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 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 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: 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). 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 , Cambridge CB4 0FZ, United Kingdom.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Interleukin-1 receptor-associated kinase 4
A, B, C, D
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
GTEx:  ENSG00000198001 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9NWZ3
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
6QX
Query on 6QX

Download Ideal Coordinates CCD File 
E [auth A],
I [auth B],
L [auth C],
O [auth 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
SO4
Query on SO4

Download Ideal Coordinates CCD File 
F [auth B]
G [auth B]
H [auth B]
J [auth C]
K [auth C]
F [auth B],
G [auth B],
H [auth B],
J [auth C],
K [auth C],
M [auth D],
N [auth D]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Modified Residues  2 Unique
IDChains TypeFormula2D DiagramParent
SEP
Query on SEP
A, B, C, D
L-PEPTIDE LINKINGC3 H8 N O6 PSER
TPO
Query on TPO
A, B, C, D
L-PEPTIDE LINKINGC4 H10 N O6 PTHR
Binding Affinity Annotations 
IDSourceBinding Affinity
6QX BindingDB:  5K75 Ki: 50 (nM) from 1 assay(s)
IC50: min: 140, max: 490 (nM) from 2 assay(s)
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



Ligand Structure Quality Assessment 


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
  • Version 1.2: 2023-09-27
    Changes: Data collection, Database references, Refinement description
  • Version 1.3: 2024-10-09
    Changes: Structure summary