6AUD | pdb_00006aud

PI3K-gamma K802T in complex with Cpd 8 10-((1-(tert-butyl)piperidin-4-yl)sulfinyl)-2-(1-isopropyl-1H-1,2,4-triazol-5-yl)-5,6-dihydrobenzo[f]imidazo[1,2-d][1,4]oxazepine

• PDB DOI: https://doi.org/10.2210/pdb6AUD/pdb

• Classification: TRANSFERASE/TRANSFERASE INHBITOR
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): Yes 


• Deposited: 2017-08-31 Released: 2017-11-15 
• Deposition Author(s): Murray, J.M., Ultsch, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.02 Å
• R-Value Free: 
  0.233 (Depositor), 0.233 (DCC) 
• R-Value Work: 
  0.203 (Depositor), 0.203 (DCC) 
• R-Value Observed: 
  0.204 (Depositor) 

Starting Model: experimental

Literature

Design of Selective Benzoxazepin PI3K delta Inhibitors Through Control of Dihedral Angles.

Safina, B.S., Elliott, R.L., Forrest, A.K., Heald, R.A., Murray, J.M., Nonomiya, J., Pang, J., Salphati, L., Seward, E.M., Staben, S.T., Ultsch, M., Wei, B., Yang, W., Sutherlin, D.P.

(2017) ACS Med Chem Lett 8: 936-940

• PubMed: 28947940 
• DOI: https://doi.org/10.1021/acsmedchemlett.7b00170
• Primary Citation Related Structures: 
  6AUD


• PubMed Abstract: 
  

  A novel selective benzoxazepin inhibitor of PI3Kδ has been discovered. Beginning from compound 3 , an αPI3K inhibitor, we utilized structure-based drug design and computational analysis of dihedral torsion angles to optimize for PI3Kδ isoform potency and isoform selectivity. Further medicinal chemistry optimization of the series led to the identification of 24 , a highly potent and selective inhibitor of PI3Kδ.

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Organizational Affiliation: 
• Discovery Chemistry, Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States.
Discovery from Charles River, 8-9 Spire Green Centre, Harlow, Essex CM 19 5TR, United Kingdom.
ChemPartner, 998 Halei Road, Zhangjiang Hi-tech Park, Pudong New Area, Shanghai 201203, China.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 111.18 kDa 
• Atom Count: 7,121 
• Modeled Residue Count: 840 
• Deposited Residue Count: 966 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform	A	966	Homo sapiens	Mutation(s): 1  Gene Names: PIK3CG EC: 2.7.1.153 (PDB Primary Data), 2.7.11.1 (PDB Primary Data), 2.7.1.137 (UniProt), 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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BWY	B [auth A]	10-[(S)-(1-tert-butylpiperidin-4-yl)sulfinyl]-2-[1-(propan-2-yl)-1H-1,2,4-triazol-5-yl]-5,6-dihydroimidazo[1,2-d][1,4]benzoxazepine C25 H34 N6 O2 S HUAOHTKULCUTBL-UMSFTDKQSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.02 Å
• R-Value Free:  0.233 (Depositor), 0.233 (DCC) 
• R-Value Work:  0.203 (Depositor), 0.203 (DCC) 
• R-Value Observed: 0.204 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 139.051	α = 90
b = 66.065	β = 98.06
c = 102.492	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
DENZO	data reduction
SCALEPACK	data scaling
PDB_EXTRACT	data extraction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-11-15 
Deposition Author(s): Murray, J.M., Ultsch, M.

Revision History  

• Version 1.0: 2017-11-15
  Type: Initial release
  
• Version 1.1: 2023-10-04
  Changes: Data collection, Database references, Refinement description