6TNR | pdb_00006tnr

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 (Depositor), 0.203 (DCC) 
  • R-Value Work: 
    0.174 (Depositor), 0.172 (DCC) 
  • R-Value Observed: 
    0.176 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 6TNR

Ligand Structure Quality Assessment 


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 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.

Macromolecule Content 

  • Total Structure Weight: 108.33 kDa 
  • Atom Count: 7,729 
  • Modeled Residue Count: 863 
  • Deposited Residue Count: 940 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  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
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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 (Depositor), 0.203 (DCC) 
  • R-Value Work:  0.174 (Depositor), 0.172 (DCC) 
  • R-Value Observed: 0.176 (Depositor) 
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



Ligand Structure Quality Assessment 


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