6HTP

Yeast 20S proteasome with human beta2c (S171G) in complex with 7


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.177 

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

    Institut für Medizinische und Pharmazeutische Chemie, Technische Universität Braunschweig, Braunschweig, Germany.,Department of Biophysics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China; Institute of Systems Biomedicine, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China; Beijing Key Laboratory of Tumor Systems Biology, Peking University Health Science Center, Beijing 100191, China. Electronic address: yunch@hsc.pku.edu.cn.,Department of Molecular Cardiology, Lerner Research Institute, Cleveland Clinic, 9500 Euclid Avenue, Cleveland, OH, 44195, USA.,Rheumatology Unit, Department of Medicine Solna, Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden.,Department of Biophysics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China; Institute of Systems Biomedicine, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China; Beijing Key Laboratory of Tumor Systems Biology, Peking University Health Science Center, Beijing 100191, China.,Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan.,Laboratório de Espectrometria de Massa, Embrapa Recursos Genéticos e Biotecnologia, Brasília, Distrito Federal, Brazil. Electronic address: carlos.bloch@embrapa.br.,Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan. kurumizaka@iam.u-tokyo.ac.jp shunichi.sekine@riken.jp.,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.,Department of Chemistry, Université de Montréal, Montréal, QC, H3C 3J7, Canada.,Center of Pharmaceutical Engeneering (PVZ), Technische Universität Braunschweig, Braunschweig, Germany.,Department of Biochemistry, School of Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA.,Computational Biochemistry, Zentrum für Medizinische Biotechnologie, Fakultät für Biologie, Universität Duisburg-Essen, Universitätsstr. 2, 45117, Essen, Germany.,Collaborative Innovation Center of New Drug Research and Safety Evaluation, Zhengzhou University, Zhengzhou 450001, China.,Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104-6059, USA.,Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China.,College of Life Sciences, Peking University, Beijing 100871, China.,Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, QC, H3C 3J7, Canada.,Université de Lorraine, CNRS, CRM2, Nancy, France. claude.didierjean@univ-lorraine.fr.,Science for Life Laboratory, Department of Medicine Solna, Karolinska Institutet, Sweden; Department of Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden.,School of Biological Sciences, Seoul National University, Seoul, Republic of Korea.,RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan.,College of Chemistry and Molecular Engineering, Zhengzhou University, Zhengzhou 450001, China.,DISFARM, Dipartimento di Scienze Farmaceutiche, Sezione Chimica Generale e Organica, Università degli Studi, Milano, Italy.,Université de Lorraine, INRA, IAM, Nancy, France.,Department of Biochemistry and the Emory Comprehensive Glycomics Core, Emory University School of Medicine, Atlanta, GA, 30322, USA.,Max-Planck Institute for Plant Breeding Research, 50829 Cologne, Germany.,Institute of Biochemistry, University of Cologne, 50674 Koeln, Germany.,Biochemistry, Cellular, and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996, USA.,Institute for Pharmaceutical Chemistry, Structural Genomics Consortium and Buchmann Institute for Molecular Life Sciences, Johann Wolfgang Goethe-University, Frankfurt am Main, Germany.,Center for RNA Research, Institute for Basic Science, Seoul, Republic of Korea.,ManRos Therapeutics, Hôtel de Recherche, Centre de Perharidy, Roscoff, France.,Olema Pharmaceuticals, San Francisco, CA, 94107, USA. leslie@olemapharma.com.,Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, 77030, USA.,Pfizer Worldwide Research & Development , 610 Main Street, Cambridge, Massachusetts 02139, United States.,RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan. kurumizaka@iam.u-tokyo.ac.jp shunichi.sekine@riken.jp.,Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104-6059, USA. blackbe@pennmedicine.upenn.edu.,Center for Integrated Protein Science at the Department Chemie, Lehrstuhl für Biochemie , Technische Universität München , 85748 Garching , Germany.,Instituto de Química, Universidade de Brasília (UnB), Brasília, Distrito Federal, Brazil; Departamento de Áreas Acadêmicas, Instituto Federal de Educação, Ciência e Tecnologia e Goiás (IFG), Luziânia, Goiás, Brazil.,Tetramer Core, BRI at Virginia Mason, Seattle, WA, USA.,Translational Research Program, BRI at Virginia Mason, Seattle, WA, USA.,Rheumatology Unit, Department of Medicine Solna, Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden. Electronic address: Vivianne.malmstrom@ki.se.,Chemical Biology, Zentrum für Medizinische Biotechnologie, Fakultät für Biologie, Universität Duisburg-Essen, Universitätsstr. 2, 45117, Essen, Germany.,Department of Pharmacology, Baylor College of Medicine, Houston, TX, 77030, USA.,Department of Chemistry , University of Florence , Via della Lastruccia 3 , 50019 Sesto Fiorentino, Florence , Italy.,Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan.,Molecular Biophysics and Integrated Bioimaging, Berkeley Center for Structural Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.,Structural Biology Group, European Synchrotron Radiation Facility, CS 40220, F-38043, Grenoble, France. christoph.mueller_dieckmann@esrf.fr.,Departamento de Química, Universidade Federal de São Carlos (UFSCar), São Carlos, São Paulo, Brazil.,Instituto de Química, Universidade de Brasília (UnB), Brasília, Distrito Federal, Brazil; Instituto de Biociências, Universidade Federal do Estado do Rio de Janeiro (UNIRIO), Rio de Janeiro, Rio de Janeiro, Brazil.,Ben May Department for Cancer Research, University of Chicago, Chicago, IL, 60637, USA. sfanning@uchicago.edu.,Max Planck Institute for Evolutionary Anthropology, D-04103, Leipzig, Germany.,Pohang Accelerator Laboratory, Pohang University of Science and Technology, Pohang, Republic of Korea.,Laboratory of Chemical Biology and Institute of, Complex Molecular Systems, Department of Biomedical Engineering, Eindhoven University of Technology, Den Dolech 2, 5612, AZ, Eindhoven, The Netherlands.,Université de Lorraine, LERMAB, Nancy, France.,Olema Pharmaceuticals, San Francisco, CA, 94107, USA.,Magnetic Resonance Center CERM , University of Florence , Via Luigi Sacconi 6 , 50019 Sesto Fiorentino, Florence , Italy.,Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, 77030, USA. vprasad@bcm.edu.,Structural Genomics Consortium, Nuffield Department of Medicine, Oxford University, Oxford, United Kingdom.,Pohang Accelerator Laboratory, Pohang University of Science and Technology, Pohang, Republic of Korea ygkim76@postech.ac.kr.,Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China.,Structural Biology Group, European Synchrotron Radiation Facility, CS 40220, F-38043, Grenoble, France.,The Francis Crick Institute, London, NW1 1AT, United Kingdom.,Rheumatology Unit, Department of Medicine Solna, Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden; Science for Life Laboratory, Department of Medicine Solna, Karolinska Institutet, Sweden; Department of Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden.,Department of Structural Biology, Weizmann Institute of Science, Rehovot, 7610001, Israel.,Department of Hematology and Oncology , Kantonsspital St. Gallen , 9007 St. Gallen , Switzerland.,Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA.,Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA. vprasad@bcm.edu.,Department of Medical Sciences, Rheumatology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden.,Université de Lorraine, CNRS, CRM2, Nancy, France.,Department of Medicine, Baylor College of Medicine, Houston, TX, 77030, USA.,Université de Lorraine, INRA, IAM, Nancy, France. eric.gelhaye@univ-lorraine.fr.,Department of Chemistry, University of Duisburg-Essen, Universitätsstr. 7, 45117, Essen, Germany.,Department of Physiology and Biophysics, School of Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA.,Ben May Department for Cancer Research, University of Chicago, Chicago, IL, 60637, USA.,Department of Biochemistry, School of Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA. qinj@ccf.org.,Department of Systems Biology, Harvard Medical School, Boston, MA, 02115, USA.,Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, QC, H3C 3J7, Canada. john.pascal@umontreal.ca.,Laboratório de Espectrometria de Massa, Embrapa Recursos Genéticos e Biotecnologia, Brasília, Distrito Federal, Brazil.,Department of Molecular Cardiology, Lerner Research Institute, Cleveland Clinic, 9500 Euclid Avenue, Cleveland, OH, 44195, USA. qinj@ccf.org.




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-7
H, V
234Homo sapiensMutation(s): 1 
Gene Names: PSMB7 (Z)
EC: 3.4.25.1
Find proteins for Q99436 (Homo sapiens)
Go to Gene View: PSMB7
Go to UniProtKB:  Q99436
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 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
b, N
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
CL
Query on CL

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

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]-4-methyl-1-oxidanylidene-pentan-2-yl]amino]-4-methyl-1-oxidanylidene-pentan-2-yl]pyrazine-2-carboxamide
C29 H44 N6 O5 S
COXIIRGPLZWLTL-DSITVLBTSA-N
 Ligand Interaction
MG
Query on MG

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.177 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 133.910α = 90.00
b = 300.420β = 112.84
c = 144.040γ = 90.00
Software Package:
Software NamePurpose
XSCALEdata scaling
XDSdata reduction
REFMACphasing
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2018-10-04 
  • 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