9GDI | pdb_00009gdi

HUMAN PI3KDELTA IN COMPLEX WITH ISOCUMARIN INHIBITOR 10


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.81 Å
  • R-Value Free: 
    0.299 (Depositor), 0.266 (DCC) 
  • R-Value Work: 
    0.246 (Depositor), 0.234 (DCC) 
  • R-Value Observed: 
    0.247 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Discovery of CHF-6523, an Inhaled Selective PI3K delta Inhibitor for the Treatment of Chronic Obstructive Pulmonary Disease.

Bruno, P.Pala, D.Micoli, A.Corsi, M.Accetta, A.Carzaniga, L.Ronchi, P.Fiorelli, C.Formica, M.Pizzirani, D.Mazzucato, R.Guariento, S.Bertolini, S.Martucci, C.Allen, A.D.Mileo, V.Capacchi, S.Gallo, P.M.Fioni, A.Xanxo Fernandez, S.Villetti, G.Puccini, P.Civelli, M.Guala, M.Retini, M.Martinelli, P.Visentini, F.Pavoni, V.Daldosso, M.Fontana, S.Biagetti, M.Capelli, A.M.

(2025) J Med Chem 68: 2444-2465

  • DOI: https://doi.org/10.1021/acs.jmedchem.4c02062
  • Primary Citation of Related Structures:  
    9GCF, 9GDI, 9GG9

  • PubMed Abstract: 

    The design of inhaled selective phosphatidylinositol 3-kinase delta (PI3Kδ) inhibitors for the treatment of inflammatory lung diseases was pursued. Knowledge-based design of a novel isocoumarin scaffold that was able to adopt a propeller-shape topology ensured the desired PI3Kδ selectivity. Achievement of low nanomolar cellular potencies through hinge binder group optimization, reduction of intrinsic permeability through head group optimization to extend lung retention, and screening of crystalline forms suitable for administration as dry powders culminated in the identification of compound 18 . This novel inhaled selective PI3Kδ inhibitor displayed durable anti-inflammatory activity in a disease-relevant rat model of Th-2-driven acute lung inflammation and safe in vitro and in vivo preclinical profiles. Therefore, compound 18 showed the appropriate discovery profile and was progressed to clinical trials in healthy volunteers and chronic obstructive pulmonary disease (COPD) patients as CHF-6523.


  • Organizational Affiliation
    • Chiesi Farmaceutici S.p.A, Centro Ricerche, Largo Belloli 11/a, 43122 Parma, Italy.

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)
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 alpha170Bos 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 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1IJ1
Query on A1IJ1

Download Ideal Coordinates CCD File 
C [auth A]3-[(1S)-1-[4-azanyl-3-(3-fluoranyl-5-oxidanyl-phenyl)pyrazolo[3,4-d]pyrimidin-1-yl]ethyl]-4-(1-methyl-3,6-dihydro-2H-pyridin-4-yl)isochromen-1-one
C28 H25 F N6 O3
QKJLXHNKHNDHAP-HNNXBMFYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
D [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.81 Å
  • R-Value Free:  0.299 (Depositor), 0.266 (DCC) 
  • R-Value Work:  0.246 (Depositor), 0.234 (DCC) 
  • R-Value Observed: 0.247 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 90.474α = 90
b = 108.618β = 90
c = 142.402γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
REFMACrefinement
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2024-12-18
    Type: Initial release
  • Version 1.1: 2025-02-26
    Changes: Database references