5K76

IRAK4 in complex with Compound 28


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.74 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.217 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Discovery and Optimization of Pyrrolopyrimidine Inhibitors of Interleukin-1 Receptor Associated Kinase 4 (IRAK4) for the Treatment of Mutant MYD88L265P Diffuse Large B-Cell Lymphoma.

Scott, J.S.Degorce, S.L.Anjum, R.Culshaw, J.Davies, R.D.M.Davies, N.L.Dillman, K.S.Dowling, J.E.Drew, L.Ferguson, A.D.Groombridge, S.D.Halsall, C.T.Hudson, J.A.Lamont, S.Lindsay, N.A.Marden, S.K.Mayo, M.F.Pease, J.E.Perkins, D.R.Pink, J.H.Robb, G.R.Rosen, A.Shen, M.McWhirter, C.Wu, D.

(2017) J. Med. Chem. 60: 10071-10091

  • DOI: 10.1021/acs.jmedchem.7b01290
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Herein we report the optimization of a series of pyrrolopyrimidine inhibitors of interleukin-1 receptor associated kinase 4 (IRAK4) using X-ray crystal structures and structure based design to identify and optimize our scaffold. Compound 28 demonstra ...

    Herein we report the optimization of a series of pyrrolopyrimidine inhibitors of interleukin-1 receptor associated kinase 4 (IRAK4) using X-ray crystal structures and structure based design to identify and optimize our scaffold. Compound 28 demonstrated a favorable physicochemical and kinase selectivity profile and was identified as a promising in vivo tool with which to explore the role of IRAK4 inhibition in the treatment of mutant MYD88 L265P diffuse large B-cell lymphoma (DLBCL). Compound 28 was shown to be capable of demonstrating inhibition of NF-κB activation and growth of the ABC subtype of DLBCL cell lines in vitro at high concentrations but showed greater effects in combination with a BTK inhibitor at lower concentrations. In vivo, the combination of compound 28 and ibrutinib led to tumor regression in an ABC-DLBCL mouse model.


    Organizational Affiliation

    Oncology, IMED Biotech Unit, AstraZeneca , Macclesfield SK10 4TG, United Kingdom.,Pharmaceutical Sciences, IMED Biotech Unit, AstraZeneca , Boston, Massachusetts 02451, United States.,Oncology, IMED Biotech Unit, AstraZeneca , Boston, Massachusetts 02451, United States.,Oncology, IMED Biotech Unit, AstraZeneca , Cambridge CB4 0FZ, United Kingdom.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Interleukin-1 receptor-associated kinase 4
A, B
301Homo sapiensMutation(s): 0 
Gene Names: IRAK4
EC: 2.7.11.1
Find proteins for Q9NWZ3 (Homo sapiens)
Go to Gene View: IRAK4
Go to UniProtKB:  Q9NWZ3
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
6R1
Query on 6R1

Download SDF File 
Download CCD File 
A, B
~{N}-(4-morpholin-4-ylcyclohexyl)-5-(oxan-4-yl)-7~{H}-pyrrolo[2,3-d]pyrimidin-4-amine
C21 H31 N5 O2
DJVYXMINSBMUHH-QAQDUYKDSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
SEP
Query on SEP
A, B
L-PEPTIDE LINKINGC3 H8 N O6 PSER
TPO
Query on TPO
A, B
L-PEPTIDE LINKINGC4 H10 N O6 PTHR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.74 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.217 
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 88.051α = 90.00
b = 127.099β = 90.00
c = 142.078γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
XDSdata reduction
BUSTERrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2016-05-25 
  • Released Date: 2017-12-06 
  • Deposition Author(s): Ferguson, A.D.

Revision History 

  • Version 1.0: 2017-12-06
    Type: Initial release
  • Version 1.1: 2018-01-10
    Type: Database references