8V2F

Crystal structure of IRAK4 kinase domain with compound 9

• PDB DOI: https://doi.org/10.2210/pdb8V2F/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens
• Expression System: Trichoplusia ni
• Mutation(s): No 


• Deposited: 2023-11-22 Released: 2024-07-03 
• Deposition Author(s): Weiss, M.M., Zheng, X., Browne, C.M., Campbell, V., Chen, D., Enerson, B., Fei, X., Huang, X., Klaus, C.R., Li, H., Mayo, M., McDonald, A.A., Paul, A., Sharma, K., Shi, Y., Slavin, A., Walter, D.M., Yuan, K., Zhang, Y., Zhu, X., Kelleher, J., Ji, N., Walker, D., Mainolfi, N.
• Funding Organization(s): Other private

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.09 Å
• R-Value Free: 0.208 
• R-Value Work: 0.168 
• R-Value Observed: 0.170 

Literature

Discovery of KT-413, a Targeted Protein Degrader of IRAK4 and IMiD Substrates Targeting MYD88 Mutant Diffuse Large B-Cell Lymphoma

Weiss, M.M., Zheng, X., Ji, N., Browne, C.M., Campbell, V., Chen, D., Enerson, B., Fei, X., Huang, X., Klaus, C.R., Li, H., Mayo, M., McDonald, A.A., Paul, A., Rong, H., Sharma, K., Shi, Y., Slavin, A., Walther, D.M., Yuan, K., Zhang, Y., Zhu, X., Kelleher, J., Walker, D., Mainolfi, N.

(2024) J Med Chem 

• DOI: https://doi.org/10.1021/acs.jmedchem.3c01823

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.

Biological Assembly 3  

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

Biological assembly 3 assigned by authors.

Biological Assembly 4  

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

Biological assembly 4 assigned by authors.

Macromolecule Content

• Total Structure Weight: 151.37 kDa 
• Atom Count: 10,225 
• Modelled Residue Count: 1,191 
• Deposited Residue Count: 1,308 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Interleukin-1 receptor-associated kinase 4	A, B, C, D	327	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 GTEx:  ENSG00000198001

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
YJU (Subject of Investigation/LOI)	E [auth A], I [auth B], M [auth C], P [auth D]	N-{2-[(1r,4r)-4-(hydroxymethyl)cyclohexyl]-6-(2-hydroxypropan-2-yl)-2H-indazol-5-yl}-6-(trifluoromethyl)pyridine-2-carboxamide C24 H27 F3 N4 O3 JQMIRXOVVPAXPB-KOMQPUFPSA-N
GOL	G [auth A], H [auth A], K [auth B], L [auth B], O [auth C], Q [auth D]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL	F [auth A], J [auth B], N [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.09 Å
• R-Value Free: 0.208 
• R-Value Work: 0.168 
• R-Value Observed: 0.170 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 142.87	α = 90
b = 140.68	β = 124
c = 89.02	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
REFMAC	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-07-03 
Deposition Author(s): Weiss, M.M., Zheng, X., Browne, C.M., Campbell, V., Chen, D., Enerson, B., Fei, X., Huang, X., Klaus, C.R., Li, H., Mayo, M., McDonald, A.A., Paul, A., Sharma, K., Shi, Y., Slavin, A., Walter, D.M., Yuan, K., Zhang, Y., Zhu, X., Kelleher, J., Ji, N., Walker, D., Mainolfi, N.

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Funding Organization	Location	Grant Number
Other private	United States	--

Revision History  

• Version 1.0: 2024-07-03
  Type: Initial release