3ZW3

Fragment based discovery of a novel and selective PI3 Kinase inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.187 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Fragment based discovery of a novel and selective PI3 kinase inhibitor.

Hughes, S.J.Millan, D.S.Kilty, I.C.Lewthwaite, R.A.Mathias, J.P.O'Reilly, M.A.Pannifer, A.Phelan, A.Stuhmeier, F.Baldock, D.A.Brown, D.G.

(2011) Bioorg Med Chem Lett 21: 6586-6590

  • DOI: https://doi.org/10.1016/j.bmcl.2011.07.117
  • Primary Citation of Related Structures:  
    3ZVV, 3ZW3

  • PubMed Abstract: 

    We report the use of fragment screening and fragment based drug design to develop a PI3γ kinase fragment hit into a lead. Initial fragment hits were discovered by high concentration biochemical screening, followed by a round of virtual screening to identify additional ligand efficient fragments. These were developed into potent and ligand efficient lead compounds using structure guided fragment growing and merging strategies. This led to a potent, selective, and cell permeable PI3γ kinase inhibitor with good metabolic stability that was useful as a preclinical tool compound.


  • Organizational Affiliation

    Worldwide Medicinal Chemistry, Pfizer Global Research and Development, Sandwich Laboratories, Ramsgate Road, Sandwich, Kent CT13 9NJ, UK. samantha.hughes@pfizer.com


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PHOSPHATIDYLINOSITOL-4,5-BISPHOSPHATE 3-KINASE CATALYTIC SUBUNIT GAMMA ISOFORM966Homo sapiensMutation(s): 0 
EC: 2.7.1.153
UniProt & NIH Common Fund Data Resources
Find proteins for P48736 (Homo sapiens)
Explore P48736 
Go to UniProtKB:  P48736
PHAROS:  P48736
GTEx:  ENSG00000105851 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP48736
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZW3
Query on ZW3

Download Ideal Coordinates CCD File 
B [auth A]N-{6-[(Z)-(2,4-dioxo-1,3-thiazolidin-5-ylidene)methyl]imidazo[1,2-a]pyridin-2-yl}acetamide
C13 H10 N4 O3 S
CCECKHDWHUIQQG-WTKPLQERSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
ZW3 PDBBind:  3ZW3 IC50: 34 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.187 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 142.23α = 90
b = 68.52β = 95.64
c = 107.13γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-09-28
    Type: Initial release
  • Version 1.1: 2011-11-16
    Changes: Database references, Other
  • Version 1.2: 2018-02-07
    Changes: Database references, Structure summary