7AWE

HUMAN IMMUNOPROTEASOME 20S PARTICLE IN COMPLEX WITH [(1R)-2-(1-benzofuran-3-yl)-1-{[(1S,2R,4R)-7-oxabicyclo[2.2.1]heptan-2-yl]formamido}ethyl]boronic acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.29 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.179 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

M3258 Is a Selective Inhibitor of the Immunoproteasome Subunit LMP7 ( beta 5i) Delivering Efficacy in Multiple Myeloma Models.

Sanderson, M.P.Friese-Hamim, M.Walter-Bausch, G.Busch, M.Gaus, S.Musil, D.Rohdich, F.Zanelli, U.Downey-Kopyscinski, S.L.Mitsiades, C.S.Schadt, O.Klein, M.Esdar, C.

(2021) Mol Cancer Ther 20: 1378-1387

  • DOI: https://doi.org/10.1158/1535-7163.MCT-21-0005
  • Primary Citation of Related Structures:  
    7AWE

  • PubMed Abstract: 

    Large multifunctional peptidase 7 (LMP7/β5i/PSMB8) is a proteolytic subunit of the immunoproteasome, which is predominantly expressed in normal and malignant hematolymphoid cells, including multiple myeloma, and contributes to the degradation of ubiquitinated proteins. Described herein for the first time is the preclinical profile of M3258; an orally bioavailable, potent, reversible and highly selective LMP7 inhibitor. M3258 demonstrated strong antitumor efficacy in multiple myeloma xenograft models, including a novel model of the human bone niche of multiple myeloma. M3258 treatment led to a significant and prolonged suppression of tumor LMP7 activity and ubiquitinated protein turnover and the induction of apoptosis in multiple myeloma cells both in vitro and in vivo Furthermore, M3258 showed superior antitumor efficacy in selected multiple myeloma and mantle cell lymphoma xenograft models compared with the approved nonselective proteasome inhibitors bortezomib and ixazomib. The differentiated preclinical profile of M3258 supported the initiation of a phase I study in patients with multiple myeloma (NCT04075721).


  • Organizational Affiliation

    Merck KGaA, Darmstadt, Germany. michael.sanderson@merckgroup.com.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-6
A, O
242Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000100902 
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UniProt GroupP60900
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-2
B, P
229Homo sapiensMutation(s): 0 
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Find proteins for P25787 (Homo sapiens)
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PHAROS:  P25787
GTEx:  ENSG00000106588 
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UniProt GroupP25787
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-4
C, Q
256Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000041357 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-7
D, R
237Homo sapiensMutation(s): 0 
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Find proteins for O14818 (Homo sapiens)
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GTEx:  ENSG00000101182 
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UniProt GroupO14818
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-5
E, S
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: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-1
F, T
236Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000129084 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-3
G, U
242Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000100567 
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UniProt GroupP25788
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-9
H, V
199Homo sapiensMutation(s): 0 
EC: 3.4.25.1
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GTEx:  ENSG00000240065 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-10
I, W
223Homo sapiensMutation(s): 0 
EC: 3.4.25.1
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GTEx:  ENSG00000205220 
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UniProt GroupP40306
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-3
J, X
204Homo sapiensMutation(s): 0 
EC: 3.4.25.1
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Find proteins for P49720 (Homo sapiens)
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GTEx:  ENSG00000277791 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-2
K, Y
197Homo sapiensMutation(s): 0 
EC: 3.4.25.1
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GTEx:  ENSG00000126067 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-8
L, Z
203Homo sapiensMutation(s): 0 
EC: 3.4.25.1
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GTEx:  ENSG00000204264 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-1AA [auth a],
M
213Homo sapiensMutation(s): 0 
EC: 3.4.25.1
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GTEx:  ENSG00000008018 
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UniProt GroupP20618
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-4BA [auth b],
N
214Homo sapiensMutation(s): 0 
EC: 3.4.25.1
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GTEx:  ENSG00000159377 
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Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
S5K (Subject of Investigation/LOI)
Query on S5K

Download Ideal Coordinates CCD File 
EA [auth H],
LA [auth L],
UA [auth V],
YA [auth Z]
[(1R)-2-(1-benzofuran-3-yl)-1-{[(1S,2R,4R)-7-oxabicyclo[2.2.1]heptan-2-yl]formamido}ethyl]boronic acid
C17 H20 B N O5
RFQDLTYXNINJON-OYNZBZHQSA-N
SCN
Query on SCN

Download Ideal Coordinates CCD File 
AB [auth Z]
CB [auth a]
DA [auth F]
DB [auth a]
JA [auth K]
AB [auth Z],
CB [auth a],
DA [auth F],
DB [auth a],
JA [auth K],
KA [auth K],
OA [auth M],
PA [auth M],
QA [auth M],
SA [auth T],
TA [auth U]
THIOCYANATE ION
C N S
ZMZDMBWJUHKJPS-UHFFFAOYSA-M
NA
Query on NA

Download Ideal Coordinates CCD File 
BB [auth a]
CA [auth A]
FA [auth H]
GA [auth I]
HA [auth J]
BB [auth a],
CA [auth A],
FA [auth H],
GA [auth I],
HA [auth J],
IA [auth J],
MA [auth L],
NA [auth M],
RA [auth O],
VA [auth V],
WA [auth W],
XA [auth X],
ZA [auth Z]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
S5K BindingDB:  7AWE IC50: min: 3.4, max: 3.00e+4 (nM) from 3 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.29 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.179 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 119.471α = 90
b = 206.048β = 106.69
c = 162.808γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
PDB_EXTRACTdata extraction
STARANISOdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-06-09
    Type: Initial release
  • Version 1.1: 2021-08-11
    Changes: Advisory, Database references
  • Version 1.2: 2024-11-20
    Changes: Data collection, Structure summary