7LQ1

HUMAN PI3KDELTA IN COMPLEX WITH COMPOUND 28

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 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history. 


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

  • 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.

    • Organizational Affiliation: 

    Computational and Structural Chemistry, Merck & Co., Inc., Boston, MA, USA. Electronic address: xavier.fradera@merck.com.


Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit delta isoform1,044Homo sapiensMutation(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)
Go to UniProtKB:  O00329
PHAROS:  O00329
GTEx:  ENSG00000171608 
Sequence Annotations
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  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Phosphatidylinositol 3-kinase regulatory subunit alpha169Homo sapiensMutation(s): 0 
Gene Names: PIK3R1, GRB1
UniProt & NIH Common Fund Data Resources
Find proteins for P27986 (Homo sapiens)
Go to UniProtKB:  P27986
PHAROS:  P27986
GTEx:  ENSG00000145675 
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
YA7 (Subject of Investigation/LOI)
Query on YA7
Download Ideal Coordinates CCD File 
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
Query on CL
Download Ideal Coordinates CCD File 
D [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Binding Affinity Annotations 
IDSourceBinding Affinity
YA7 BindingDB:  7LQ1 IC50: 1.4 (nM) from 1 assay(s)
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 = 90.551α = 90
b = 108.59β = 90
c = 142.424γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
REFMACphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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