6ZAD

PI3K Delta in complex with methoxymethyloxathiatetraazatetracyclodocosahexaenedione


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.24 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.177 

wwPDB Validation 3D Report Full Report



Literature

Design and Development of a Macrocyclic Series Targeting Phosphoinositide 3-Kinase delta.

Spencer, J.A.Baldwin, I.R.Barton, N.Chung, C.W.Convery, M.A.Edwards, C.D.Jamieson, C.Mallett, D.N.Rowedder, J.E.Rowland, P.Thomas, D.A.Hardy, C.J.

(2020) ACS Med Chem Lett 11: 1386-1391

  • DOI: 10.1021/acsmedchemlett.0c00061
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • A macrocyclization approach has been explored on a series of benzoxazine phosphoinositide 3-kinase δ inhibitors, resulting in compounds with improved potency, permeability, and in vivo clearance while maintaining good solubility. The thermod ...

    A macrocyclization approach has been explored on a series of benzoxazine phosphoinositide 3-kinase δ inhibitors, resulting in compounds with improved potency, permeability, and in vivo clearance while maintaining good solubility. The thermodynamics of binding was explored via surface plasmon resonance, and the binding of lead macrocycle 19 was found to be almost exclusively entropically driven compared with progenitor 18 , which demonstrated both enthalpic and entropic contributions. The pharmacokinetics of macrocycle 19 was also explored in vivo , where it showed reduced clearance when compared with the progenitor 18 . This work adds to the growing body of evidence that macrocyclization could provide an alternative and complementary approach to the design of small-molecule inhibitors, with the potential to deliver differentiated properties.


    Organizational Affiliation

    GSK Medicines Research Centre, Gunnels Wood Road, Stevenage SG1 2NY, United Kingdom.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit delta isoformA940Mus musculusMutation(s): 0 
Gene Names: Pik3cd
EC: 2.7.1.153
Find proteins for O35904 (Mus musculus)
Explore O35904 
Go to UniProtKB:  O35904
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
QDW
Query on QDW

Download CCD File 
A
methoxymethyloxathiatetraazatetracyclodocosahexaenedione
C18 H22 N4 O4 S
GANNRSDWVBVNOE-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.24 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.177 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 141.43α = 90
b = 64.48β = 103.03
c = 116.66γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling
BUSTERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2020-07-29
    Type: Initial release