7LXV

Structure of human 20S proteasome with bound MPI-5


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Design of proteasome inhibitors with oral efficacy in vivo against Plasmodium falciparum and selectivity over the human proteasome.

Xie, S.C.Metcalfe, R.D.Mizutani, H.Puhalovich, T.Hanssen, E.Morton, C.J.Du, Y.Dogovski, C.Huang, S.C.Ciavarri, J.Hales, P.Griffin, R.J.Cohen, L.H.Chuang, B.C.Wittlin, S.Deni, I.Yeo, T.Ward, K.E.Barry, D.C.Liu, B.Gillett, D.L.Crespo-Fernandez, B.F.Ottilie, S.Mittal, N.Churchyard, A.Ferguson, D.Aguiar, A.C.C.Guido, R.V.C.Baum, J.Hanson, K.K.Winzeler, E.A.Gamo, F.J.Fidock, D.A.Baud, D.Parker, M.W.Brand, S.Dick, L.R.Griffin, M.D.W.Gould, A.E.Tilley, L.

(2021) Proc Natl Acad Sci U S A 118

  • DOI: 10.1073/pnas.2107213118
  • Primary Citation of Related Structures:  
    7LXT, 7LXU, 7LXV

  • PubMed Abstract: 
  • The Plasmodium falciparum proteasome is a potential antimalarial drug target. We have identified a series of amino-amide boronates that are potent and specific inhibitors of the P. falciparum 20S proteasome ( Pf 20S) β5 active site and that exhibit fast-acting antimalarial activity ...

    The Plasmodium falciparum proteasome is a potential antimalarial drug target. We have identified a series of amino-amide boronates that are potent and specific inhibitors of the P. falciparum 20S proteasome ( Pf 20S) β5 active site and that exhibit fast-acting antimalarial activity. They selectively inhibit the growth of P. falciparum compared with a human cell line and exhibit high potency against field isolates of P. falciparum and Plasmodium vivax They have a low propensity for development of resistance and possess liver stage and transmission-blocking activity. Exemplar compounds, MPI-5 and MPI-13, show potent activity against P. falciparum infections in a SCID mouse model with an oral dosing regimen that is well tolerated. We show that MPI-5 binds more strongly to Pf 20S than to human constitutive 20S ( Hs 20Sc). Comparison of the cryo-electron microscopy (EM) structures of Pf 20S and Hs 20Sc in complex with MPI-5 and Pf 20S in complex with the clinically used anti-cancer agent, bortezomib, reveal differences in binding modes that help to explain the selectivity. Together, this work provides insights into the 20S proteasome in P. falciparum , underpinning the design of potent and selective antimalarial proteasome inhibitors.


    Organizational Affiliation

    Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC 3010, Australia; ltilley@unimelb.edu.au sandy.gould@takeda.com.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-2A, O234Homo sapiensMutation(s): 0 
Gene Names: PSMA2HC3PSC3
EC: 3.4.25.1
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UniProt GroupP25787
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-4B, P261Homo sapiensMutation(s): 0 
Gene Names: PSMA4HC9PSC9
EC: 3.4.25.1
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-7C, Q248Homo sapiensMutation(s): 0 
Gene Names: PSMA7HSPC
EC: 3.4.25.1
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-5D, R241Homo sapiensMutation(s): 0 
Gene Names: PSMA5
EC: 3.4.25.1
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-1E, S263Homo sapiensMutation(s): 0 
Gene Names: PSMA1HC2NUPROS30PSC2
EC: 3.4.25.1
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-3F, T255Homo sapiensMutation(s): 0 
Gene Names: PSMA3HC8PSC8
EC: 3.4.25.1
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-6G, U246Homo sapiensMutation(s): 0 
Gene Names: PSMA6PROS27
EC: 3.4.25.1
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit beta type-7H, V234Homo sapiensMutation(s): 0 
Gene Names: PSMB7Z
EC: 3.4.25.1
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit beta type-3I, W205Homo sapiensMutation(s): 0 
Gene Names: PSMB3
EC: 3.4.25.1
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit beta type-2J, X201Homo sapiensMutation(s): 0 
Gene Names: PSMB2
EC: 3.4.25.1
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit beta type-5K, Y204Homo sapiensMutation(s): 0 
Gene Names: PSMB5LMPXMB1X
EC: 3.4.25.1
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit beta type-1L, Z213Homo sapiensMutation(s): 0 
Gene Names: PSMB1PSC5
EC: 3.4.25.1
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit beta type-4M,
AA [auth a]
219Homo sapiensMutation(s): 0 
Gene Names: PSMB4PROS26
EC: 3.4.25.1
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit beta type-6N,
BA [auth b]
205Homo sapiensMutation(s): 0 
Gene Names: PSMB6LMPYY
EC: 3.4.25.1
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Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
YHD (Subject of Investigation/LOI)
Query on YHD

Download Ideal Coordinates CCD File 
CA [auth K],
DA [auth Y]
N-[(1R)-2-([1,1'-biphenyl]-4-yl)-1-boronoethyl]-1-methyl-L-prolinamide
C20 H25 B N2 O3
VGGVSZZQWVUBBQ-OALUTQOASA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Global Health Innovative Technology FundUnited StatesRFP-HTLP-H2019-101
Australian Research Council (ARC)AustraliaFL150100106

Revision History  (Full details and data files)

  • Version 1.0: 2021-09-22
    Type: Initial release
  • Version 1.1: 2022-04-13
    Changes: Database references