1W6H

Novel plasmepsin II-inhibitor complex

• PDB DOI: https://doi.org/10.2210/pdb1W6H/pdb

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


• Deposited: 2004-08-18 Released: 2006-07-05 
• Deposition Author(s): Lindberg, J., Johansson, P.-O., Rosenquist, A., Kvarnstroem, I., Vrang, L., Samuelsson, B., Unge, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.24 Å
• R-Value Free: 
  0.246 (Depositor), 0.239 (DCC) 
• R-Value Work: 
  0.197 (Depositor), 0.204 (DCC) 
• R-Value Observed: 
  0.200 (Depositor) 

Literature

Structural Study of a Novel Inhibitor with Bulky P1 Side Chain in Complex with Plasmepsin II -Implications for Drug Design

Lindberg, J., Johansson, P.-O., Rosenquist, A., Kvarnstroem, I., Vrang, L., Samuelsson, B., Unge, T.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content

• Total Structure Weight: 75.66 kDa 
• Atom Count: 5,470 
• Modelled Residue Count: 650 
• Deposited Residue Count: 662 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PLASMEPSIN 2	A, B	331	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
TIT	C [auth A], D [auth B]	N-((3S,4S)-5-[(4-BROMOBENZYL)OXY]-3-HYDROXY-4-{[N-(PYRIDIN-2-YLCARBONYL)-L-VALYL]AMINO}PENTANOYL)-L-ALANYL-L-LEUCINAMIDE C32 H45 Br N6 O7 QXHNYZQKWOKULQ-QPGFMSSHSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
TIT	BindingDB:  1W6H	Ki: min: 0.5, max: 2.2 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.24 Å
• R-Value Free:  0.246 (Depositor), 0.239 (DCC) 
• R-Value Work:  0.197 (Depositor), 0.204 (DCC) 
• R-Value Observed: 0.200 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.21	α = 90
b = 77.614	β = 90
c = 84.237	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-07-05 
Deposition Author(s): Lindberg, J., Johansson, P.-O., Rosenquist, A., Kvarnstroem, I., Vrang, L., Samuelsson, B., Unge, T.

Revision History  

• Version 1.0: 2006-07-05
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2018-01-17
  Changes: Data collection
• Version 1.4: 2024-10-23
  Changes: Data collection, Database references, Other, Structure summary