Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 41.76 kDa 
• Atom Count: 2935 
• Modelled Residue Count: 340 
• Deposited Residue Count: 348 
• Unique protein chains: 1

2PMN

Crystal structure of PfPK7 in complex with an ATP-site inhibitor

• PDB DOI: 10.2210/pdb2PMN/pdb

• Classification: TRANSFERASE
• Organism(s): Plasmodium falciparum
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2007-04-23 Released: 2008-01-22 
• Deposition Author(s): Merckx, A., Echalier, A., Noble, M., Endicott, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.296 
• R-Value Work: 0.219 
• R-Value Observed: 0.223 

Literature

Structures of P. falciparum protein kinase 7 identify an activation motif and leads for inhibitor design.

Merckx, A., Echalier, A., Langford, K., Sicard, A., Langsley, G., Joore, J., Doerig, C., Noble, M., Endicott, J.

(2008) Structure 16: 228-238

• PubMed: 18275814 
• DOI: 10.1016/j.str.2007.11.014
• Primary Citation of Related Structures:  
  2PMN, 2PMO


• PubMed Abstract: 
  

Malaria is a major threat to world health. The identification of parasite targets for drug development is a priority and parasitic protein kinases suggest themselves as suitable targets as many display profound structural and functional divergences from their host counterparts. In this paper, we describe the structure of the orphan protein kinase, Plasmodium falciparum protein kinase 7 (PFPK7). Several Plasmodium protein kinases contain extensive insertions, and the structure of PFPK7 reveals how these may be accommodated as excursions from the canonical eukaryotic protein kinase fold. The constitutively active conformation of PFPK7 is stabilized by a structural motif in which the role of the conserved phosphorylated residue that assists in structuring the activation loop of many protein kinases is played by an arginine residue. We identify two series of PFPK7 ATP-competitive inhibitors and suggest further developments for the design of selective and potent PFPK7 lead compounds as potential antimalarials.

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Organizational Affiliation: 

The Laboratory of Molecular Biophysics, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ser/Thr protein kinase, putative	A [auth X]	348	Plasmodium falciparum	Mutation(s): 0  Gene Names: PFB0605w EC: 2.7.11.1
UniProt
Find proteins for Q7YTF7 (Plasmodium falciparum (isolate 3D7)) Explore Q7YTF7  Go to UniProtKB:  Q7YTF7

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
K51	B [auth X]	4-(6-{[(1S)-1-(HYDROXYMETHYL)-2-METHYLPROPYL]AMINO}IMIDAZO[1,2-B]PYRIDAZIN-3-YL)BENZONITRILE C18 H19 N5 O CQZVJEKKNHOFNB-OAHLLOKOSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
K51	PDBBind:  2PMN	IC50: 6300 (nM) from 1 assay(s)
	BindingDB:  2PMN	IC50: 280 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.296 
• R-Value Work: 0.219 
• R-Value Observed: 0.223 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.406	α = 90
b = 82.084	β = 90
c = 138.962	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DNA	data collection
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2007-04-23 
• Released Date: 2008-01-22 
Deposition Author(s): Merckx, A., Echalier, A., Noble, M., Endicott, J.

Revision History  

• Version 1.0: 2008-01-22
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance