4URK | pdb_00004urk

PI3Kg in complex with AZD6482

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 
    0.309 (Depositor), 0.305 (DCC) 
  • R-Value Work: 
    0.250 (Depositor), 0.243 (DCC) 
  • R-Value Observed: 
    0.254 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history. 

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

  • DOI: https://doi.org/10.1016/j.bmcl.2014.07.007
  • Primary Citation 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: fgiordanetto@tarosdiscovery.com.

Macromolecule Content 

  • Total Structure Weight: 111.14 kDa 
  • Atom Count: 6,823 
  • Modeled Residue Count: 837 
  • Deposited Residue Count: 966 
  • Unique protein chains: 1

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
PHOSPHATIDYLINOSITOL 4,5-BISPHOSPHATE 3-KINASE CATALYTIC SUBUNIT GAMMA ISOFORM966Homo sapiensMutation(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 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP48736
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A82

Query on A82


Download:Ideal Coordinates CCD File
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 
IDSourceBinding 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), 0.305 (DCC) 
  • R-Value Work:  0.250 (Depositor), 0.243 (DCC) 
  • R-Value Observed: 0.254 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 143.179α = 90
b = 67.521β = 95.71
c = 106.167γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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