6RFJ

IRAK4 IN COMPLEX WITH inhibitor

• PDB DOI:  https://doi.org/10.2210/pdb6RFJ/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2019-04-15 Released: 2019-10-30 
• Deposition Author(s): Xue, Y., Degorce, S.L., Robb, G.R., Ferguson, A.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.61 Å
• R-Value Free: 0.254 
• R-Value Work: 0.245 
• R-Value Observed: 0.245 

Literature

Discovery of a Series of 5-Azaquinazolines as Orally Efficacious IRAK4 Inhibitors Targeting MyD88L265PMutant Diffuse Large B Cell Lymphoma.

Degorce, S.L., Anjum, R., Bloecher, A., Carbajo, R.J., Dillman, K.S., Drew, L., Halsall, C.T., Lenz, E.M., Lindsay, N.A., Mayo, M.F., Pink, J.H., Robb, G.R., Rosen, A., Scott, J.S., Xue, Y.

(2019) J Med Chem 62: 9918-9930

• PubMed: 31622099 
• DOI: https://doi.org/10.1021/acs.jmedchem.9b01346
• Primary Citation of Related Structures:  
  6RFI, 6RFJ


• PubMed Abstract: 
  

In this article, we report the discovery of a series of 5-azaquinazolines as selective IRAK4 inhibitors. From modestly potent quinazoline 4 , we introduced a 5-aza substitution to mask the 4-NH hydrogen bond donor (HBD). This allowed us to substitute the core with a 2-aminopyrazole, which showed large gains in cellular potency despite the additional formal HBD. Further optimization led to 6-cyanomethyl-5-azaquinazoline 13 , a selective IRAK4 inhibitor, which proved efficacious in combination with ibrutinib, while showing very little activity as a single agent up to 100 mg/kg. This contrasted to previously reported IRAK4 inhibitors that exhibited efficacy in the same model as single agents and was attributed to the enhanced specificity of 13 toward IRAK4.

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Organizational Affiliation: 

Discovery Sciences, R&D , AstraZeneca , Gothenburg SE-431 83 , Mölndal , Sweden.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 74.16 kDa 
• Atom Count: 4,450 
• Modelled Residue Count: 547 
• Deposited Residue Count: 644 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Interleukin-1 receptor-associated kinase 4	A, B	322	Homo sapiens	Mutation(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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
K1E	C [auth A], E [auth B]	methyl 4-[4-[[6-(cyanomethyl)-2-[(1-methylpyrazol-4-yl)amino]pyrido[3,2-d]pyrimidin-4-yl]amino]cyclohexyl]piperazine-1-carboxylate C25 H32 N10 O2 RPGMSHCJIWHISY-IRJFHVNHSA-N
SO4	D [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SEP	A, B	L-PEPTIDE LINKING	C3 H8 N O6 P		SER
TPO	A, B	L-PEPTIDE LINKING	C4 H10 N O6 P		THR

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.61 Å
• R-Value Free: 0.254 
• R-Value Work: 0.245 
• R-Value Observed: 0.245 
• Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 87.607	α = 90
b = 118.925	β = 90
c = 140.507	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
Aimless	data scaling
BUSTER	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-10-30 
Deposition Author(s): Xue, Y., Degorce, S.L., Robb, G.R., Ferguson, A.D.

Revision History  

• Version 1.0: 2019-10-30
  Type: Initial release
  
• Version 1.1: 2019-11-27
  Changes: Database references