6FTN | pdb_00006ftn

mPI3Kd IN COMPLEX WITH AZ2

• PDB DOI: https://doi.org/10.2210/pdb6FTN/pdb

• Classification: TRANSFERASE
• Organism(s): Mus musculus
• Expression System: Insect cell expression vector pTIE1
• Mutation(s): No 


• Deposited: 2018-02-22 Released: 2018-06-20 
• Deposition Author(s): Petersen, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.272 (Depositor), 0.279 (DCC) 
• R-Value Work: 
  0.248 (Depositor), 0.251 (DCC) 
• R-Value Observed: 
  0.249 (Depositor) 

Starting Model: other

Literature

Discovery of Highly Isoform Selective Orally Bioavailable Phosphoinositide 3-Kinase (PI3K)-gamma Inhibitors.

Pemberton, N., Mogemark, M., Arlbrandt, S., Bold, P., Cox, R.J., Gardelli, C., Holden, N.S., Karabelas, K., Karlsson, J., Lever, S., Li, X., Lindmark, H., Norberg, M., Perry, M.W.D., Petersen, J., Rodrigo Blomqvist, S., Thomas, M., Tyrchan, C., Westin Eriksson, A., Zlatoidsky, P., Oster, L.

(2018) J Med Chem 61: 5435-5441

• PubMed: 29852070 
• DOI: https://doi.org/10.1021/acs.jmedchem.8b00447
• Primary Citation Related Structures: 
  6FTN


• PubMed Abstract: 
  

  In this paper, we describe the discovery and optimization of a new chemotype of isoform selective PI3Kγ inhibitors. Starting from an HTS hit, potency and physicochemical properties could be improved to give compounds such as 15, which is a potent and remarkably selective PI3Kγ inhibitor with ADME properties suitable for oral administration. Compound 15 was advanced into in vivo studies showing dose-dependent inhibition of LPS-induced airway neutrophilia in rats when administered orally.

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Organizational Affiliation: 
• Pharmaron Beijing Co., Ltd. , No. 6 Taihe Road, BDA , Beijing 100176 , P. R. China.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 108.14 kDa 
• Atom Count: 6,899 
• Modeled Residue Count: 827 
• Deposited Residue Count: 939 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphor inositol 3 kinase	A	939	Mus musculus	Mutation(s): 0  EC: 2.7.1.137 (UniProt), 2.7.1.153 (UniProt)
UniProt
Find proteins for O35904 (Mus musculus) Explore O35904  Go to UniProtKB:  O35904

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
E78	B [auth A]	~{N}-[5-[2-[(1~{S})-1-cyclopropylethyl]-7-methyl-1-oxidanylidene-3~{H}-isoindol-5-yl]-4-methyl-1,3-thiazol-2-yl]ethanamide C20 H23 N3 O2 S CNCRCDLWUGCPSJ-LBPRGKRZSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
E78	BindingDB:  6FTN	IC50: min: 200, max: 1780 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.272 (Depositor), 0.279 (DCC) 
• R-Value Work:  0.248 (Depositor), 0.251 (DCC) 
• R-Value Observed: 0.249 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 141.227	α = 90
b = 65.012	β = 103.38
c = 116.341	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-06-20 
Deposition Author(s): Petersen, J.

Revision History  

• Version 1.0: 2018-06-20
  Type: Initial release
  
• Version 1.1: 2018-07-11
  Changes: Data collection, Database references
• Version 1.2: 2024-05-01
  Changes: Data collection, Database references, Refinement description