4J4N

Crystal structure of FK506 binding domain of plasmodium falciparum FKBP35 in complex with D44


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.229 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Small molecule Plasmodium FKBP35 inhibitor as a potential antimalaria agent.

Harikishore, A.Niang, M.Rajan, S.Preiser, P.R.Yoon, H.S.

(2013) Sci Rep 3: 2501-2501

  • DOI: https://doi.org/10.1038/srep02501
  • Primary Citation of Related Structures:  
    4J4N, 4J4O

  • PubMed Abstract: 

    Malaria parasite strains have emerged to tolerate the therapeutic effects of the prophylactics and drugs presently available. This resistance now poses a serious challenge to researchers in the bid to overcome malaria parasitic infection. Recent studies have shown that FK520 and its analogs inhibit malaria parasites growth by binding to FK506 binding proteins (FKBPs) of the parasites. Structure based drug screening efforts based on three-dimensional structural information of FKBPs from Plasmodium falciparum led us to identify new chemical entities that bind to the parasite FKBP35 and inhibit its growth. Our experimental results verify that this novel compound (D44) modulate the PPIase activity of Plasmodium FKBP35 and demonstrate the stage-specific growth inhibition of Plasmodium falciparum strains. Here, we present the X-ray crystallographic structures of FK506 binding domains (FKBDs) of PfFKBP35 and PvFKBP35 in complex with the newly identified inhibitor providing molecular insights into its mode of action.


  • Organizational Affiliation

    1] School of Biological Science, Nanyang Technological University, 60 Nanyang Drive, Singapore 637665 [2].


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
FK506-binding protein (FKBP)-type peptidyl-propyl isomerase
A, B, C
129Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: FKBP35PFL2275C
EC: 5.2.1.8
UniProt
Find proteins for Q8I4V8 (Plasmodium falciparum (isolate 3D7))
Explore Q8I4V8 
Go to UniProtKB:  Q8I4V8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8I4V8
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
D44 PDBBind:  4J4N IC50: 132 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.229 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 69.927α = 90
b = 69.927β = 90
c = 186.877γ = 90
Software Package:
Software NamePurpose
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-09-11
    Type: Initial release
  • Version 1.1: 2023-11-08
    Changes: Data collection, Database references, Derived calculations, Refinement description