6TNS | pdb_00006tns

PI3K delta in complex with 2methoxyN[2methoxy5(7{[(2R)4(oxetan3 yl)morpholin2yl]methoxy}1,3dihydro2 benzofuran5yl)pyridin3yl]ethane1 sulfonamide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 
    0.244 (Depositor) 
  • R-Value Work: 
    0.187 (Depositor) 
  • R-Value Observed: 
    0.190 (Depositor) 

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
NQ5 (Subject of Investigation/LOI)
Query on NQ5

Download Ideal Coordinates CCD File 
B [auth A]2-methoxy-~{N}-[2-methoxy-5-[7-[[(2~{R})-4-(oxetan-3-yl)morpholin-2-yl]methoxy]-1,3-dihydro-2-benzofuran-5-yl]pyridin-3-yl]ethanesulfonamide
C25 H33 N3 O8 S
ZWPJBXLFZFLGMV-OAQYLSRUSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
NQ5 BindingDB:  6TNS Kd: 0.2 (nM) from 1 assay(s)
IC50: min: 5, max: 63 (nM) from 3 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free:  0.244 (Depositor) 
  • R-Value Work:  0.187 (Depositor) 
  • R-Value Observed: 0.190 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 141.749α = 90
b = 64.582β = 103.1
c = 116.105γ = 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