4CKU | pdb_00004cku

Three dimensional structure of plasmepsin II in complex with hydroxyethylamine-based inhibitor

• PDB DOI: https://doi.org/10.2210/pdb4CKU/pdb

• Classification: HYDROLASE
• Organism(s): Plasmodium falciparum
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2014-01-08 Released: 2014-06-18 
• Deposition Author(s): Tars, K., Leitans, J., Jaudzems, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 
  0.209 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.158 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.160 (Depositor) 

Starting Model: experimental

Literature

Plasmepsin Inhibitory Activity and Structure-Guided Optimization of a Potent Hydroxyethylamine-Based Antimalarial Hit.

Jaudzems, K., Tars, K., Maurops, G., Ivdra, N., Otikovs, M., Leitans, J., Kanepe-Lapsa, I., Domraceva, I., Mutule, I., Trapencieris, P., Blackman, M.J., Jirgensons, A.

(2014) ACS Med Chem Lett 5: 373

• PubMed: 24900843 
• DOI: https://doi.org/10.1021/ml4004952
• Primary Citation of Related Structures:  
  4CKU


• PubMed Abstract: 
  

  Antimalarial hit 1 SR (TCMDC-134674) identified in a GlaxoSmithKline cell based screening campaign was evaluated for inhibitory activity against the digestive vacuole plasmepsins (Plm I, II, and IV). It was found to be a potent Plm IV inhibitor with no selectivity over Cathepsin D. A cocrystal structure of 1 SR bound to Plm II was solved, providing structural insight for the design of more potent and selective analogues. Structure-guided optimization led to the identification of structurally simplified analogues 17 and 18 as low nanomolar inhibitors of both, plasmepsin Plm IV activity and P. falciparum growth in erythrocytes.

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Organizational Affiliation: 
• Latvian Institute of Organic Synthesis , Aizkraukles 21, Riga LV-1006, Latvia.
Biomedical Research and Study Centre , Ratsupites 1, Riga LV-1067, Latvia.
Division of Parasitology, MRC National Institute for Medical Research , The Ridgeway, Mill, Hill, London NW7 1AA, U.K.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 225.62 kDa 
• Atom Count: 16,812 
• Modeled Residue Count: 1,946 
• Deposited Residue Count: 1,974 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PLASMEPSIN-2	A, B, C, D, E, F	329	Plasmodium falciparum	Mutation(s): 0  EC: 3.4.23.39
UniProt
Find proteins for P46925 (Plasmodium falciparum (isolate HB3)) Explore P46925  Go to UniProtKB:  P46925

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
P2F	G [auth A], H [auth B], I [auth C], J [auth D], K [auth E], L [auth F]	5-[1,1-bis(oxidanylidene)-1,2-thiazinan-2-yl]-N3-[(2S,3R)-4-[2-(3-methoxyphenyl)propan-2-ylamino]-3-oxidanyl-1-phenyl-butan-2-yl]-N1,N1-dipropyl-benzene-1,3-dicarboxamide C38 H52 N4 O6 S KCQAMDDVQXZDMS-OIDHKYIRSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
P2F	BindingDB:  4CKU	IC50: 150 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free:  0.209 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.158 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.160 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 201.95	α = 90
b = 115.25	β = 110.75
c = 93.17	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-06-18 
Deposition Author(s): Tars, K., Leitans, J., Jaudzems, K.

Revision History  

• Version 1.0: 2014-06-18
  Type: Initial release
  
• Version 1.1: 2018-01-17
  Changes: Data collection
• Version 1.2: 2019-01-30
  Changes: Data collection, Experimental preparation
• Version 1.3: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description
• Version 1.4: 2024-10-23
  Changes: Structure summary