8Q6H | pdb_00008q6h

HUMAN PI4KIIIB IN COMPLEX WITH COVALENTLY BOUND INHIBITOR (COMPOUND 11)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.94 Å
  • R-Value Free: 
    0.237 (Depositor), 0.244 (DCC) 
  • R-Value Work: 
    0.170 (Depositor), 0.179 (DCC) 
  • R-Value Observed: 
    0.173 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 8Q6H

Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history. 

Literature

Covalent targeting of non-cysteine residues in PI4KIII beta.

Cosgrove, B., Grant, E.K., Bertrand, S., Down, K.D., Somers, D.O., P Evans, J., Tomkinson, N.C.O., Barker, M.D.

(2023) RSC Chem Biol 4: 1111-1122

  • DOI: https://doi.org/10.1039/d3cb00142c
  • Primary Citation Related Structures: 
    8Q6F, 8Q6G, 8Q6H

  • PubMed Abstract: 

    The synthesis and characterisation of fluorosulfate covalent inhibitors of the lipid kinase PI4KIIIβ is described. The conserved lysine residue located within the ATP binding site was targeted, and optimised compounds based upon reversible inhibitors with good activity and physicochemical profile showed strong reversible interactions and slow onset times for the covalent inhibition, resulting in an excellent selectivity profile for the lipid kinase target. X-Ray crystallography demonstrated a distal tyrosine residue could also be targeted using a fluorosulfate strategy. Combination of this knowledge showed that a dual covalent inhibitor could be developed which reveals potential in addressing the challenges associated with drug resistant mutations.

    • Organizational Affiliation: 
    • Medicinal Chemistry, GlaxoSmithKline Medicines Research Centre Stevenage SG1 2NY UK.

Macromolecule Content 

  • Total Structure Weight: 49.04 kDa 
  • Atom Count: 3,420 
  • Modeled Residue Count: 385 
  • Deposited Residue Count: 424 
  • Unique protein chains: 1

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Phosphatidylinositol 4-kinase beta424Homo sapiensMutation(s): 2 
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
GTEx:  ENSG00000143393 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UBF8
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
KI7
(Subject of Investigation/LOI)

Query on KI7


Download:Ideal Coordinates CCD File
C [auth A]3-(3-fluorosulfonyloxy-4-methoxy-phenyl)-7-[(4-fluorosulfonyloxyphenyl)methylamino]-2,5-dimethyl-pyrazolo[1,5-a]pyrimidine
C22 H20 F2 N4 O7 S2
QRZXRBNRQIPFIW-UHFFFAOYSA-N
EDO

Query on EDO


Download:Ideal Coordinates CCD File
D [auth A]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
MG

Query on MG


Download:Ideal Coordinates CCD File
B [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.94 Å
  • R-Value Free:  0.237 (Depositor), 0.244 (DCC) 
  • R-Value Work:  0.170 (Depositor), 0.179 (DCC) 
  • R-Value Observed: 0.173 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.839α = 90
b = 67.845β = 90
c = 107.033γ = 90
Software Package:
Software NamePurpose
autoPROCdata processing
XDSdata reduction
Aimlessdata scaling
STARANISOdata scaling
REFMACphasing
REFMACrefinement

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

& Funding Information

Deposition Data

  • Released Date: 2023-12-13 
    • Deposition Author(s): Somers, D.O.
Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2023-12-13
    Type: Initial release
  • Version 1.1: 2024-11-13
    Changes: Structure summary