1W6H

Novel plasmepsin II-inhibitor complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.24 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.200 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


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.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PLASMEPSIN 2A, B331Plasmodium falciparumMutation(s): 0 
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
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TIT
Query on TIT

Download Ideal Coordinates CCD File 
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
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
TIT PDBBind:  1W6H Ki: 0.5 (nM) from 1 assay(s)
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 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.200 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 44.21α = 90
b = 77.614β = 90
c = 84.237γ = 90
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

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Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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