7POR

PI3 kinase delta in complex with N-[2-(2-fluoro-4-{[4-(propan-2-yl)piperazin-1-yl]methyl}phenyl)pyridin-4-yl]-2-methoxy-5-(morpholin-4-yl)pyridine-3-sulfonamide

• PDB DOI: https://doi.org/10.2210/pdb7POR/pdb

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


• Deposited: 2021-09-09 Released: 2021-09-29 
• Deposition Author(s): Rowland, P., Convery, M.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.26 Å
• R-Value Free: 0.222 
• R-Value Work: 0.188 
• R-Value Observed: 0.190 

Literature

Discovery of GSK251: A Highly Potent, Highly Selective, Orally Bioavailable Inhibitor of PI3K delta with a Novel Binding Mode.

Down, K., Amour, A., Anderson, N.A., Barton, N., Campos, S., Cannons, E.P., Clissold, C., Convery, M.A., Coward, J.J., Doyle, K., Duempelfeld, B., Edwards, C.D., Goldsmith, M.D., Krause, J., Mallett, D.N., McGonagle, G.A., Patel, V.K., Rowedder, J., Rowland, P., Sharpe, A., Sriskantharajah, S., Thomas, D.A., Thomson, D.W., Uddin, S., Hamblin, J.N., Hessel, E.M.

(2021) J Med Chem 64: 13780-13792

• PubMed: 34510892 
• DOI: https://doi.org/10.1021/acs.jmedchem.1c01102
• Primary Citation of Related Structures:  
  7POP, 7POR, 7POS, 7POT


• PubMed Abstract: 
  

  Optimization of a previously reported lead series of PI3Kδ inhibitors with a novel binding mode led to the identification of a clinical candidate compound 31 (GSK251). Removal of an embedded Ames-positive heteroaromatic amine by reversing a sulfonamide followed by locating an interaction with Trp760 led to a highly selective compound 9 . Further optimization to avoid glutathione trapping, to enhance potency and selectivity, and to optimize an oral pharmacokinetic profile led to the discovery of compound 31 (GSK215) that had a low predicted daily dose (45 mg, b.i.d) and a rat toxicity profile suitable for further development.

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Organizational Affiliation: 

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

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 108.41 kDa 
• Atom Count: 7,272 
• Modelled Residue Count: 859 
• 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
7XH (Subject of Investigation/LOI)	B [auth A]	~{N}-[2-[2-fluoranyl-4-[(4-propan-2-ylpiperazin-1-yl)methyl]phenyl]pyridin-4-yl]-2-methoxy-5-morpholin-4-yl-pyridine-3-sulfonamide C29 H37 F N6 O4 S ODQVPYNCHSLNGV-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
7XH	BindingDB:  7POR	Ki: 0.01 (nM) from 1 assay(s)
		IC50: min: 0.79, max: 6.3 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.26 Å
• R-Value Free: 0.222 
• R-Value Work: 0.188 
• R-Value Observed: 0.190 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 142	α = 90
b = 64.2	β = 102.27
c = 115.46	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
Aimless	data scaling

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-09-29 
Deposition Author(s): Rowland, P., Convery, M.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2021-09-29
  Type: Initial release
  
• Version 1.1: 2021-10-06
  Changes: Data collection, Database references
• Version 1.2: 2024-06-19
  Changes: Data collection