4CKU

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.158 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

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

  • DOI: 10.1021/ml4004952
  • Also Cited By: 4Y6M

  • 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 ...

    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.


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PLASMEPSIN-2
A, B, C, D, E, F
329Plasmodium falciparumMutation(s): 0 
EC: 3.4.23.39
Find proteins for P46925 (Plasmodium falciparum)
Go to UniProtKB:  P46925
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
P2F
Query on P2F

Download SDF File 
Download CCD File 
A, B, C, D, E, 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
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
P2FIC50: 150 nM (99) BINDINGDB
P2FIC50: 150 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.158 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 201.950α = 90.00
b = 115.250β = 110.75
c = 93.170γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-06-18
    Type: Initial release
  • Version 1.1: 2018-01-17
    Type: Data collection
  • Version 1.2: 2019-01-30
    Type: Data collection, Experimental preparation