6TNR

PI3K delta in complex with N[5(7{2[4(2hydroxypropan2yl)piperidin1 yl]ethoxy}1,3dihydro2benzofuran5yl)2 methoxypyridin3yl]methanesulfonamide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.176 

wwPDB Validation   3D Report Full Report


This is version 1.5 of the entry. See complete history


Literature

Optimization of Orally Bioavailable PI3K delta Inhibitors and Identification of Vps34 as a Key Selectivity Target.

Henley, Z.A.Amour, A.Barton, N.Bantscheff, M.Bergamini, G.Bertrand, S.M.Convery, M.Down, K.Dumpelfeld, B.Edwards, C.D.Grandi, P.Gore, P.M.Keeling, S.Livia, S.Mallett, D.Maxwell, A.Price, M.Rau, C.Reinhard, F.B.M.Rowedder, J.Rowland, P.Taylor, J.A.Thomas, D.A.Hessel, E.M.Hamblin, J.N.

(2020) J Med Chem 63: 638-655

  • DOI: https://doi.org/10.1021/acs.jmedchem.9b01585
  • Primary Citation of Related Structures:  
    6TNR, 6TNS

  • PubMed Abstract: 

    Optimization of a lead series of PI3Kδ inhibitors based on a dihydroisobenzofuran core led to the identification of potent, orally bioavailable compound 19 . Selectivity profiling of compound 19 showed similar potency for class III PI3K, Vps34, and PI3Kδ, and compound 19 was not well-tolerated in a 7-day rat toxicity study. Structure-based design led to an improvement in selectivity for PI3Kδ over Vps34 and, a focus on oral phramacokinetics properties resulted in the discovery of compound 41 , which showed improved toxicological outcomes at similar exposure levels to compound 19 .


  • Organizational Affiliation

    Cellzome GmbH , GlaxoSmithKline , Meyerhofstrasse 1 , 69117 Heidelberg , Germany.


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 isoform940Mus musculusMutation(s): 0 
Gene Names: Pik3cd
EC: 2.7.1.153 (PDB Primary Data), 2.7.1.137 (UniProt)
UniProt
Find proteins for O35904 (Mus musculus)
Explore O35904 
Go to UniProtKB:  O35904
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO35904
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NQ2 (Subject of Investigation/LOI)
Query on NQ2

Download Ideal Coordinates CCD File 
B [auth A]~{N}-[2-methoxy-5-[7-[2-[4-(2-oxidanylpropan-2-yl)piperidin-1-yl]ethoxy]-1,3-dihydro-2-benzofuran-5-yl]pyridin-3-yl]methanesulfonamide
C25 H35 N3 O6 S
YTBODSVQSOILIJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.176 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 141.661α = 90
b = 64.723β = 103.1
c = 116.306γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
PDB_EXTRACTdata extraction
autoPROCdata reduction
autoPROCdata scaling
BUSTERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-01-01
    Type: Initial release
  • Version 1.1: 2020-01-15
    Changes: Database references
  • Version 1.2: 2020-02-05
    Changes: Database references
  • Version 1.3: 2020-03-04
    Changes: Data collection
  • Version 1.4: 2021-09-29
    Changes: Database references, Refinement description, Source and taxonomy
  • Version 1.5: 2024-06-19
    Changes: Data collection