4URK

PI3Kg in complex with AZD6482

• PDB DOI: https://doi.org/10.2210/pdb4URK/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2014-06-30 Released: 2014-10-22 
• Deposition Author(s): Giordanetto, F., Barlaam, B., Berglund, S., Edman, K., Karlsson, O., Lindberg, J., Nylander, S., Inghardt, T.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 
  0.309 (Depositor), 0.310 (DCC) 
• R-Value Work: 
  0.250 (Depositor), 0.240 (DCC) 
• R-Value Observed: 
  0.254 (Depositor) 

Starting Model: experimental

Literature

Discovery of 9-(1-Phenoxyethyl)-2-Morpholino-4-Oxo-Pyrido[1, 2-A]Pyrimidine-7-Carboxamides as Oral Pi3Kbeta Inhibitors, Useful as Antiplatelet Agents.

Giordanetto, F., Barlaam, B., Berglund, S., Edman, K., Karlsson, O., Lindberg, J., Nylander, S., Inghardt, T.

(2014) Bioorg Med Chem Lett 24: 3936

• PubMed: 25042253 
• DOI: https://doi.org/10.1016/j.bmcl.2014.07.007
• Primary Citation of Related Structures:  
  4URK


• PubMed Abstract: 
  

  Optimization of AZD6482 (2), the first antiplatelet PI3Kβ inhibitor evaluated in man, focused on improving the pharmacokinetic profile to a level compatible with once daily oral dosing as well as achieving adequate selectivity towards PI3Kα to minimize the risk for insulin resistance. Structure-based design and optimization of DMPK properties resulted in (R)-16, a novel, orally bioavailable PI3Kβ inhibitor with potent in vivo anti-thrombotic effect with excellent separation to bleeding risk and insulin resistance.

---

Organizational Affiliation: 

Medicinal Chemistry, AstraZeneca R&D, CVMD iMed, Mölndal, Pepparedsleden 1, SE-431 83 Mölndal, Sweden. Electronic address: [e-mail].

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: 111.14 kDa 
• Atom Count: 6,823 
• Modelled Residue Count: 837 
• 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): 0  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
A82	B [auth A]	2-[[(1R)-1-(7-methyl-2-morpholin-4-yl-4-oxidanylidene-pyrido[1,2-a]pyrimidin-9-yl)ethyl]amino]benzoic acid C22 H24 N4 O4 IRTDIKMSKMREGO-OAHLLOKOSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
A82	BindingDB:  4URK	IC50: min: 870, max: 1090 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free:  0.309 (Depositor), 0.310 (DCC) 
• R-Value Work:  0.250 (Depositor), 0.240 (DCC) 
• R-Value Observed: 0.254 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 143.179	α = 90
b = 67.521	β = 95.71
c = 106.167	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: 2014-10-22 
Deposition Author(s): Giordanetto, F., Barlaam, B., Berglund, S., Edman, K., Karlsson, O., Lindberg, J., Nylander, S., Inghardt, T.

Revision History  

• Version 1.0: 2014-10-22
  Type: Initial release
  
• Version 1.1: 2024-01-10
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description