6MUM

Murine PI3K delta kinsae domain - cpd 3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.06 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.230 
  • R-Value Observed: 0.232 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structure Overhaul Affords a Potent Purine PI3K delta Inhibitor with Improved Tolerability.

Methot, J.L.Zhou, H.Kattar, S.D.McGowan, M.A.Wilson, K.Garcia, Y.Deng, Y.Altman, M.Fradera, X.Lesburg, C.Fischmann, T.Li, C.Alves, S.Shah, S.Fernandez, R.Goldenblatt, P.Hill, A.Shaffer, L.Chen, D.Tong, V.McLeod, R.L.Yu, H.Bass, A.Kemper, R.Gatto, N.T.LaFranco-Scheuch, L.Trotter, B.W.Guzi, T.Katz, J.D.

(2019) J Med Chem 62: 4370-4382

  • DOI: 10.1021/acs.jmedchem.8b01818
  • Primary Citation of Related Structures:  
    6MUM, 6MUL

  • PubMed Abstract: 
  • PI3Kδ catalytic activity is required for immune cell activation, and has been implicated in inflammatory diseases as well as hematological malignancies in which the AKT pathway is overactive. A purine PI3Kδ inhibitor bearing a benzimidazolone-piperidine motif was found to be poorly tolerated in dog, which was attributed to diffuse vascular injury ...

    PI3Kδ catalytic activity is required for immune cell activation, and has been implicated in inflammatory diseases as well as hematological malignancies in which the AKT pathway is overactive. A purine PI3Kδ inhibitor bearing a benzimidazolone-piperidine motif was found to be poorly tolerated in dog, which was attributed to diffuse vascular injury. Several strategies were implemented to mitigate this finding, including reconstruction of the benzimidazolone-piperidine selectivity motif. Structure-based design led to the identification of O- and N-linked heterocycloalkyls, with pyrrolidines being particularly ligand efficient and kinome selective, and having an improved safety pharmacology profile. A representative was advanced into a dog tolerability study where it was found to be well tolerated, with no histopathological evidence of vascular injury.


    Organizational Affiliation

    Novartis Pharma AG, Basel, CH-4056, Switzerland.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit delta isoformA, B940Mus musculusMutation(s): 0 
Gene Names: Pik3cd
EC: 2.7.1.153
UniProt
Find proteins for O35904 (Mus musculus)
Explore O35904 
Go to UniProtKB:  O35904
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K47
Query on K47

Download Ideal Coordinates CCD File 
C [auth A], D [auth B][(3S)-3-{[8-(1-ethyl-5-methyl-1H-pyrazol-4-yl)-9-methyl-9H-purin-6-yl]oxy}pyrrolidin-1-yl](oxan-4-yl)methanone
C22 H29 N7 O3
FHKPLLOSJHHKNU-INIZCTEOSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.06 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.230 
  • R-Value Observed: 0.232 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.35α = 90
b = 220.68β = 114.02
c = 78.19γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XDSdata reduction
SCALAdata scaling
BUSTERrefinement
BUSTER-TNTphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2018-10-23 
  • Released Date: 2019-05-01 
  • Deposition Author(s): Fischmann, T.O.

Revision History  (Full details and data files)

  • Version 1.0: 2019-05-01
    Type: Initial release
  • Version 1.1: 2019-05-22
    Changes: Data collection, Database references