6T2W

Crystal structure of the CSF1R kinase domain with a dihydropurinone inhibitor (compound 4)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.187 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.167 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

The Discovery of 7-Methyl-2-[(7-methyl[1,2,4]triazolo[1,5-a]pyridin-6-yl)amino]-9-(tetrahydro-2H-pyran-4-yl)-7,9-dihydro-8H-purin-8-one (AZD7648), a Potent and Selective DNA-Dependent Protein Kinase (DNA-PK) Inhibitor.

Goldberg, F.W.Finlay, M.R.V.Ting, A.K.T.Beattie, D.Lamont, G.M.Fallan, C.Wrigley, G.L.Schimpl, M.Howard, M.R.Williamson, B.Vazquez-Chantada, M.Barratt, D.G.Davies, B.R.Cadogan, E.B.Ramos-Montoya, A.Dean, E.

(2020) J Med Chem 63: 3461-3471

  • DOI: 10.1021/acs.jmedchem.9b01684
  • Primary Citation of Related Structures:  
    6T3B, 6T3C, 6T2W

  • PubMed Abstract: 
  • DNA-PK is a key component within the DNA damage response, as it is responsible for recognizing and repairing double-strand DNA breaks (DSBs) via non-homologous end joining. Historically it has been challenging to identify inhibitors of the DNA-PK catalytic subunit (DNA-PKcs) with good selectivity versus the structurally related PI3 (lipid) and PI3K-related protein kinases ...

    DNA-PK is a key component within the DNA damage response, as it is responsible for recognizing and repairing double-strand DNA breaks (DSBs) via non-homologous end joining. Historically it has been challenging to identify inhibitors of the DNA-PK catalytic subunit (DNA-PKcs) with good selectivity versus the structurally related PI3 (lipid) and PI3K-related protein kinases. We screened our corporate collection for DNA-PKcs inhibitors with good PI3 kinase selectivity, identifying compound 1 . Optimization focused on further improving selectivity while improving physical and pharmacokinetic properties, notably co-optimization of permeability and metabolic stability, to identify compound 16 (AZD7648). Compound 16 had no significant off-target activity in the protein kinome and only weak activity versus PI3Kα/γ lipid kinases. Monotherapy activity in murine xenograft models was observed, and regressions were observed when combined with inducers of DSBs (doxorubicin or irradiation) or PARP inhibition (olaparib). These data support progression into clinical studies (NCT03907969).


    Organizational Affiliation

    Oncology R&D, AstraZeneca, Cambridge CB4 0FZ, U.K.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Macrophage colony-stimulating factor 1 receptor A332Homo sapiensMutation(s): 0 
Gene Names: CSF1RFMS
EC: 2.7.10.1
Find proteins for P07333 (Homo sapiens)
Explore P07333 
Go to UniProtKB:  P07333
NIH Common Fund Data Resources
PHAROS:  P07333
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
M9T
Query on M9T

Download Ideal Coordinates CCD File 
A
2-[(4-methoxy-2-methyl-phenyl)amino]-7-methyl-9-(4-oxidanylcyclohexyl)purin-8-one
C20 H25 N5 O3
MFVOIPKDSOFMQO-HDJSIYSDSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
M9TIC50:  10   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.187 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.167 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.04α = 90
b = 81.04β = 90
c = 146γ = 120
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
BUSTERrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-01-01
    Type: Initial release
  • Version 1.1: 2020-01-22
    Changes: Database references
  • Version 1.2: 2020-04-22
    Changes: Database references