9O3F | pdb_00009o3f

Plasmodium falciparum 20S proteasome bound to inhibitor 296

  • Classification: CYTOSOLIC PROTEIN
  • Organism(s): Plasmodium falciparum 3D7
  • Mutation(s): No 

  • Deposited: 2025-04-07 Released: 2025-11-12 
  • Deposition Author(s): Han, Y., Deng, X., Ray, S., Phillips, M.
  • Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), Cancer Prevention and Research Institute of Texas (CPRIT)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.28 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Optimization of Species-Selective Reversible Proteasome Inhibitors for the Treatment of Malaria.

Gahalawat, S.Ray, S.Zhang, X.Deng, X.Han, Y.Chen, Z.Lawong, A.Shackleford, D.M.Katneni, K.Chen, G.Li, P.Ng, A.Zhong, L.Hu, M.McInerney, M.Wang, W.Saunders, J.Collins, D.Jayaseelan, J.Noack, C.L.C Maity, B.De, N.Laleu, B.Campbell, S.F.Phillips, M.A.Charman, S.A.Ready, J.M.

(2025) J Med Chem 68: 23485-23520

  • DOI: https://doi.org/10.1021/acs.jmedchem.5c02394
  • Primary Citation of Related Structures:  
    9O3E, 9O3F

  • PubMed Abstract: 

    Malaria remains a critical global health challenge, with increasing resistance to frontline therapies necessitating novel drug targets. The proteasome has emerged as a promising target for antimalarial drug discovery. This study describes efforts to optimize a series of species-selective reversible inhibitors targeting the Plasmodium falciparum 20S proteasome. Starting from the carboxypiperidine scaffold identified through a high-throughput viability screen, we conducted iterative structure-activity relationship studies, leading to the development of highly potent and selective inhibitors with good oral bioavailability. Lead compounds demonstrated nanomolar potency against P. falciparum blood-stage parasites and selective inhibition of the parasite proteasome over the human counterpart. Cryo-EM structural studies confirmed binding at the β5 subunit, while in vivo pharmacokinetic studies identified promising candidates for further development. These findings support proteasome inhibition as a viable strategy for novel antimalarial drug development.


  • Organizational Affiliation
    • Department of Biochemistry, UT Southwestern Medical Center, Dallas, Texas 75390, United States.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome endopeptidase complexA,
N [auth O]
260Plasmodium falciparum 3D7Mutation(s): 0 
EC: 3.4.25.1
UniProt
Find proteins for Q8IAR3 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome endopeptidase complexB,
O [auth P]
235Plasmodium falciparum 3D7Mutation(s): 0 
EC: 3.4.25.1
UniProt
Find proteins for C6KST3 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha typeC,
P [auth Q]
242Plasmodium falciparum 3D7Mutation(s): 0 
UniProt
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha typeD,
Q [auth R]
241Plasmodium falciparum 3D7Mutation(s): 0 
EC: 3.4.25.1
UniProt
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha typeE,
R [auth S]
256Plasmodium falciparum 3D7Mutation(s): 0 
EC: 3.4.25.1
UniProt
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome endopeptidase complexF,
S [auth T]
254Plasmodium falciparum 3D7Mutation(s): 0 
EC: 3.4.25.1
UniProt
Find proteins for Q8IK90 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-3, putativeG,
T [auth U]
252Plasmodium falciparum 3D7Mutation(s): 0 
EC: 3.4.25.1
UniProt
Find proteins for O77396 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-6, putativeH,
U [auth V]
252Plasmodium falciparum 3D7Mutation(s): 0 
EC: 3.4.25.1
UniProt
Find proteins for Q8I0U7 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit betaI,
V [auth W]
229Plasmodium falciparum 3D7Mutation(s): 0 
EC: 3.4.25.1
UniProt
Find proteins for Q8I6T3 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit betaJ,
W [auth X]
218Plasmodium falciparum 3D7Mutation(s): 0 
EC: 3.4.25.1
UniProt
Find proteins for Q8I261 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit betaK,
X [auth Y]
195Plasmodium falciparum 3D7Mutation(s): 0 
EC: 3.4.25.1
UniProt
Find proteins for Q8IKC9 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta typeL,
Y [auth Z]
211Plasmodium falciparum 3D7Mutation(s): 0 
EC: 3.4.25.1
UniProt
Find proteins for Q8IJT1 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit betaM [auth N],
Z [auth b]
284Plasmodium falciparum 3D7Mutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit betaAA [auth M],
BA [auth a]
240Plasmodium falciparum 3D7Mutation(s): 0 
EC: 3.4.25.1
UniProt
Find proteins for A0A5K1K7U1 (Plasmodium falciparum (isolate 3D7))
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Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1B73 (Subject of Investigation/LOI)
Query on A1B73

Download Ideal Coordinates CCD File 
CA [auth M],
DA [auth a]
(3S)-1-({[(3S)-piperidin-3-yl]oxy}acetyl)-N-({4-[4-(trifluoromethyl)phenyl]-1,3-thiazol-2-yl}methyl)piperidine-3-carboxamide
C24 H29 F3 N4 O3 S
OVPLOMYZPJLWSF-HKUYNNGSSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.28 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX
RECONSTRUCTIONRELION4.0.1

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR01AI103947
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR01AI155784
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM007062
Cancer Prevention and Research Institute of Texas (CPRIT)United StatesRP220582

Revision History  (Full details and data files)

  • Version 1.0: 2025-11-12
    Type: Initial release
  • Version 1.1: 2025-11-26
    Changes: Data collection, Database references