9R9K: IRAK4

IRAK4 in complex with inhibitor. Determined by X-ray diffraction at 1.87 Å resolution. Released 1 Oct 2025.

Method: X-ray diffraction
Resolution: 1.87 Å
Organism: Homo sapiens
Chains: 4
Atoms: 9,831
Mol. weight: 140.22 kDa
Ligands: A1JDQ
Released: 1 Oct 2025

Explore 9R9K in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9R9K contains 83 α-helices and 70 β-strands across 4 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 21 helices, 17 β-strands

Element	Residues	Length	Sheet
α-helix	165	1
β-strand	166-167	2	1
α-helix	168-169	2
α-helix	170-176	7
β-strand	184	1	1
α-helix	185-187	3
β-strand	191-194	4	1
β-strand	198-205	8	1
β-strand	208-215	8	1
α-helix	224-239	16
β-strand	245	1	2
α-helix	246-247	2
β-strand	248-252	5	1
β-strand	259-263	5	1
β-strand	269	1	2
α-helix	270-274	5
α-helix	277-279	3
α-helix	280-284	5
α-helix	285-304	20
β-strand	308	1	3
α-helix	314-316	3
β-strand	317-319	3	2
β-strand	325-327	3	2
β-strand	334	1	3
β-strand	344	1	4
α-helix	352-354	3
α-helix	357-360	4
β-strand	363	1	4
α-helix	366-382	17
β-strand	387	1	5
β-strand	395	1	5
α-helix	396-398	3
α-helix	399-404	6
α-helix	410-413	4
α-helix	423-436	14
α-helix	441-443	3
α-helix	445-446	2
α-helix	447-458	12

Chain B: 21 helices, 18 β-strands

Element	Residues	Length	Sheet
α-helix	159-161	3
α-helix	165	1
β-strand	166-167	2	6
α-helix	170-176	7
β-strand	184	1	6
α-helix	185-187	3
β-strand	191-195	5	6
β-strand	198-205	8	6
β-strand	208-215	8	6
α-helix	224-239	16
β-strand	245	1	7
α-helix	246-247	2
β-strand	248-252	5	6
β-strand	258-263	6	6
β-strand	269	1	7
α-helix	270-275	6
α-helix	277-279	3
α-helix	280-284	5
α-helix	285-304	20
β-strand	308	1	8
α-helix	314-316	3
β-strand	317-319	3	7
β-strand	325-327	3	7
β-strand	334	1	8
β-strand	344	1	9
α-helix	352-354	3
α-helix	357-360	4
β-strand	363	1	9
α-helix	366-382	17
β-strand	387	1	10
β-strand	391	1	11
β-strand	395	1	10
α-helix	396-398	3
α-helix	399-404	6
α-helix	410-413	4
α-helix	423-436	14
α-helix	441-443	3
α-helix	445-446	2
α-helix	447-458	12

Chain C: 21 helices, 18 β-strands

Element	Residues	Length	Sheet
α-helix	165	1
β-strand	166-167	2	12
α-helix	168-169	2
α-helix	170-176	7
β-strand	184	1	12
α-helix	185-187	3
β-strand	191-194	4	12
β-strand	198-205	8	12
β-strand	208-215	8	12
α-helix	223-239	17
β-strand	245	1	13
α-helix	246-247	2
β-strand	248-252	5	12
β-strand	259-263	5	12
β-strand	269	1	13
α-helix	270-275	6
α-helix	277-279	3
α-helix	280-284	5
α-helix	285-304	20
β-strand	308	1	14
α-helix	314-316	3
β-strand	317-319	3	13
β-strand	325-327	3	13
β-strand	334	1	14
β-strand	344	1	15
α-helix	352-354	3
α-helix	357-360	4
β-strand	363	1	15
α-helix	366-382	17
β-strand	387	1	16
β-strand	391	1	11
β-strand	395	1	16
α-helix	396-398	3
α-helix	399-404	6
α-helix	410-413	4
α-helix	423-436	14
α-helix	441-443	3
α-helix	445-446	2
α-helix	447-458	12

Chain D: 20 helices, 17 β-strands

Element	Residues	Length	Sheet
α-helix	165	1
β-strand	166-167	2	17
α-helix	170-176	7
β-strand	184	1	17
α-helix	185-187	3
β-strand	191-194	4	17
β-strand	198-205	8	17
β-strand	208-215	8	17
α-helix	223-239	17
β-strand	245	1	18
α-helix	246-247	2
β-strand	248-252	5	17
β-strand	259-263	5	17
β-strand	269	1	18
α-helix	270-275	6
α-helix	277-279	3
α-helix	280-284	5
α-helix	285-304	20
β-strand	308	1	19
α-helix	314-316	3
β-strand	317-319	3	18
β-strand	325-327	3	18
β-strand	334	1	19
β-strand	344	1	20
α-helix	352-354	3
α-helix	357-360	4
β-strand	363	1	20
α-helix	366-382	17
β-strand	387	1	21
β-strand	395	1	21
α-helix	396-398	3
α-helix	399-404	6
α-helix	410-413	4
α-helix	423-436	14
α-helix	441-443	3
α-helix	445-446	2
α-helix	447-458	12

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Interleukin-1 receptor-associated kinase 4	A, B, C, D	protein	308	Homo sapiens	Q9NWZ3 (AlphaFold model)

Sequence of entity 1 (A, B, C, D), FASTA

>9R9K_1 Interleukin-1 receptor-associated kinase 4 (chains A, B, C, D)
GENKSLEVSDTRFHSFSFYELKNVTNNFDERPISVGGNKMGEGGFGVVYKGYVNNTTVAV
KKLAAMVDITTEELKQQFDQEIKVMAKCQHENLVELLGFSSDGDDLCLVYVYMPNGSLLD
RLSCLDGTPPLSWHMRCKIAQGAANGINFLHENHHIHRDIKSANILLDEAFTAKISDFGL
ARASEKFAQTVMTSRIVGTTAYMAPEALRGEITPKSDIYSFGVVLLEIITGLPAVDEHRE
PQLLLDIKEEIEDEEKTIEDYIDKKMNDADSTSVEAMYSVASQCLHEKKNKRPDIKKVQQ
LLQEMTAS

Ligands and cofactors

ID	Name	Formula	Copies
A1JDQ	~{N}-[3-aminocarbonyl-1-(oxan-4-yl)pyrazol-4-yl]-2-(2-methylpyridin-4-yl)-1,3-o…	C19 H20 N6 O4	4

Water and common crystallization additives (SO4) are not listed.

Primary citation

Generation of a potent & selective series of IRAK4 inhibitors based on a structure based, hybridization approach. Terstiege, I., Aagaard, A., Berggren, K. et al. Bioorg Med Chem (2025) 131:118333-118333. DOI 10.1016/j.bmc.2025.118333 · PubMed

Other PDB entries of the same protein (UniProt Q9NWZ3 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6EGE 1.4 Å, Crystal structure of the unphosphorylated IRAK4 kinase domain Bound to a type I inhibitor
9NA5 1.73 Å, IRAK4 in Complex with Compound 24
6UYA 1.74 Å, Crystal structure of Compound 19 bound to IRAK4
8W3X 1.76 Å, Crystal structure of IRAK4 in complex with compound 6
6O95 1.77 Å, Structure of the IRAK4 kinase domain with compound 41
6O8U 1.8 Å, Crystal structure of IRAK4 in complex with compound 23
8UCC 1.8 Å, IRAK4 in complex with compound 20
5UIT 1.84 Å, Crystal structure of IRAK4 in complex with compound 14
8UCB 1.85 Å, IRAK4 in complex with compound 8
9R9G 1.88 Å, IRAK4 in complex with inhibitor
8SCE 1.89 Å, Crystal structure of IRAK4-HSA complexed with N-[(2R)-2-FLUORO-3-HYDROXY-3-METHYLBUTYL]-6…
9PSS 1.93 Å, IRAK4 in Complex with Compound 3

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