7POT

PI3 kinase delta in complex with N-[5-(3,6-dihydro-2H-pyran-4-yl)-2-methoxypyridin-3-yl]benzenesulfonamide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.39 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.199 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Discovery of GSK251: A Highly Potent, Highly Selective, Orally Bioavailable Inhibitor of PI3K delta with a Novel Binding Mode.

Down, K.Amour, A.Anderson, N.A.Barton, N.Campos, S.Cannons, E.P.Clissold, C.Convery, M.A.Coward, J.J.Doyle, K.Duempelfeld, B.Edwards, C.D.Goldsmith, M.D.Krause, J.Mallett, D.N.McGonagle, G.A.Patel, V.K.Rowedder, J.Rowland, P.Sharpe, A.Sriskantharajah, S.Thomas, D.A.Thomson, D.W.Uddin, S.Hamblin, J.N.Hessel, E.M.

(2021) J Med Chem 64: 13780-13792

  • DOI: https://doi.org/10.1021/acs.jmedchem.1c01102
  • Primary Citation of Related Structures:  
    7POP, 7POR, 7POS, 7POT

  • PubMed Abstract: 

    Optimization of a previously reported lead series of PI3Kδ inhibitors with a novel binding mode led to the identification of a clinical candidate compound 31 (GSK251). Removal of an embedded Ames-positive heteroaromatic amine by reversing a sulfonamide followed by locating an interaction with Trp760 led to a highly selective compound 9 . Further optimization to avoid glutathione trapping, to enhance potency and selectivity, and to optimize an oral pharmacokinetic profile led to the discovery of compound 31 (GSK215) that had a low predicted daily dose (45 mg, b.i.d) and a rat toxicity profile suitable for further development.


  • Organizational Affiliation

    Medicines Research Centre, GlaxoSmithKline R&D, Gunnels Wood Road, Stevenage SG1 2NY, U.K.


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
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
7XW (Subject of Investigation/LOI)
Query on 7XW

Download Ideal Coordinates CCD File 
B [auth A]N-[5-(3,6-dihydro-2H-pyran-4-yl)-2-methoxy-pyridin-3-yl]benzenesulfonamide
C17 H18 N2 O4 S
OZEVUWLUKNYTLV-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.39 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.199 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 141.446α = 90
b = 64.324β = 102.2
c = 116.485γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
autoPROCdata reduction
STARANISOdata scaling

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2021-09-29
    Type: Initial release
  • Version 1.1: 2021-10-06
    Changes: Data collection, Database references