5M2B

Yeast 20S proteasome with human beta5i (1-138) and human beta6 (97-111; 118-133) in complex with thiazole based inhibitor Ro19

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.201 

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Ligand Structure Quality Assessment 


This is version 2.0 of the entry. See complete history. 


Literature

Structural Elucidation of a Nonpeptidic Inhibitor Specific for the Human Immunoproteasome.

Cui, H., Baur, R., Le Chapelain, C., Dubiella, C., Heinemeyer, W., Huber, E.M., Groll, M.

(2017) Chembiochem 18: 523-526

  • DOI: https://doi.org/10.1002/cbic.201700021
  • Primary Citation of Related Structures:  
    5M2B

  • PubMed Abstract: 

    • Selective inhibition of the immunoproteasome is a promising approach towards the development of immunomodulatory drugs. Recently, a class of substituted thiazole compounds that combine a nonpeptidic scaffold with the absence of an electrophile was reported in a patent ...

    Selective inhibition of the immunoproteasome is a promising approach towards the development of immunomodulatory drugs. Recently, a class of substituted thiazole compounds that combine a nonpeptidic scaffold with the absence of an electrophile was reported in a patent. Here, we investigated the mode of action of the lead compound by using a sophisticated chimeric yeast model of the human immunoproteasome for structural studies. The inhibitor adopts a unique orientation perpendicular to the β5i substrate-binding channel. Distinct interactions between the inhibitor and the subpockets of the human immunoproteasome account for its isotype selectivity.

    Organizational Affiliation: 

    Center for Integrated Protein Science Munich (CIPSM), Department of Chemistry, Technische Universität München, Lichtenbergstrasse 4, 85748, Garching, Germany.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-2A, O250Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRE8, PRS4, YML092C
EC: 3.4.25.1
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-3B, P258Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRE9, PRS5, YGR135W
EC: 3.4.25.1
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-4C, Q254Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRE6, YOL038W
EC: 3.4.25.1
UniProt
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-5D, R260Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PUP2, DOA5, YGR253C, G9155
EC: 3.4.25.1
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-6E, S234Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRE5, YMR314W, YM9924.06
EC: 3.4.25.1
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Probable proteasome subunit alpha type-7F, T288Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRE10, PRC1, PRS1, YOR362C, O6650
EC: 3.4.25.1
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-1G, U252Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SCL1, PRC2, PRS2, YGL011C
EC: 3.4.25.1
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit beta type-2H, V232Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PUP1, YOR157C
EC: 3.4.25.1
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit beta type-3I, W205Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PUP3, YER094C
EC: 3.4.25.1
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Entity ID: 10
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Proteasome subunit beta type-4J, X198Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRE1, YER012W
EC: 3.4.25.1
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit beta type-8,Proteasome subunit beta type-5K, Y211Homo sapiens, Saccharomyces cerevisiae S288C
This entity is chimeric		Mutation(s): 0 
Gene Names: PSMB8, LMP7, PSMB5i, RING10, Y2, PRE2, DOA3, PRG1, YPR103W, P8283.10
EC: 3.4.25.1
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PHAROS:  P28062
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UniProt GroupsP30656P28062
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit beta type-6,Proteasome subunit beta type,Proteasome subunit beta type-6,Proteasome subunit beta type,Proteasome subunit beta type-6L, Z222Saccharomyces cerevisiae S288C, Homo sapiensMutation(s): 0 
Gene Names: PRE7, PRS3, PTS1, YBL041W, YBL0407, PSMB1
EC: 3.4.25.1
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PHAROS:  P20618
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit beta type-7AA [auth a],
M		246Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRE4, YFR050C
EC: 3.4.25.1
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit beta type-1BA [auth b],
N		196Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRE3, YJL001W, J1407
EC: 3.4.25.1
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Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
7DX
Query on 7DX
Download Ideal Coordinates CCD File 
GA [auth K],
MA [auth Y]		(2~{S})-2-cyclohexyl-4-oxidanylidene-4-[[7-(4-phenyl-1,3-thiazol-2-yl)quinolin-2-yl]amino]butanoic acid
C28 H27 N3 O3 S
APWRCWKBBYBSJJ-QFIPXVFZSA-N		 Ligand Interaction
CL
Query on CL
Download Ideal Coordinates CCD File 
DA [auth G],
KA [auth N],
LA [auth U],
OA [auth b]		CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M		 Ligand Interaction
MG
Query on MG
Download Ideal Coordinates CCD File 
CA [auth G],
EA [auth I],
FA [auth J],
HA [auth K],
IA [auth L],
CA [auth G],
EA [auth I],
FA [auth J],
HA [auth K],
IA [auth L],
JA [auth N],
NA [auth Z]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.201 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 135.16α = 90
b = 301.15β = 112.81
c = 145.98γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
REFMACphasing
REFMACrefinement

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History & Funding Information

Deposition Data

  • Released Date: 2017-01-25 
    • Deposition Author(s): Groll, M.
Funding OrganizationLocationGrant Number
German Research FoundationGermanyGR1861/10-1

Revision History  (Full details and data files)

  • Version 1.0: 2017-01-25
    Type: Initial release
  • Version 1.1: 2017-03-29
    Changes: Database references
  • Version 2.0: 2019-12-04
    Changes: Atomic model, Author supporting evidence, Data collection, Source and taxonomy, Structure summary