4WWP

Crystal structure of human PI3K-gamma in complex with pyridinylquinoline inhibitor N-{(1S)-1-[8-chloro-2-(2-methylpyridin-3-yl)quinolin-3-yl]ethyl}-9H-purin-6-amine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.213 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Discovery and in Vivo Evaluation of (S)-N-(1-(7-Fluoro-2-(pyridin-2-yl)quinolin-3-yl)ethyl)-9H-purin-6-amine (AMG319) and Related PI3K delta Inhibitors for Inflammation and Autoimmune Disease.

Cushing, T.D.Hao, X.Shin, Y.Andrews, K.Brown, M.Cardozo, M.Chen, Y.Duquette, J.Fisher, B.Gonzalez-Lopez de Turiso, F.He, X.Henne, K.R.Hu, Y.L.Hungate, R.Johnson, M.G.Kelly, R.C.Lucas, B.McCarter, J.D.McGee, L.R.Medina, J.C.San Miguel, T.Mohn, D.Pattaropong, V.Pettus, L.H.Reichelt, A.Rzasa, R.M.Seganish, J.Tasker, A.S.Wahl, R.C.Wannberg, S.Whittington, D.A.Whoriskey, J.Yu, G.Zalameda, L.Zhang, D.Metz, D.P.

(2015) J Med Chem 58: 480-511

  • DOI: 10.1021/jm501624r
  • Primary Citation of Related Structures:  
    4WWN, 4WWO, 4WWP

  • PubMed Abstract: 
  • The development and optimization of a series of quinolinylpurines as potent and selective PI3Kδ kinase inhibitors with excellent physicochemical properties are described. This medicinal chemistry effort led to the identification of 1 (AMG319), a compound with an IC50 of 16 nM in a human whole blood assay (HWB), excellent selectivity over a large panel of protein kinases, and a high level of in vivo efficacy as measured by two rodent disease models of inflammation ...

    The development and optimization of a series of quinolinylpurines as potent and selective PI3Kδ kinase inhibitors with excellent physicochemical properties are described. This medicinal chemistry effort led to the identification of 1 (AMG319), a compound with an IC50 of 16 nM in a human whole blood assay (HWB), excellent selectivity over a large panel of protein kinases, and a high level of in vivo efficacy as measured by two rodent disease models of inflammation.


    Organizational Affiliation

    Department of Therapeutic Discovery, ‡Department of Pharmacokinetics and Drug Metabolism, and §Department of Pharmaceutics Research and Development, Amgen Inc. , 1120 Veterans Boulevard, South San Francisco, California 94080, United States.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoformA959Homo sapiensMutation(s): 0 
Gene Names: PIK3CG
EC: 2.7.1.153 (PDB Primary Data), 2.7.11.1 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P48736 (Homo sapiens)
Explore P48736 
Go to UniProtKB:  P48736
PHAROS:  P48736
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
3VE
Query on 3VE

Download Ideal Coordinates CCD File 
E [auth A]N-{(1S)-1-[8-chloro-2-(2-methylpyridin-3-yl)quinolin-3-yl]ethyl}-9H-purin-6-amine
C22 H18 Cl N7
DHDVJIWYMLZLBX-ZDUSSCGKSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
B [auth A], C [auth A], D [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
F [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
3VEIC50:  120   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.213 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 143.013α = 90
b = 67.633β = 95.27
c = 105.981γ = 90
Software Package:
Software NamePurpose
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
DENZOdata reduction
REFMACphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-12-17
    Type: Initial release
  • Version 1.1: 2015-01-28
    Changes: Database references
  • Version 1.2: 2017-11-22
    Changes: Database references, Derived calculations, Other, Refinement description, Source and taxonomy, Structure summary