8S3R

HUMAN PI3KDELTA IN COMPLEX WITH PYRIDAZINONE INHIBITOR 7


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.28 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.204 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Discovery and Optimization of Pyridazinones as PI3K delta Selective Inhibitors for Administration by Inhalation.

Bruno, P.Micoli, A.Corsi, M.Pala, D.Guariento, S.Fiorelli, C.Ronchi, P.Fioni, A.Gallo, P.M.Marenghi, G.Bertolini, S.Capacchi, S.Mileo, V.Biagetti, M.Capelli, A.M.

(2024) J Med Chem 67: 11103-11124

  • DOI: https://doi.org/10.1021/acs.jmedchem.4c00610
  • Primary Citation of Related Structures:  
    8S3R

  • PubMed Abstract: 

    A hit-to-lead campaign pursuing the identification of novel inhalant small-molecule phosphatidylinositol 3-kinase (PI3K) inhibitors for the treatment of inflammatory respiratory diseases is disclosed. A synthetically versatile pyridazin-3(2 H )-one scaffold was designed, and three exit vectors on the core moiety were used to explore chemical diversity and optimize pharmacological and absorption, distribution, metabolism, and excretion (ADME) properties. Desired modulation of PI3Kδ selectivity and cellular potency as well as ADME properties in view of administration by inhalation was achieved. Intratracheal administration of lead compound 26 resulted in a promising pharmacokinetic profile, thus demonstrating that the optimization strategy of in vitro profiles successfully translated to an in vivo setting.


  • Organizational Affiliation

    Medicinal Chemistry and Drug Design Technologies Department, Chiesi Farmaceutici S.p.A, Nuovo 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 isoform1,018Homo 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
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1H48 (Subject of Investigation/LOI)
Query on A1H48

Download Ideal Coordinates CCD File 
C [auth A]5-[(1~{S})-1-[4-azanyl-3-(5-oxidanylpyridin-3-yl)pyrazolo[3,4-d]pyrimidin-1-yl]ethyl]-4-cyclopentyl-2-(phenylmethyl)pyridazin-3-one
C28 H28 N8 O2
DRNLTPZVKYHLED-KRWDZBQOSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.28 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.204 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 90.121α = 90
b = 108.35β = 90
c = 142.411γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
REFMACrefinement
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: 2024-07-03
    Type: Initial release
  • Version 1.1: 2024-07-24
    Changes: Database references