8ATB

Discovery of IRAK4 Inhibitor 16

• PDB DOI: https://doi.org/10.2210/pdb8ATB/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): Yes 


• Deposited: 2022-08-22 Released: 2023-11-29 
• Deposition Author(s): Schafer, M., Bothe, U., Schmidt, N., Gunther, J., Nubbemeyer, R., Siebeneicher, H., Ring, S., Boemer, U., Peters, M., Denner, K., Himmel, H., Sutter, A., Terebesi, I., Lange, M., Wenger, A.M., Guimond, N., Thaler, T., Platzek, J., Eberspaecher, U., Steuber, H., Steinmeyer, A., Zollner, T.M.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 0.260 
• R-Value Work: 0.212 

Literature

Discovery of IRAK4 Inhibitors BAY1834845 (Zabedosertib) and BAY1830839 .

Bothe, U., Gunther, J., Nubbemeyer, R., Siebeneicher, H., Ring, S., Bomer, U., Peters, M., Rausch, A., Denner, K., Himmel, H., Sutter, A., Terebesi, I., Lange, M., Wengner, A.M., Guimond, N., Thaler, T., Platzek, J., Eberspacher, U., Schafer, M., Steuber, H., Zollner, T.M., Steinmeyer, A., Schmidt, N.

(2024) J Med Chem 67: 1225-1242

• PubMed: 38228402 
• DOI: https://doi.org/10.1021/acs.jmedchem.3c01714
• Primary Citation of Related Structures:  
  8ATB, 8ATL, 8ATN, 8BR5, 8BR6, 8BR7


• PubMed Abstract: 
  

  Interleukin-1 receptor-associated kinase 4 (IRAK4) plays a critical role in innate inflammatory processes. Here, we describe the discovery of two clinical candidate IRAK4 inhibitors, BAY1834845 (zabedosertib) and BAY1830839 , starting from a high-throughput screening hit derived from Bayer's compound library. By exploiting binding site features distinct to IRAK4 using an in-house docking model, liabilities of the original hit could surprisingly be overcome to confer both candidates with a unique combination of good potency and selectivity. Favorable DMPK profiles and activity in animal inflammation models led to the selection of these two compounds for clinical development in patients.

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Organizational Affiliation: 

Bayer AG, Research & Development, Pharmaceuticals, 13353 Berlin, Germany.

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: 67.71 kDa 
• Atom Count: 4,594 
• Modelled Residue Count: 562 
• Deposited Residue Count: 596 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Interleukin-1 receptor-associated kinase 4	A [auth AAA], B [auth BBB]	298	Homo sapiens	Mutation(s): 3  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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
O0H (Subject of Investigation/LOI)	C [auth AAA], E [auth BBB]	~{N}-[6-ethoxy-2-[2-(4-methylpiperazin-1-yl)-2-oxidanylidene-ethyl]indazol-5-yl]-6-(trifluoromethyl)pyridine-2-carboxamide C23 H25 F3 N6 O3 AIMNCVIDWQOVPW-UHFFFAOYSA-N
GOL	D [auth AAA]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Modified Residues  3 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSO	A [auth AAA], B [auth BBB]	L-PEPTIDE LINKING	C3 H7 N O3 S		CYS
SEP	A [auth AAA], B [auth BBB]	L-PEPTIDE LINKING	C3 H8 N O6 P		SER
TPO	A [auth AAA], B [auth BBB]	L-PEPTIDE LINKING	C4 H10 N O6 P		THR

Binding Affinity Annotations
ID	Source	Binding Affinity
O0H	BindingDB:  8ATB	IC50: 5 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 0.260 
• R-Value Work: 0.212 
• Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 87.2	α = 90
b = 117.5	β = 90
c = 136.6	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-11-29 
Deposition Author(s): Schafer, M., Bothe, U., Schmidt, N., Gunther, J., Nubbemeyer, R., Siebeneicher, H., Ring, S., Boemer, U., Peters, M., Denner, K., Himmel, H., Sutter, A., Terebesi, I., Lange, M., Wenger, A.M., Guimond, N., Thaler, T., Platzek, J., Eberspaecher, U., Steuber, H., Steinmeyer, A., Zollner, T.M.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2023-11-29
  Type: Initial release
  
• Version 1.1: 2024-01-31
  Changes: Database references
• Version 1.2: 2024-02-07
  Changes: Database references
• Version 1.3: 2024-11-13
  Changes: Structure summary