5NCY

mPI3Kd IN COMPLEX WITH inh1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.222 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Design and Synthesis of Soluble and Cell-Permeable PI3K delta Inhibitors for Long-Acting Inhaled Administration.

Perry, M.W.D.Bjorhall, K.Bonn, B.Carlsson, J.Chen, Y.Eriksson, A.Fredlund, L.Hao, H.Holden, N.S.Karabelas, K.Lindmark, H.Liu, F.Pemberton, N.Petersen, J.Rodrigo Blomqvist, S.Smith, R.W.Svensson, T.Terstiege, I.Tyrchan, C.Yang, W.Zhao, S.Oster, L.

(2017) J. Med. Chem. 60: 5057-5071

  • DOI: 10.1021/acs.jmedchem.7b00401
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • PI3Kδ is a lipid kinase that is believed to be important in the migration and activation of cells of the immune system. Inhibition is hypothesized to provide a powerful yet selective immunomodulatory effect that may be beneficial for the treatment of ...

    PI3Kδ is a lipid kinase that is believed to be important in the migration and activation of cells of the immune system. Inhibition is hypothesized to provide a powerful yet selective immunomodulatory effect that may be beneficial for the treatment of conditions such as asthma or rheumatoid arthritis. In this work, we describe the identification of inhibitors based on a thiazolopyridone core structure and their subsequent optimization for inhalation. The initially identified compound (13) had good potency and isoform selectivity but was not suitable for inhalation. Addition of basic substituents to a region of the molecule pointing to solvent was tolerated (enzyme inhibition pIC50 > 9), and by careful manipulation of the pKa and lipophilicity, we were able to discover compounds (20b, 20f) with good lung retention and cell potency that could be taken forward to in vivo studies where significant target engagement could be demonstrated.


    Organizational Affiliation

    Respiratory, Inflammation and Autoimmunity, Innovative Medicines and Early Development, AstraZeneca Gothenburg , Pepparedsleden 1, SE-431 83 Mölndal, Sweden.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit delta isoform
A
939Mus musculusMutation(s): 0 
Gene Names: Pik3cd
EC: 2.7.1.153
Find proteins for O35904 (Mus musculus)
Go to UniProtKB:  O35904
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
8TK
Query on 8TK

Download SDF File 
Download CCD File 
A
4-azanyl-6-[[(1~{S})-1-(3-methyl-5-oxidanylidene-6-phenyl-[1,3]thiazolo[3,2-a]pyridin-7-yl)ethyl]amino]pyrimidine-5-carbonitrile
C21 H18 N6 O S
XLCBQUCCOPILIO-ZDUSSCGKSA-N
 Ligand Interaction
EDO
Query on EDO

Download SDF File 
Download CCD File 
A
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
8TKIC50: 0.4 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.222 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 140.989α = 90.00
b = 64.549β = 103.59
c = 116.013γ = 90.00
Software Package:
Software NamePurpose
BUSTERrefinement
MOLREPphasing
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2017-03-06 
  • Released Date: 2017-06-21 
  • Deposition Author(s): Petersen, J.

Revision History 

  • Version 1.0: 2017-06-21
    Type: Initial release
  • Version 1.1: 2017-07-05
    Type: Database references