8BCY

HUMAN PI3KDELTA IN COMPLEX WITH COMPOUND 13


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.43 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.224 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Application of an "inhalation by design" approach to the identification and in-vitro evaluation of novel purine based PI3K delta inhibitors.

Mazzucato, R.Roberti, M.Capelli, A.M.Rancati, F.Biagetti, M.Fiorelli, C.Bruno, P.Ronchi, P.Bertolini, S.Corsi, M.Pala, D.

(2023) Eur J Med Chem 254: 115331-115331

  • DOI: https://doi.org/10.1016/j.ejmech.2023.115331
  • Primary Citation of Related Structures:  
    8BCY

  • PubMed Abstract: 

    PI3Kδ is a lipid kinase which plays a key role in airway inflammatory conditions. Accordingly, the inhibition of PI3Kδ can be considered a valuable strategy for the treatment of chronic respiratory diseases such as Asthma and Chronic obstructive pulmonary disease (COPD). In this work, we describe our efforts to identify new PI3Kδ inhibitors following an "inhalation by design" strategy. Starting from the identification of a purine scaffold, we carried out a preliminary SAR expansion which led to the identification of a new hit characterized by a high enzymatic potency and moderate PI3Kδ selectivity. A subsequent optimization led to novel purine based derivatives with favorable in vitro ADME profiles, which might represent promising starting points for future development of new inhaled drug candidates.


  • Organizational Affiliation

    Chemistry Research and Drug Design Department, Chiesi Farmaceutici S.p.A, Nuovo Centro Ricerche, Largo Belloli 11/a, 43122, Parma, Italy. Electronic address: R.Mazzucato@chiesi.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 isoform1,018Homo 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)
Explore O00329 
Go to UniProtKB:  O00329
PHAROS:  O00329
GTEx:  ENSG00000171608 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO00329
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 alpha169Bos taurusMutation(s): 0 
Gene Names: PIK3R1
UniProt
Find proteins for P23727 (Bos taurus)
Explore P23727 
Go to UniProtKB:  P23727
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP23727
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
I3H (Subject of Investigation/LOI)
Query on I3H

Download Ideal Coordinates CCD File 
C [auth A]9-[2-(3,4-dichlorophenyl)ethyl]-2-(3-hydroxyphenyl)-8-oxidanylidene-7~{H}-purine-6-carboxamide
C20 H15 Cl2 N5 O3
ZOEBAQBSIASRNL-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.43 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.224 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 90.603α = 90
b = 108.809β = 90
c = 142.623γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XSCALEdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other private--

Revision History  (Full details and data files)

  • Version 1.0: 2023-05-10
    Type: Initial release
  • Version 1.1: 2024-06-19
    Changes: Data collection