7Z61 | pdb_00007z61

Crystal structure of PI3Kgamma with a dihydropurinone inhibitor (compound 18)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.74 Å
  • R-Value Free: 
    0.276 (Depositor), 0.280 (DCC) 
  • R-Value Work: 
    0.217 (Depositor), 0.216 (DCC) 
  • R-Value Observed: 
    0.220 (Depositor) 

Starting Model: other
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Optimization of hERG and Pharmacokinetic Properties for Basic Dihydro-8 H -purin-8-one Inhibitors of DNA-PK.

Goldberg, F.W.Ting, A.K.T.Beattie, D.Lamont, G.M.Fallan, C.Finlay, M.R.V.Williamson, B.Schimpl, M.Harmer, A.R.Adeyemi, O.B.Nordell, P.Cronin, A.S.Vazquez-Chantada, M.Barratt, D.Ramos-Montoya, A.Cadogan, E.B.Davies, B.R.

(2022) ACS Med Chem Lett 13: 1295-1301

  • DOI: https://doi.org/10.1021/acsmedchemlett.2c00172
  • Primary Citation Related Structures: 
    7Z61

  • PubMed Abstract: 

    The DNA-PK complex is activated by double-strand DNA breaks and regulates the non-homologous end-joining repair pathway; thus, targeting DNA-PK by inhibiting the DNA-PK catalytic subunit (DNA-PKcs) is potentially a useful therapeutic approach for oncology. A previously reported series of neutral DNA-PKcs inhibitors were modified to incorporate a basic group, with the rationale that increasing the volume of distribution while maintaining good metabolic stability should increase the half-life. However, adding a basic group introduced hERG activity, and basic compounds with modest hERG activity (IC 50 = 10-15 μM) prolonged QTc (time from the start of the Q wave to the end of the T wave, corrected by heart rate) in an anaesthetized guinea pig cardiovascular model. Further optimization was necessary, including modulation of p K a , to identify compound 18 , which combines low hERG activity (IC 50 = 75 μM) with excellent kinome selectivity and favorable pharmacokinetic properties.


  • Organizational Affiliation
    • Oncology R&D, AstraZeneca, Cambridge CB2 0AA, U.K.

Macromolecule Content 

  • Total Structure Weight: 111.12 kDa 
  • Atom Count: 6,778 
  • Modeled Residue Count: 834 
  • Deposited Residue Count: 966 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform966Homo sapiensMutation(s): 0 
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 
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
IGJ
(Subject of Investigation/LOI)

Query on IGJ



Download:Ideal Coordinates CCD File
B [auth A]9-[(3~{R},4~{R})-4-fluoranylpyrrolidin-3-yl]-7-methyl-2-[(7-methylquinolin-6-yl)amino]purin-8-one
C20 H20 F N7 O
VHGGSMHLKWIQAF-CZUORRHYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
IGJ BindingDB:  7Z61 IC50: 4800 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.74 Å
  • R-Value Free:  0.276 (Depositor), 0.280 (DCC) 
  • R-Value Work:  0.217 (Depositor), 0.216 (DCC) 
  • R-Value Observed: 0.220 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 142.894α = 90
b = 67.95β = 95.92
c = 107.464γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
AMoREphasing
BUSTERrefinement
PDB_EXTRACTdata extraction
DIALSdata reduction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not fundedUnited Kingdom--

Revision History  (Full details and data files)

  • Version 1.0: 2022-07-13
    Type: Initial release
  • Version 1.1: 2022-08-31
    Changes: Database references
  • Version 1.2: 2024-05-01
    Changes: Data collection, Refinement description