3BPF

Crystal Structure of Falcipain-2 with Its inhibitor, E64


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.325 
  • R-Value Work: 0.275 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structures of falcipain-2 and falcipain-3 bound to small molecule inhibitors: implications for substrate specificity.

Kerr, I.D.Lee, J.H.Pandey, K.C.Harrison, A.Sajid, M.Rosenthal, P.J.Brinen, L.S.

(2009) J.Med.Chem. 52: 852-857

  • DOI: 10.1021/jm8013663
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Falcipain-2 and falcipain-3 are critical hemoglobinases of Plasmodium falciparum, the most virulent human malaria parasite. We have determined the 2.9 A crystal structure of falcipain-2 in complex with the epoxysuccinate E64 and the 2.5 A crystal str ...

    Falcipain-2 and falcipain-3 are critical hemoglobinases of Plasmodium falciparum, the most virulent human malaria parasite. We have determined the 2.9 A crystal structure of falcipain-2 in complex with the epoxysuccinate E64 and the 2.5 A crystal structure of falcipain-3 in complex with the aldehyde leupeptin. These complexes represent the first crystal structures of plasmodial cysteine proteases with small molecule inhibitors and the first reported crystal structure of falcipain-3. Our structural analyses indicate that the relative shape and flexibility of the S2 pocket are affected by a number of discrete amino acid substitutions. The cumulative effect of subtle differences, including those at "gatekeeper" positions, may explain the observed kinetic differences between these two closely related enzymes.


    Organizational Affiliation

    Department of Cellular and Molecular Pharmacology and Department of Pathology, University of California, San Francisco, California 94158, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cysteine protease falcipain-2
A, B, C, D
241Plasmodium falciparumMutation(s): 0 
EC: 3.4.22.-
Find proteins for Q9N6S8 (Plasmodium falciparum)
Go to UniProtKB:  Q9N6S8
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
C
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
E64
Query on E64

Download SDF File 
Download CCD File 
A, B, C, D
N-[N-[1-HYDROXYCARBOXYETHYL-CARBONYL]LEUCYLAMINO-BUTYL]-GUANIDINE
C15 H30 N5 O5
QPQNJAXBPHVASB-QWRGUYRKSA-O
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.325 
  • R-Value Work: 0.275 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 143.778α = 90.00
b = 167.810β = 90.00
c = 177.758γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
PHASERphasing
MOSFLMdata reduction
XSCALEdata scaling
ADSCdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-12-30
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Refinement description, Version format compliance