6Q74 | pdb_00006q74

PI3K delta in complex with 1benzylN[5(3,6dihydro2Hpyran4yl)2methoxypyridin3yl]2methyl1Himidazole4sulfonamide

• PDB DOI: https://doi.org/10.2210/pdb6Q74/pdb

• Classification: TRANSFERASE
• Organism(s): Mus musculus
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2018-12-12 Released: 2018-12-26 
• Deposition Author(s): Convery, M.A., Rowland, P., Down, K., Barton, N.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.48 Å
• R-Value Free: 
  0.249 (Depositor), 0.255 (DCC) 
• R-Value Work: 
  0.174 (Depositor), 0.181 (DCC) 
• R-Value Observed: 
  0.178 (Depositor) 

Literature

Discovery of Potent, Efficient, and Selective Inhibitors of Phosphoinositide 3-Kinase delta through a Deconstruction and Regrowth Approach.

Barton, N., Convery, M., Cooper, A.W.J., Down, K., Hamblin, J.N., Inglis, G., Peace, S., Rowedder, J., Rowland, P., Taylor, J.A., Wellaway, N.

(2018) J Med Chem 61: 11061-11073

• PubMed: 30532965 
• DOI: https://doi.org/10.1021/acs.jmedchem.8b01556
• Primary Citation Related Structures: 
  6Q6Y, 6Q73, 6Q74


• PubMed Abstract: 
  

  A deconstruction of previously reported phosphoinositide 3-kinase δ (PI3Kδ) inhibitors and subsequent regrowth led to the identification of a privileged fragment for PI3Kδ, which was exploited to deliver a potent, efficient, and selective lead series with a novel binding mode observed in the PI3Kδ crystal structure.

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Organizational Affiliation: 
• GlaxoSmithKline R&D, Medicines Research Centre , Gunnels Wood Road , SG1 2NY Stevenage , U.K.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 108.26 kDa 
• Atom Count: 7,120 
• Modeled Residue Count: 854 
• Deposited Residue Count: 940 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit delta isoform	A	940	Mus musculus	Mutation(s): 0  Gene Names: Pik3cd EC: 2.7.1.153 (PDB Primary Data), 2.7.1.137 (UniProt)
UniProt
Find proteins for O35904 (Mus musculus) Explore O35904  Go to UniProtKB:  O35904

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HKN (Subject of Investigation/LOI)	B [auth A]	~{N}-[5-(3,6-dihydro-2~{H}-pyran-4-yl)-2-methoxy-pyridin-3-yl]-2-methyl-1-(phenylmethyl)imidazole-4-sulfonamide C22 H24 N4 O4 S HEYCQGPIBKDOSR-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
HKN	BindingDB:  6Q74	IC50: 6.3 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.48 Å
• R-Value Free:  0.249 (Depositor), 0.255 (DCC) 
• R-Value Work:  0.174 (Depositor), 0.181 (DCC) 
• R-Value Observed: 0.178 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 141.28	α = 90
b = 63.96	β = 102.16
c = 116.22	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
autoPROC	data scaling
BUSTER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-12-26 
Deposition Author(s): Convery, M.A., Rowland, P., Down, K., Barton, N.

Revision History  

• Version 1.0: 2018-12-26
  Type: Initial release
  
• Version 1.1: 2019-04-24
  Changes: Data collection, Database references
• Version 1.2: 2021-09-29
  Changes: Data collection, Database references, Refinement description, Source and taxonomy
• Version 1.3: 2024-06-19
  Changes: Data collection