Phosphatidylinositol 4-kinase III beta crystallized with MI103 inhibitor

Experimental Data Snapshot

  • Resolution: 3.41 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.212 

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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

  • DOI: https://doi.org/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.

  • Organizational Affiliation

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

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Phosphatidylinositol 4-kinase beta,Phosphatidylinositol 4-kinase beta572Homo sapiensMutation(s): 0 
Gene Names: PI4KBPIK4CB
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UBF8 (Homo sapiens)
Explore Q9UBF8 
Go to UniProtKB:  Q9UBF8
GTEx:  ENSG00000143393 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UBF8
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 3K7

Download Ideal Coordinates CCD File 
B [auth A]6-chloro-3-(3,4-dimethoxyphenyl)-2-methylimidazo[1,2-b]pyridazin-8-amine
C15 H15 Cl N4 O2
Experimental Data & Validation

Experimental Data

  • 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 = 108.353α = 90
b = 108.353β = 90
c = 55.138γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Ministry of Education, Youth and Sports of the Czech RepublicCzech RepublicLO1302

Revision History  (Full details and data files)

  • 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
  • Version 1.3: 2024-05-08
    Changes: Data collection, Database references