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 
  • R-Value Observed: 0.218 

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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: https://doi.org/10.1021/acs.jmedchem.7b01290
  • Primary Citation of Related Structures:  
    5K72, 5K75, 5K76, 5K7G, 5K7I

  • 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 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) ...

    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
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Interleukin-1 receptor-associated kinase 4
A, B
301Homo sapiensMutation(s): 0 
Gene Names: IRAK4
EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NWZ3 (Homo sapiens)
Explore Q9NWZ3 
Go to UniProtKB:  Q9NWZ3
PHAROS:  Q9NWZ3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9NWZ3
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
6R1
Query on 6R1
Download Ideal Coordinates CCD File 
C [auth A],
D [auth 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
Binding Affinity Annotations 
IDSourceBinding Affinity
6R1 BindingDB:  5K76 Kd: 0.7 (nM) from 1 assay(s)
IC50: min: 4, max: 52 (nM) from 4 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.74 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.218 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 88.051α = 90
b = 127.099β = 90
c = 142.078γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata 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: 2017-12-06
    Type: Initial release
  • Version 1.1: 2018-01-10
    Changes: Database references