5EUQ

Crystal structure of an engineered construct of phosphatidylinositol 4 kinase III beta with a potent and selective inhibitor in complex with GDP loaded Rab11


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.233 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Design and Structural Characterization of Potent and Selective Inhibitors of Phosphatidylinositol 4 Kinase III beta.

Rutaganira, F.U.Fowler, M.L.McPhail, J.A.Gelman, M.A.Nguyen, K.Xiong, A.Dornan, G.L.Tavshanjian, B.Glenn, J.S.Shokat, K.M.Burke, J.E.

(2016) J.Med.Chem. 59: 1830-1839

  • DOI: 10.1021/acs.jmedchem.5b01311

  • PubMed Abstract: 
  • Type III phosphatidylinositol 4-kinase (PI4KIIIβ) is an essential enzyme in mediating membrane trafficking and is implicated in a variety of pathogenic processes. It is a key host factor mediating replication of RNA viruses. The design of potent and ...

    Type III phosphatidylinositol 4-kinase (PI4KIIIβ) is an essential enzyme in mediating membrane trafficking and is implicated in a variety of pathogenic processes. It is a key host factor mediating replication of RNA viruses. The design of potent and specific inhibitors of this enzyme will be essential to define its cellular roles and may lead to novel antiviral therapeutics. We previously reported the PI4K inhibitor PIK93, and this compound has defined key functions of PI4KIIIβ. However, this compound showed high cross reactivity with class I and III PI3Ks. Using structure-based drug design, we have designed novel potent and selective (>1000-fold over class I and class III PI3Ks) PI4KIIIβ inhibitors. These compounds showed antiviral activity against hepatitis C virus. The co-crystal structure of PI4KIIIβ bound to one of the most potent compounds reveals the molecular basis of specificity. This work will be vital in the design of novel PI4KIIIβ inhibitors, which may play significant roles as antiviral therapeutics.


    Organizational Affiliation

    Howard Hughes Medical Institute and Department of Cellular and Molecular Pharmacology, University of California, San Francisco (UCSF) , San Francisco, California 94143, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ras-related protein Rab-11A
B
219Homo sapiensMutation(s): 0 
Gene Names: RAB11A (RAB11)
Find proteins for P62491 (Homo sapiens)
Go to Gene View: RAB11A
Go to UniProtKB:  P62491
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Phosphatidylinositol 4-kinase beta
E
529Homo sapiensMutation(s): 1 
Gene Names: PI4KB (PIK4CB)
EC: 2.7.1.67
Find proteins for Q9UBF8 (Homo sapiens)
Go to Gene View: PI4KB
Go to UniProtKB:  Q9UBF8
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GDP
Query on GDP

Download SDF File 
Download CCD File 
B
GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
 Ligand Interaction
SO4
Query on SO4

Download SDF File 
Download CCD File 
E
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
5S8
Query on 5S8

Download SDF File 
Download CCD File 
E
~{N}-[5-[3-[[(4-hydroxyphenyl)amino]-bis(oxidanyl)-$l^{4}-sulfanyl]-4-methoxy-phenyl]-4-methyl-1,3-thiazol-2-yl]cyclopentanecarboxamide
C23 H27 N3 O5 S2
CBCKCOMPEQUVAG-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.233 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 48.900α = 90.00
b = 103.490β = 90.00
c = 188.940γ = 90.00
Software Package:
Software NamePurpose
Aimlessdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
MOSFLMdata reduction
iMOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Canadian Institutes of Health ResearchCanadaFRN 142393

Revision History 

  • Version 1.0: 2016-02-24
    Type: Initial release
  • Version 1.1: 2016-03-23
    Type: Database references
  • Version 1.2: 2017-09-06
    Type: Advisory, Author supporting evidence, Database references, Derived calculations
  • Version 1.3: 2017-11-22
    Type: Refinement description