5T2D | pdb_00005t2d

mPI3Kd IN COMPLEX WITH 7j

• PDB DOI: https://doi.org/10.2210/pdb5T2D/pdb

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


• Deposited: 2016-08-23 Released: 2017-04-19 
• Deposition Author(s): Petersen, J., Terstige, I., Perry, M., Svensson, T., Tyrchan, C., Lindmark, H., Oster, L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 
  0.287 (Depositor), 0.290 (DCC) 
• R-Value Work: 
  0.223 (Depositor), 0.230 (DCC) 
• R-Value Observed: 
  0.226 (Depositor) 

Literature

Discovery of triazole aminopyrazines as a highly potent and selective series of PI3K delta inhibitors.

Terstiege, I., Perry, M., Petersen, J., Tyrchan, C., Svensson, T., Lindmark, H., Oster, L.

(2017) Bioorg Med Chem Lett 27: 679-687

• PubMed: 28017532 
• DOI: https://doi.org/10.1016/j.bmcl.2016.11.004
• Primary Citation of Related Structures:  
  5T23, 5T27, 5T28, 5T2B, 5T2D, 5T2G, 5T2I, 5T2L, 5T2M


• PubMed Abstract: 
  

  A novel class of potent PI3Kδ inhibitors with >1000-fold selectivity against other class I PI3K isoforms is described. Optimization of the substituents on a triazole aminopyrazine scaffold, emerging from an in-house PI3Kα program, turned moderately selective PI3Kδ compounds into highly potent and selective PI3Kδ inhibitors. These efforts resulted in a series of aminopyrazines with PI3Kδ IC ₅₀ ⩽1nM in the enzyme assay, some of the most selective PI3Kδ inhibitors published to date, with a cell potency in a JeKo-cell assay of 20-120nM.

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Organizational Affiliation: 

Respiratory, Inflammation & Autoimmunity, Innovative Medicines and Early Development Biotech Unit, AstraZeneca, Pepparedsleden 1, Mölndal, 43183, Sweden. Electronic address: [e-mail].

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 108.23 kDa 
• Atom Count: 6,657 
• Modelled Residue Count: 820 
• Deposited Residue Count: 939 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit delta isoform	A	939	Mus musculus	Mutation(s): 0  Gene Names: Pik3cd EC: 2.7.1.153 (PDB Primary Data), 2.7.1.137 (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
74L	B [auth A]	4-[3-azanyl-6-[1-methyl-5-(1-phenylcyclopropyl)-1,2,4-triazol-3-yl]pyrazin-2-yl]-~{N},~{N}-dimethyl-pyrazole-1-sulfonamide C21 H23 N9 O2 S GMLLOWVABPADNX-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
74L	BindingDB:  5T2D	IC50: min: 0.79, max: 90 (nM) from 3 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free:  0.287 (Depositor), 0.290 (DCC) 
• R-Value Work:  0.223 (Depositor), 0.230 (DCC) 
• R-Value Observed: 0.226 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.916	α = 90
b = 142.418	β = 90
c = 220.671	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-04-19 
Deposition Author(s): Petersen, J., Terstige, I., Perry, M., Svensson, T., Tyrchan, C., Lindmark, H., Oster, L.

Revision History  

• Version 1.0: 2017-04-19
  Type: Initial release
  
• Version 1.1: 2024-05-08
  Changes: Data collection, Database references