5K75

IRAK4 in complex with Compound 1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.03 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.239 
  • R-Value Observed: 0.240 

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:  
    5K72, 5K76, 5K75, 5K7I, 5K7G

  • 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

    Pharmaceutical Sciences, IMED Biotech Unit, AstraZeneca , Boston, Massachusetts 02451, United States.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Interleukin-1 receptor-associated kinase 4ABCD301Homo sapiensMutation(s): 0 
Gene Names: IRAK4
EC: 2.7.11.1
Find proteins for Q9NWZ3 (Homo sapiens)
Explore Q9NWZ3 
Go to UniProtKB:  Q9NWZ3
NIH Common Fund Data Resources
PHAROS  Q9NWZ3
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
6QX
Query on 6QX

Download CCD File 
A, B, C, D
~{N}1-(7,8-dihydro-6~{H}-cyclopenta[2,3]thieno[2,4-~{c}]pyrimidin-1-yl)-~{N}4,~{N}4-dimethyl-cyclohexane-1,4-diamine
C17 H24 N4 S
URDBLCLSFRUNRD-HAQNSBGRSA-N
 Ligand Interaction
SO4
Query on SO4

Download CCD File 
B, C, D
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
SEP
Query on SEP
A,B,C,DL-PEPTIDE LINKINGC3 H8 N O6 PSER
TPO
Query on TPO
A,B,C,DL-PEPTIDE LINKINGC4 H10 N O6 PTHR
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
6QXIC50:  140   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.03 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.239 
  • R-Value Observed: 0.240 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 144.87α = 90
b = 141.62β = 125.92
c = 88.06γ = 90
Software Package:
Software NamePurpose
BUSTER-TNTrefinement
Aimlessdata scaling
MOLREPphasing
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

View Full Validation Report



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
    Changes: Database references