8Q6F

HUMAN PI4KIIIB IN COMPLEX WITH COVALENTLY BOUND INHIBITOR (COMPOUND 4)

PDB DOI: https://doi.org/10.2210/pdb8Q6F/pdb

Classification: TRANSFERASE
Organism(s): Homo sapiens
Expression System: Baculovirus expression vector pFastBac1-HM
Mutation(s): Yes

Deposited: 2023-08-11 Released: 2023-12-13
Deposition Author(s): Somers, D.O.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.51 Å
R-Value Free: 0.224
R-Value Work: 0.179
R-Value Observed: 0.181

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 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

PubMed: 38033723 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1039/d3cb00142c
Primary Citation of 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: 49.41 kDa
Atom Count: 3,631
Modelled Residue Count: 389
Deposited Residue Count: 424
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphatidylinositol 4-kinase beta	A	424	Homo sapiens	Mutation(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 Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9UBF8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
KHR (Subject of Investigation/LOI) Query on KHR Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	3-(3-fluorosulfonyloxy-4-methoxy-phenyl)-2,5-dimethyl-7-(pyridin-4-ylmethylamino)pyrazolo[1,5-a]pyrimidine C₂₁ H₂₀ F N₅ O₄ S GIEBWLKAVFAUAV-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain K [auth A] MOL2 format, chain K [auth A]	K [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain K [auth A] Interactions & Density Focus chain K [auth A]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A]	D [auth A] E [auth A] F [auth A] G [auth A] H [auth A] D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A]	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]