4ANX

Complexes of PI3Kgamma with isoform selective inhibitors.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.73 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.225 
  • R-Value Observed: 0.228 

Starting Model: other
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

The Discovery of a Novel Series of Potent and Orally Bioavailable Phosphoinositide 3-Kinase Gamma Inhibitors

Leahy, J.W.Buhr, C.A.Johnson, H.W.B.Kim, B.G.Baik, T.Cannoy, J.Forsyth, T.P.Jeong, J.W.Lee, M.S.Ma, S.Noson, K.Wang, L.Williams, M.Nuss, J.M.Brooks, E.Heald, N.Holst, C.Jaeger, C.Lam, S.Lougheed, J.C.Nguyen, L.Plonowski, A.Stout, T.Foster, P.G.Wu, X.Yakes, M.F.Yu, R.Zhang, W.Lamb, P.Raeber, O.

(2012) J Med Chem 55: 5467

  • DOI: https://doi.org/10.1021/jm300403a
  • Primary Citation of Related Structures:  
    4ANU, 4ANV, 4ANW, 4ANX

  • PubMed Abstract: 

    The phosphoinositide 3-kinases (PI3Ks) have been linked to an extraordinarily diversified group of cellular functions making these enzymes compelling targets for the treatment of disease. A large body of evidence has linked PI3Kγ to the modulation of autoimmune and inflammatory processes making it an intriguing target for drug discovery. Our high-throughput screening (HTS) campaign revealed two hits that were nominated for further optimization studies. The in vitro activity of the first HTS hit, designated as the sulfonylpiperazine scaffold, was optimized utilizing structure-based design. However, nonoptimal pharmacokinetic properties precluded this series from further studies. An overlay of the X-ray structures of the sulfonylpiperazine scaffold and the second HTS hit within their complexes with PI3Kγ revealed a high degree of overlap. This feature was utilized to design a series of hybrid analogues including advanced leads such as 31 with desirable potency, selectivity, and oral bioavailability.


  • Organizational Affiliation

    Department of Drug Discovery, Exelixis, 169 Harbor Way, South San Francisco, California 94083, United States.


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 ISOFORM980Homo sapiensMutation(s): 0 
EC: 2.7.1.137 (PDB Primary Data), 2.7.1.153 (PDB Primary Data), 2.7.11.1 (PDB Primary Data), 2.7.1.154 (UniProt)
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
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
534
Query on 534

Download Ideal Coordinates CCD File 
B [auth A]5-{3-[(4-{3-[4-(1-methylethyl)phenyl]pyrazin-2-yl}piperazin-1-yl)sulfonyl]phenyl}pyrimidin-2-amine
C27 H29 N7 O2 S
IVXKQJAJTVBVLV-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
534 PDBBind:  4ANX IC50: 18 (nM) from 1 assay(s)
BindingDB:  4ANX IC50: min: 18, max: 182 (nM) from 2 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.73 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.225 
  • R-Value Observed: 0.228 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 143.424α = 90
b = 68.531β = 95.26
c = 106.263γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-05-09
    Type: Initial release
  • Version 1.1: 2012-06-27
    Changes: Other
  • Version 1.2: 2019-05-08
    Changes: Data collection, Experimental preparation, Other
  • Version 1.3: 2024-05-01
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description