5AE9 | pdb_00005ae9

Crystal structure of mouse PI3 kinase delta in complex with GSK2292767


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.44 Å
  • R-Value Free: 
    0.263 (Depositor), 0.285 (DCC) 
  • R-Value Work: 
    0.186 (Depositor), 0.199 (DCC) 
  • R-Value Observed: 
    0.190 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 5AE9

Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

Optimization of Novel Indazoles as Highly Potent and Selective Inhibitors of Phosphoinositide 3-Kinase Gamma for the Treatment of Respiratory Disease.

Down, K.Amour, A.Baldwin, I.R.Cooper, A.W.J.Deakin, A.M.Felton, L.M.Guntrip, S.B.Hardy, C.Harrison, Z.A.Jones, K.L.Jones, P.Keeling, S.E.Le, J.Livia, S.Lucas, F.Lunniss, C.J.Parr, N.J.Robinson, E.Rowland, P.Smith, S.Thomas, D.A.Vitulli, G.Washio, Y.Hamblin, J.N.

(2015) J Med Chem 58: 7381

  • DOI: https://doi.org/10.1021/acs.jmedchem.5b00767
  • Primary Citation Related Structures: 
    5AE8, 5AE9

  • PubMed Abstract: 

    Optimization of lead compound 1, through extensive use of structure-based design and a focus on PI3Kδ potency, isoform selectivity, and inhaled PK properties, led to the discovery of clinical candidates 2 (GSK2269557) and 3 (GSK2292767) for the treatment of respiratory indications via inhalation. Compounds 2 and 3 are both highly selective for PI3Kδ over the closely related isoforms and are active in a disease relevant brown Norway rat acute OVA model of Th2-driven lung inflammation.


  • Organizational Affiliation
    • Refractory Respiratory Inflammation DPU, and ‡Allergic Inflammation DPU, Respiratory Therapeutic Area, GlaxoSmithKline R&D , Gunnels Wood Road, Stevenage, SG1 2NY, U.K.

Macromolecule Content 

  • Total Structure Weight: 108.34 kDa 
  • Atom Count: 7,494 
  • Modeled Residue Count: 858 
  • 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: 2.7.1.137 (PDB Primary Data), 2.7.1.153 (PDB Primary Data)
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
OKO

Query on OKO



Download:Ideal Coordinates CCD File
B [auth A]N-[5-[4-(5-{[(2R,6S)-2,6-DIMETHYL-4-MORPHOLINYL]METHYL}-1,3-OXAZOL-2-YL)-1H-INDAZOL-6-YL]-2-(METHYLOXY)-3-PYRIDINYL]METHANESULFONAMIDE
C24 H28 N6 O5 S
NLUPPCTVKHDVIQ-GASCZTMLSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.44 Å
  • R-Value Free:  0.263 (Depositor), 0.285 (DCC) 
  • R-Value Work:  0.186 (Depositor), 0.199 (DCC) 
  • R-Value Observed: 0.190 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 142.3α = 90
b = 64.62β = 103.32
c = 116.37γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
autoPROCdata reduction
Aimlessdata scaling
BUSTERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2015-09-16
    Type: Initial release
  • Version 1.1: 2015-10-07
    Changes: Database references
  • Version 1.2: 2021-09-29
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description, Source and taxonomy, Structure summary
  • Version 1.3: 2024-06-19
    Changes: Data collection