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- PDB-9pss: IRAK4 in Complex with Compound 3 -

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Basic information

Entry
Database: PDB / ID: 9pss
TitleIRAK4 in Complex with Compound 3
ComponentsInterleukin-1 receptor-associated kinase 4
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / Kinase / Phosphorylated / Signaling Protein / Inhibitor Complex / Immune System / TRANSFERASE / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


IRAK4 deficiency (TLR5) / MyD88 dependent cascade initiated on endosome / TRAF6 mediated induction of NFkB and MAP kinases upon TLR7/8 or 9 activation / MyD88 cascade initiated on plasma membrane / Toll signaling pathway / interleukin-33-mediated signaling pathway / neutrophil migration / toll-like receptor 9 signaling pathway / neutrophil mediated immunity / interleukin-1 receptor binding ...IRAK4 deficiency (TLR5) / MyD88 dependent cascade initiated on endosome / TRAF6 mediated induction of NFkB and MAP kinases upon TLR7/8 or 9 activation / MyD88 cascade initiated on plasma membrane / Toll signaling pathway / interleukin-33-mediated signaling pathway / neutrophil migration / toll-like receptor 9 signaling pathway / neutrophil mediated immunity / interleukin-1 receptor binding / interleukin-1-mediated signaling pathway / IRAK4 deficiency (TLR2/4) / MyD88:MAL(TIRAP) cascade initiated on plasma membrane / MyD88-dependent toll-like receptor signaling pathway / extrinsic component of plasma membrane / toll-like receptor 4 signaling pathway / toll-like receptor signaling pathway / JNK cascade / positive regulation of smooth muscle cell proliferation / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / lipopolysaccharide-mediated signaling pathway / cytokine-mediated signaling pathway / Interleukin-1 signaling / kinase activity / PIP3 activates AKT signaling / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / positive regulation of canonical NF-kappaB signal transduction / non-specific serine/threonine protein kinase / endosome membrane / intracellular signal transduction / innate immune response / protein serine kinase activity / protein serine/threonine kinase activity / protein kinase binding / magnesium ion binding / cell surface / extracellular space / ATP binding / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Interleukin-1 receptor-associated kinase 4 / IRAK4, Death domain / : / Death-like domain superfamily / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Serine/Threonine protein kinases, catalytic domain / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
: / Interleukin-1 receptor-associated kinase 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 Å
AuthorsFerrao, R.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Acs Med.Chem.Lett. / Year: 2026
Title: Examination of Noncanonical Kinase Hinge Binders Leads to Thiadiazoles as Potent IRAK4 Inhibitors.
Authors: Ammann, S.E. / Brizgys, G. / Ferrao, R.D. / Wright, N.E. / Mukherjee, P.K. / Bacon, E.M. / Chin, E. / Chou, C. / Cottell, J.J. / Hammond, A. / Ndukwe, M.S. / Park, G.Y. / Shatskikh, M.E. / ...Authors: Ammann, S.E. / Brizgys, G. / Ferrao, R.D. / Wright, N.E. / Mukherjee, P.K. / Bacon, E.M. / Chin, E. / Chou, C. / Cottell, J.J. / Hammond, A. / Ndukwe, M.S. / Park, G.Y. / Shatskikh, M.E. / Suekawa-Pirrone, K. / Warr, M.R. / Yang, Z.Y. / Zipfel, S.M. / Taylor, J.G.
History
DepositionJul 26, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 28, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Interleukin-1 receptor-associated kinase 4
B: Interleukin-1 receptor-associated kinase 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,5767
Polymers68,4312
Non-polymers1,1455
Water3,675204
1
A: Interleukin-1 receptor-associated kinase 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,8364
Polymers34,2161
Non-polymers6213
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Interleukin-1 receptor-associated kinase 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,7403
Polymers34,2161
Non-polymers5252
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)86.630, 109.420, 141.080
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Space group name HallI22
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: x+1/2,-y+1/2,-z+1/2
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-688-

HOH

21B-709-

HOH

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Components

#1: Protein Interleukin-1 receptor-associated kinase 4 / IRAK-4 / Renal carcinoma antigen NY-REN-64


Mass: 34215.516 Da / Num. of mol.: 2 / Fragment: kinase domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IRAK4 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q9NWZ3, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-A1CKP / (7P,8S)-7-{(5M)-5-[1-(oxan-4-yl)-1H-1,2,3-triazol-4-yl]-4-[(propan-2-yl)amino]pyridin-2-yl}pyrrolo[1,2-b]pyridazine-3-carbonitrile


Mass: 428.490 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H24N8O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 204 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.44 Å3/Da / Density % sol: 49.65 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: 100 mM sodium acetate, 2.0M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.97741 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 25, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97741 Å / Relative weight: 1
ReflectionResolution: 1.93→48.93 Å / Num. obs: 50246 / % possible obs: 99.61 % / Redundancy: 6.6 % / Biso Wilson estimate: 31.02 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.1049 / Rpim(I) all: 0.04424 / Rrim(I) all: 0.114 / Net I/σ(I): 11.2
Reflection shellResolution: 1.93→2 Å / Redundancy: 6.4 % / Rmerge(I) obs: 1.082 / Mean I/σ(I) obs: 1.78 / Num. unique obs: 4832 / CC1/2: 0.458 / CC star: 0.793 / Rpim(I) all: 0.4663 / Rrim(I) all: 1.196 / % possible all: 97.52

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Processing

Software
NameVersionClassification
PHENIX1.21_5207refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.93→48.93 Å / SU ML: 0.2964 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 35.0257
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2826 1997 3.98 %
Rwork0.247 48181 -
obs0.2485 50178 99.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 49.99 Å2
Refinement stepCycle: LAST / Resolution: 1.93→48.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4422 0 79 204 4705
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01254577
X-RAY DIFFRACTIONf_angle_d1.16886193
X-RAY DIFFRACTIONf_chiral_restr0.0649693
X-RAY DIFFRACTIONf_plane_restr0.0105785
X-RAY DIFFRACTIONf_dihedral_angle_d15.38621675
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.93-1.980.44571370.42963288X-RAY DIFFRACTION96.56
1.98-2.040.40881410.39383408X-RAY DIFFRACTION99.97
2.04-2.10.36231410.36043413X-RAY DIFFRACTION99.94
2.1-2.160.35561420.32173442X-RAY DIFFRACTION99.94
2.16-2.240.32291420.28633403X-RAY DIFFRACTION99.8
2.24-2.330.28231410.26433412X-RAY DIFFRACTION99.75
2.33-2.440.28981420.25113418X-RAY DIFFRACTION99.69
2.44-2.570.29411430.25863431X-RAY DIFFRACTION99.75
2.57-2.730.33911420.26433443X-RAY DIFFRACTION99.94
2.73-2.940.32651430.25743432X-RAY DIFFRACTION99.89
2.94-3.230.29541430.24513465X-RAY DIFFRACTION99.7
3.23-3.70.26221430.21663470X-RAY DIFFRACTION99.94
3.7-4.660.22971470.20053513X-RAY DIFFRACTION99.95
4.66-48.930.24571500.21953643X-RAY DIFFRACTION99.71

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