Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 65.58 kDa 
• Atom Count: 3,711 
• Modelled Residue Count: 462 
• Deposited Residue Count: 572 
• Unique protein chains: 1

 4WAG

Phosphatidylinositol 4-kinase III beta crystallized with MI103 inhibitor

• PDB DOI: 10.2210/pdb4WAG/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2014-08-29 Released: 2015-05-20 
• Deposition Author(s): Chalupska, D., Boura, E.
• Funding Organization(s): Ministry of Education, Youth and Sports of the Czech Republic

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.41 Å
• R-Value Free: 0.251 
• R-Value Work: 0.209 
• R-Value Observed: 0.212 

Literature

Highly Selective Phosphatidylinositol 4-Kinase III beta Inhibitors and Structural Insight into Their Mode of Action.

Mejdrova, I., Chalupska, D., Kogler, M., Sala, M., Plackova, P., Baumlova, A., Hrebabecky, H., Prochazkova, E., Dejmek, M., Guillon, R., Strunin, D., Weber, J., Lee, G., Birkus, G., Mertlikova-Kaiserova, H., Boura, E., Nencka, R.

(2015) J Med Chem 58: 3767-3793

• PubMed: 25897704 
• DOI: 10.1021/acs.jmedchem.5b00499
• Primary Citation of Related Structures:  
  4WAE, 4WAG


• PubMed Abstract: 
  

Phosphatidylinositol 4-kinase IIIβ is a cellular lipid kinase pivotal to pathogenesis of various RNA viruses. These viruses hijack the enzyme in order to modify the structure of intracellular membranes and use them for the construction of functional replication machinery. Selective inhibitors of this enzyme are potential broad-spectrum antiviral agents, as inhibition of this enzyme results in the arrest of replication of PI4K IIIβ-dependent viruses. Herein, we report a detailed study of novel selective inhibitors of PI4K IIIβ, which exert antiviral activity against a panel of single-stranded positive-sense RNA viruses. Our crystallographic data show that the inhibitors occupy the binding site for the adenine ring of the ATP molecule and therefore prevent the phosphorylation reaction.

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Organizational Affiliation: 

‡Gilead Sciences, Inc., 333 Lakeside Drive, Foster City, California 94404, United States.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphatidylinositol 4-kinase beta,Phosphatidylinositol 4-kinase beta	A	572	Homo sapiens	Mutation(s): 0  Gene Names: PI4KB, PIK4CB EC: 2.7.1.67
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UBF8 (Homo sapiens) Explore Q9UBF8  Go to UniProtKB:  Q9UBF8
PHAROS:  Q9UBF8

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
3K7	B [auth A]	6-chloro-3-(3,4-dimethoxyphenyl)-2-methylimidazo[1,2-b]pyridazin-8-amine C15 H15 Cl N4 O2 QKMGMIGTYUUELE-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.41 Å
• R-Value Free: 0.251 
• R-Value Work: 0.209 
• R-Value Observed: 0.212 
• Space Group: P 4₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 108.353	α = 90
b = 108.353	β = 90
c = 55.138	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2015-05-20 
Deposition Author(s): Chalupska, D., Boura, E.

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Funding Organization	Location	Grant Number
Ministry of Education, Youth and Sports of the Czech Republic	Czech Republic	LO1302

Revision History  

• Version 1.0: 2015-05-20
  Type: Initial release
  
• Version 1.1: 2015-05-27
  Changes: Database references
• Version 1.2: 2017-09-06
  Changes: Author supporting evidence