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 1.1 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 ...

    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.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-6A, O242Homo sapiensMutation(s): 0 
Gene Names: PSMA6, PROS27
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-2B, P229Homo sapiensMutation(s): 0 
Gene Names: PSMA2, HC3, PSC3
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-4C, Q256Homo sapiensMutation(s): 0 
Gene Names: PSMA4, HC9, PSC9
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-7D, R237Homo sapiensMutation(s): 0 
Gene Names: PSMA7, HSPC
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-5E, S232Homo sapiensMutation(s): 0 
Gene Names: PSMA5
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-1F, T236Homo sapiensMutation(s): 0 
Gene Names: PSMA1, HC2, NU, PROS30, PSC2
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-3G, U242Homo sapiensMutation(s): 0 
Gene Names: PSMA3, HC8, PSC8
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit beta type-9H, V199Homo sapiensMutation(s): 0 
Gene Names: PSMB9, LMP2, PSMB6i, RING12
EC: 3.4.25.1
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit beta type-10I, W223Homo sapiensMutation(s): 0 
Gene Names: PSMB10, LMP10, MECL1
EC: 3.4.25.1
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit beta type-3J, X204Homo sapiensMutation(s): 0 
Gene Names: PSMB3
EC: 3.4.25.1
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit beta type-2K, Y197Homo sapiensMutation(s): 0 
Gene Names: PSMB2
EC: 3.4.25.1
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit beta type-8L, Z203Homo sapiensMutation(s): 0 
Gene Names: PSMB8, LMP7, PSMB5i, RING10, Y2
EC: 3.4.25.1
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit beta type-1AA [auth a],
M		213Homo sapiensMutation(s): 0 
Gene Names: PSMB1, PSC5
EC: 3.4.25.1
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit beta type-4BA [auth b],
N		214Homo sapiensMutation(s): 0 
Gene Names: PSMB4, PROS26
EC: 3.4.25.1
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Small Molecules
Ligands 3 Unique
IDChainsName / 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		 Ligand Interaction
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		 Ligand Interaction
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		 Ligand Interaction
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 


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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