4Z22 | pdb_00004z22

structure of plasmepsin II from Plasmodium Falciparum complexed with inhibitor DR718A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.62 Å
  • R-Value Free: 
    0.253 (Depositor), 0.246 (DCC) 
  • R-Value Work: 
    0.206 (Depositor) 
  • R-Value Observed: 
    0.208 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history

Literature

Fragment-Based Discovery of 2-Aminoquinazolin-4(3H)-ones As Novel Class Nonpeptidomimetic Inhibitors of the Plasmepsins I, II, and IV.

Rasina, D.Otikovs, M.Leitans, J.Recacha, R.Borysov, O.V.Kanepe-Lapsa, I.Domraceva, I.Pantelejevs, T.Tars, K.Blackman, M.J.Jaudzems, K.Jirgensons, A.

(2016) J Med Chem 59: 374-387

  • DOI: https://doi.org/10.1021/acs.jmedchem.5b01558
  • Primary Citation Related Structures: 
    4Z22

  • PubMed Abstract: 

    2-Aminoquinazolin-4(3H)-ones were identified as a novel class of malaria digestive vacuole plasmepsin inhibitors by using NMR-based fragment screening against Plm II. Initial fragment hit optimization led to a submicromolar inhibitor, which was cocrystallized with Plm II to produce an X-ray structure of the complex. The structure showed that 2-aminoquinazolin-4(3H)-ones bind to the open flap conformation of the enzyme and provided clues to target the flap pocket. Further improvement in potency was achieved via introduction of hydrophobic substituents occupying the flap pocket. Most of the 2-aminoquinazolin-4(3H)-one based inhibitors show a similar activity against digestive Plms I, II, and IV and >10-fold selectivity versus CatD, although varying the flap pocket substituent led to one Plm IV selective inhibitor. In cell-based assays, the compounds show growth inhibition of Plasmodium falciparum 3D7 with IC50 ∼ 1 μM. Together, these results suggest 2-aminoquinazolin-4(3H)-ones as perspective leads for future development of an antimalarial agent.


  • Organizational Affiliation
    • Latvian Institute of Organic Synthesis , Aizkraukles 21, Riga LV-1006, Latvia.

Macromolecule Content 

  • Total Structure Weight: 74.61 kDa 
  • Atom Count: 5,382 
  • Modeled Residue Count: 658 
  • Deposited Residue Count: 658 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Plasmepsin-2
A, B
329Plasmodium falciparumMutation(s): 1 
Gene Names: PFAG_05140
EC: 3.4.23.39
UniProt
Find proteins for P46925 (Plasmodium falciparum (isolate HB3))
Explore P46925 
Go to UniProtKB:  P46925
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP46925
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
4KG

Query on 4KG



Download:Ideal Coordinates CCD File
C [auth A],
D [auth B]
2-amino-7-phenyl-3-{[(2R,5S)-5-phenyltetrahydrofuran-2-yl]methyl}quinazolin-4(3H)-one
C25 H23 N3 O2
ZFQQCJCOZGMLDR-OFNKIYASSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.62 Å
  • R-Value Free:  0.253 (Depositor), 0.246 (DCC) 
  • R-Value Work:  0.206 (Depositor) 
  • R-Value Observed: 0.208 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 52.45α = 90
b = 174.69β = 90
c = 138.97γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling
PDB_EXTRACTdata extraction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-01-13
    Type: Initial release
  • Version 1.1: 2016-01-27
    Changes: Database references
  • Version 1.2: 2018-01-17
    Changes: Data collection
  • Version 1.3: 2024-01-10
    Changes: Data collection, Database references, Refinement description
  • Version 1.4: 2024-10-09
    Changes: Structure summary