation

    Merck KGaA, Frankfurter Str. 250, Darmstadt 64293, Germany.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-1A [auth 1],
N [auth M]
213Homo sapiensMutation(s): 0 
EC: 3.4.25.1
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PHAROS:  P20618
GTEx:  ENSG00000008018 
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UniProt GroupP20618
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-4B [auth 2],
O [auth N]
214Homo sapiensMutation(s): 0 
EC: 3.4.25.1
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Find proteins for P28070 (Homo sapiens)
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PHAROS:  P28070
GTEx:  ENSG00000159377 
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UniProt GroupP28070
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-6C [auth A],
P [auth O]
242Homo sapiensMutation(s): 0 
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PHAROS:  P60900
GTEx:  ENSG00000100902 
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UniProt GroupP60900
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-2D [auth B],
Q [auth P]
229Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000106588 
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UniProt GroupP25787
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-4E [auth C],
R [auth Q]
248Homo sapiensMutation(s): 0 
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Find proteins for P25789 (Homo sapiens)
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GTEx:  ENSG00000041357 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-7F [auth D],
Z [auth r]
235Homo sapiensMutation(s): 0 
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PHAROS:  O14818
GTEx:  ENSG00000101182 
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UniProt GroupO14818
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-5AA [auth s],
G [auth E]
232Homo sapiensMutation(s): 0 
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Find proteins for P28066 (Homo sapiens)
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GTEx:  ENSG00000143106 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-1H [auth F],
S [auth T]
236Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000129084 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-3I [auth G],
T [auth U]
244Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000100567 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-9J [auth H],
U [auth V]
199Homo sapiensMutation(s): 0 
EC: 3.4.25.1
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Find proteins for P28065 (Homo sapiens)
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GTEx:  ENSG00000240065 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-3K [auth J],
V [auth X]
204Homo sapiensMutation(s): 0 
EC: 3.4.25.1
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GTEx:  ENSG00000277791 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-2L [auth K],
W [auth Y]
197Homo sapiensMutation(s): 0 
EC: 3.4.25.1
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GTEx:  ENSG00000126067 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-8M [auth L],
X [auth Z]
203Homo sapiensMutation(s): 0 
EC: 3.4.25.1
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GTEx:  ENSG00000204264 
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UniProt GroupP28062
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-10BA [auth w],
Y [auth i]
223Homo sapiensMutation(s): 0 
EC: 3.4.25.1
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Find proteins for P40306 (Homo sapiens)
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GTEx:  ENSG00000205220 
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UniProt GroupP40306
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Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SKN (Subject of Investigation/LOI)
Query on SKN

Download Ideal Coordinates CCD File 
FA [auth H]
HA [auth L]
LA [auth V]
NA [auth Z]
PA [auth i]
FA [auth H],
HA [auth L],
LA [auth V],
NA [auth Z],
PA [auth i],
RA [auth w]
((R)-2-(3-ethylphenyl)-1-((S)-3-phenyl-2-(pyrazine-2-carboxamido)propanamido)ethyl)boronic acid
C24 H27 B N4 O4
RQXXOBNVVACHIB-UNMCSNQZSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
CA [auth 1],
DA [auth 1],
GA [auth K],
JA [auth L],
MA [auth Y]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
NA
Query on NA

Download Ideal Coordinates CCD File 
EA [auth A]
IA [auth L]
KA [auth O]
OA [auth Z]
QA [auth i]
EA [auth A],
IA [auth L],
KA [auth O],
OA [auth Z],
QA [auth i],
SA [auth w]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
SKN BindingDB:  7B12 IC50: min: 1.7, max: 11 (nM) from 2 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.43 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.182 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 118.995α = 90
b = 201.736β = 106.83
c = 161.932γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
PHASERphasing
PDB_EXTRACTdata extraction
autoPROCdata scaling
autoPROCdata processing
STARANISOdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-12-01
    Type: Initial release
  • Version 1.1: 2021-12-08
    Changes: Refinement description
  • Version 1.2: 2023-06-14
    Changes: Database references
  • Version 1.3: 2024-11-06
    Changes: Data collection, Structure summary