7LQ1

HUMAN PI3KDELTA IN COMPLEX WITH COMPOUND 28

• PDB DOI: https://doi.org/10.2210/pdb7LQ1/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2021-02-12 Released: 2022-02-16 
• Deposition Author(s): Lesburg, C.A., Augustin, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.96 Å
• R-Value Free: 0.281 
• R-Value Work: 0.213 
• R-Value Observed: 0.215 

Literature

Discovery of a new series of PI3K-delta inhibitors from Virtual Screening.

Fradera, X., Deng, Q., Achab, A., Garcia, Y., Kattar, S.D., McGowan, M.A., Methot, J.L., Wilson, K., Zhou, H., Shaffer, L., Goldenblatt, P., Tong, V., Augustin, M.A., Altman, M.D., Lesburg, C.A., Shah, S., Katz, J.D.

(2021) Bioorg Med Chem Lett 42: 128046-128046

• PubMed: 33865969 
• DOI: https://doi.org/10.1016/j.bmcl.2021.128046
• Primary Citation of Related Structures:  
  7LQ1


• PubMed Abstract: 
  

  PI3K-δ mediates key immune cell signaling pathways and is a target of interest for treatment of oncological and immunological disorders. Here we describe the discovery and optimization of a novel series of PI3K-δ selective inhibitors. We first identified hits containing an isoindolinone scaffold using a combined ligand- and receptor-based virtual screening workflow, and then improved potency and selectivity guided by structural data and modeling. Careful optimization of molecular properties led to compounds with improved permeability and pharmacokinetic profile, and high potency in a whole blood assay.

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Organizational Affiliation: 

Computational and Structural Chemistry, Merck & Co., Inc., Boston, MA, USA. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Macromolecule Content

• Total Structure Weight: 141.07 kDa 
• Atom Count: 9,190 
• Modelled Residue Count: 1,119 
• Deposited Residue Count: 1,213 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit delta isoform	A	1,044	Homo sapiens	Mutation(s): 0  Gene Names: PIK3CD EC: 2.7.1.137 (PDB Primary Data), 2.7.1.153 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for O00329 (Homo sapiens) Explore O00329  Go to UniProtKB:  O00329
PHAROS:  O00329 GTEx:  ENSG00000171608

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphatidylinositol 3-kinase regulatory subunit alpha	B	169	Homo sapiens	Mutation(s): 0  Gene Names: PIK3R1, GRB1
UniProt & NIH Common Fund Data Resources
Find proteins for P27986 (Homo sapiens) Explore P27986  Go to UniProtKB:  P27986
PHAROS:  P27986 GTEx:  ENSG00000145675

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
YA7 (Subject of Investigation/LOI)	C [auth A]	N-(5-(6-(2-((2S,6R)-2,6-dimethylmorpholino)pyridin-4-yl)-1-oxoisoindolin-4-yl)-2-methoxypyridin-3-yl)methanesulfonamide C26 H29 N5 O5 S BTLBFTXHIOZUGF-IYBDPMFKSA-N
CL	D [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.96 Å
• R-Value Free: 0.281 
• R-Value Work: 0.213 
• R-Value Observed: 0.215 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.551	α = 90
b = 108.59	β = 90
c = 142.424	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
REFMAC	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2022-02-16 
Deposition Author(s): Lesburg, C.A., Augustin, M.

Revision History  

• Version 1.0: 2022-02-16
  Type: Initial release
  
• Version 1.1: 2022-08-31
  Changes: Database references
• Version 1.2: 2024-04-03
  Changes: Data collection, Refinement description