6HVU

Yeast 20S proteasome with human beta2i (1-53) in complex with 29


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.190 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structure-Based Design of Inhibitors Selective for Human Proteasome beta 2c or beta 2i Subunits.

Xin, B.T.Huber, E.M.de Bruin, G.Heinemeyer, W.Maurits, E.Espinal, C.Du, Y.Janssens, M.Weyburne, E.S.Kisselev, A.F.Florea, B.I.Driessen, C.van der Marel, G.A.Groll, M.Overkleeft, H.S.

(2019) J.Med.Chem. 62: 1626-1642

  • DOI: 10.1021/acs.jmedchem.8b01884
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Subunit-selective proteasome inhibitors are valuable tools to assess the biological and medicinal relevance of individual proteasome active sites. Whereas the inhibitors for the β1c, β1i, β5c, and β5i subunits exploit the differences in the substrate ...

    Subunit-selective proteasome inhibitors are valuable tools to assess the biological and medicinal relevance of individual proteasome active sites. Whereas the inhibitors for the β1c, β1i, β5c, and β5i subunits exploit the differences in the substrate-binding channels identified by X-ray crystallography, compounds selectively targeting β2c or β2i could not yet be rationally designed because of the high structural similarity of these two subunits. Here, we report the development, chemical synthesis, and biological screening of a compound library that led to the identification of the β2c- and β2i-selective compounds LU-002c (4; IC 50 β2c: 8 nM, IC 50 β2i/β2c: 40-fold) and LU-002i (5; IC 50 β2i: 220 nM, IC 50 β2c/β2i: 45-fold), respectively. Co-crystal structures with β2 humanized yeast proteasomes visualize protein-ligand interactions crucial for subunit specificity. Altogether, organic syntheses, activity-based protein profiling, yeast mutagenesis, and structural biology allowed us to decipher significant differences of β2 substrate-binding channels and to complete the set of subunit-selective proteasome inhibitors.


    Organizational Affiliation

    Center for Integrated Protein Science at the Department Chemie, Lehrstuhl für Biochemie , Technische Universität München , 85748 Garching , Germany.,Department of Hematology and Oncology , Kantonsspital St. Gallen , 9007 St. Gallen , Switzerland.,Gorlaeus Laboratories , Leiden Institute of Chemistry and Netherlands Proteomics Centre , Einsteinweg 55 , 2333 CC Leiden , Netherlands.,Department of Molecular and Systems Biology and Norris Cotton Cancer Center , Geisel School of Medicine at Dartmouth , 1 Medical Centre Drive HB7936 , Lebanon , New Hampshire 03756 , United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit alpha type-2
A, O
250Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: PRE8 (PRS4)
EC: 3.4.25.1
Find proteins for P23639 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P23639
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit alpha type-3
B, P
258Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: PRE9 (PRS5)
EC: 3.4.25.1
Find proteins for P23638 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P23638
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit alpha type-4
C, Q
254Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: PRE6
EC: 3.4.25.1
Find proteins for P40303 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P40303
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit alpha type-5
D, R
260Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: PUP2 (DOA5)
EC: 3.4.25.1
Find proteins for P32379 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P32379
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit alpha type-6
E, S
234Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: PRE5
EC: 3.4.25.1
Find proteins for P40302 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P40302
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
Probable proteasome subunit alpha type-7
F, T
288Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: PRE10 (PRC1, PRS1)
EC: 3.4.25.1
Find proteins for P21242 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P21242
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit alpha type-1
G, U
252Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: SCL1 (PRC2, PRS2)
EC: 3.4.25.1
Find proteins for P21243 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P21243
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit beta type-10,Proteasome subunit beta type-2
H, V
226Homo sapiensSaccharomyces cerevisiae (strain ATCC 204508 / S288c)
This entity is chimeric
Mutation(s): 0 
Gene Names: PSMB10 (LMP10, MECL1), PUP1
EC: 3.4.25.1 3.4.25.1
Find proteins for P40306 (Homo sapiens)
Go to Gene View: PSMB10
Go to UniProtKB:  P40306
Find proteins for P25043 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P25043
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit beta type-3
I, W
205Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: PUP3
EC: 3.4.25.1
Find proteins for P25451 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P25451
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit beta type-4
J, X
198Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: PRE1
EC: 3.4.25.1
Find proteins for P22141 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P22141
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit beta type-5
K, Y
212Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: PRE2 (DOA3, PRG1)
EC: 3.4.25.1
Find proteins for P30656 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P30656
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit beta type-6
L, Z
222Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: PRE7 (PRS3, PTS1)
EC: 3.4.25.1
Find proteins for P23724 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P23724
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit beta type-7
M, a
246Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: PRE4
EC: 3.4.25.1
Find proteins for P30657 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P30657
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit beta type-1
N, b
196Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: PRE3
EC: 3.4.25.1
Find proteins for P38624 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P38624
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
G, U
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
GTW
Query on GTW

Download SDF File 
Download CCD File 
H, K, V, Y
~{N}-[(2~{S})-1-[[(2~{S})-1-[[(2~{S})-1-[4-(aminomethyl)phenyl]-4-methylsulfonyl-butan-2-yl]amino]-3-cyclohexyl-1-oxidanylidene-propan-2-yl]amino]-4-methyl-1-oxidanylidene-pentan-2-yl]-2-methyl-1,3-thiazole-5-carboxamide
C32 H49 N5 O5 S2
ZGJWOTGESBPCTA-PKTNWEFCSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
G, I, K, N, V, W, Y, Z
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.190 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 135.310α = 90.00
b = 299.460β = 112.44
c = 143.920γ = 90.00
Software Package:
Software NamePurpose
REFMACphasing
REFMACrefinement
XSCALEdata scaling
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2018-10-11 
  • Released Date: 2019-01-30 
  • Deposition Author(s): Huber, E.M., Groll, M.

Funding OrganizationLocationGrant Number
German Research FoundationGermanyGR1861/10-1

Revision History 

  • Version 1.0: 2019-01-30
    Type: Initial release
  • Version 1.1: 2019-04-24
    Type: Data collection, Database references