6G6W

HUMAN PI3KDELTA IN COMPLEX WITH LIGAND LASW1976


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.72 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.219 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Discovery of a Novel Inhaled PI3K delta Inhibitor for the Treatment of Respiratory Diseases.

Erra, M.Taltavull, J.Bernal, F.J.Caturla, J.F.Carrascal, M.Pages, L.Mir, M.Espinosa, S.Gracia, J.Dominguez, M.Sabate, M.Paris, S.Maldonado, M.Hernandez, B.Bravo, M.Calama, E.Miralpeix, M.Lehner, M.D.Calbet, M.

(2018) J Med Chem 61: 9551-9567

  • DOI: 10.1021/acs.jmedchem.8b00873
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Oral PI3Kδ inhibitors such as Idelalisib and Duvelisib have shown efficacy as anticancer agents and Idelalisib has been approved for the treatment of three B-cell cancers. However, Idelalisib has a black box warning on its product label regarding the ...

    Oral PI3Kδ inhibitors such as Idelalisib and Duvelisib have shown efficacy as anticancer agents and Idelalisib has been approved for the treatment of three B-cell cancers. However, Idelalisib has a black box warning on its product label regarding the risks of fatal and serious toxicities including hepatic toxicity, severe diarrhea, colitis, pneumonitis, infections, and intestinal perforation. Some of these side effects are mechanism-related and could hinder the development of Idelalisib for less severe conditions. For respiratory diseases, compounds administered by inhalation are delivered directly to the site of action and may improve the therapeutic index of a drug, minimizing undesired side effects. This work describes the discovery and optimization of inhaled PI3Kδ inhibitors intended for the treatment of severe asthma and COPD. Once the potency was in the desired range, efforts were focused on identifying the particular physicochemical properties that could translate into better lung retention. This medicinal chemistry exercise led to the identification of LAS195319 as a candidate for clinical development.


    Organizational Affiliation

    Department of Chemistry and Biochemistry , University of California, San Diego , La Jolla , California 92093 , United States.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit delta isoformA1072Homo sapiensMutation(s): 0 
Gene Names: PIK3CD
EC: 2.7.1.153
Find proteins for O00329 (Homo sapiens)
Explore O00329 
Go to UniProtKB:  O00329
NIH Common Fund Data Resources
PHAROS  O00329
Protein Feature View
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  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Phosphatidylinositol 3-kinase regulatory subunit alphaB170Bos taurusMutation(s): 0 
Gene Names: PIK3R1
Find proteins for P23727 (Bos taurus)
Explore P23727 
Go to UniProtKB:  P23727
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EO5
Query on EO5

Download CCD File 
A
~{N}-[3-[4-[[(1~{S})-1-(5-methyl-4-oxidanylidene-3-phenyl-pyrrolo[2,1-f][1,2,4]triazin-2-yl)ethyl]amino]-7~{H}-pyrrolo[ 2,3-d]pyrimidin-5-yl]-5-oxidanyl-phenyl]methanesulfonamide
C28 H26 N8 O4 S
AYLIBFXIKSYUIG-KRWDZBQOSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.72 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.219 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 90.452α = 90
b = 108.951β = 90
c = 142.481γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-11-07
    Type: Initial release
  • Version 1.1: 2018-11-21
    Changes: Data collection, Database references