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- PDB-9psu: IRAK4 in Complex with Compound 12 -

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Basic information

Entry
Database: PDB / ID: 9psu
TitleIRAK4 in Complex with Compound 12
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 / MOLECULAR REPLACEMENT / Resolution: 2.43 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
C: Interleukin-1 receptor-associated kinase 4
D: Interleukin-1 receptor-associated kinase 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)138,94111
Polymers136,5424
Non-polymers2,3997
Water3,387188
1
A: Interleukin-1 receptor-associated kinase 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,6632
Polymers34,1361
Non-polymers5281
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)34,8554
Polymers34,1361
Non-polymers7203
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Interleukin-1 receptor-associated kinase 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,7593
Polymers34,1361
Non-polymers6242
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Interleukin-1 receptor-associated kinase 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,6632
Polymers34,1361
Non-polymers5281
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)136.613, 141.246, 87.350
Angle α, β, γ (deg.)90.000, 126.720, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

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


Mass: 34135.539 Da / Num. of mol.: 4
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-A1CKS / N-[(1R,5S,8R)-3-(5-{(6P)-6-[(8S)-3-cyanopyrrolo[1,2-b]pyridazin-7-yl]-4-[(propan-2-yl)amino]pyridin-3-yl}-1,3,4-thiadiazol-2-yl)-3-azabicyclo[3.2.1]octan-8-yl]acetamide


Mass: 527.644 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H29N9OS / 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.: 188 / 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: 2.47 Å3/Da / Density % sol: 50.28 %
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: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.542 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Nov 18, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.542 Å / Relative weight: 1
ReflectionResolution: 2.43→49.72 Å / Num. obs: 49871 / % possible obs: 99.73 % / Redundancy: 3.7 % / Biso Wilson estimate: 33.11 Å2 / CC1/2: 0.987 / CC star: 0.997 / Rmerge(I) obs: 0.1931 / Rpim(I) all: 0.1176 / Rrim(I) all: 0.2266 / Net I/σ(I): 4.04
Reflection shellResolution: 2.43→2.517 Å / Rmerge(I) obs: 0.897 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 4938 / CC1/2: 0.688 / Rpim(I) all: 0.5501 / Rrim(I) all: 1.055

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.43→49.72 Å / SU ML: 0.3668 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 33.8104
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.295 2368 4.75 %
Rwork0.2454 47474 -
obs0.2478 49842 99.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 50.32 Å2
Refinement stepCycle: LAST / Resolution: 2.43→49.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8902 0 167 188 9257
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00259232
X-RAY DIFFRACTIONf_angle_d0.549212485
X-RAY DIFFRACTIONf_chiral_restr0.04171389
X-RAY DIFFRACTIONf_plane_restr0.00421596
X-RAY DIFFRACTIONf_dihedral_angle_d13.4711242
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.43-2.480.38131320.32742602X-RAY DIFFRACTION93.28
2.48-2.530.35291330.31222816X-RAY DIFFRACTION99.9
2.53-2.590.3571380.30152816X-RAY DIFFRACTION100
2.59-2.660.38481120.31932828X-RAY DIFFRACTION99.97
2.66-2.730.37781590.31212795X-RAY DIFFRACTION99.97
2.73-2.810.36271420.30722764X-RAY DIFFRACTION99.93
2.81-2.90.33751450.2952789X-RAY DIFFRACTION99.97
2.9-30.3751260.27982788X-RAY DIFFRACTION99.83
3-3.120.35721400.25962801X-RAY DIFFRACTION99.86
3.12-3.260.28351550.25392793X-RAY DIFFRACTION99.97
3.26-3.440.28531560.24052780X-RAY DIFFRACTION99.9
3.44-3.650.28631660.22732784X-RAY DIFFRACTION99.9
3.65-3.930.30411550.2232771X-RAY DIFFRACTION99.93
3.93-4.330.23971330.1982806X-RAY DIFFRACTION99.93
4.33-4.950.24151410.19282821X-RAY DIFFRACTION99.9
4.95-6.240.28691290.23732836X-RAY DIFFRACTION99.87
6.24-49.720.20941060.22082884X-RAY DIFFRACTION99.43
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.86366356917-1.0847863405-3.361522782135.746389383962.530417922565.02818804825-0.828958046257-0.402205506624-0.5760035816220.2503498765970.5281447914110.08873382870550.6384361413330.5189945624830.2824693010280.4299194826140.07711849050320.01799705072080.303925486107-0.007953279994180.56505940087943.9752751199-6.0887238746622.6797273677
22.109598646791.037358254130.3129115316660.8125596538360.1617573584971.27249069886-0.05008652074960.214174779515-0.174349471139-0.2364678715180.107893577024-0.24014881650.1459156693350.174258203405-0.0525786763250.596249764919-0.003615802631770.1985910231220.193842502982-0.01452087217030.47869716967834.894781072-8.559250031739.95403964051
31.131777844811.568201114040.3148947481582.202789342570.7751392244813.32538426879-0.6246152118660.469785730967-0.653782170491-1.084959335140.353758607834-1.324951063490.4127061308640.5085342823740.2690939808571.07283314133-0.1134565241620.4480143031310.383297858875-0.1220038143710.86032367160135.9326189072-27.11475359472.34277283912
43.55135353566-0.667071573863-0.2646684593424.04510612165-0.6624317399045.15104089319-0.3273457253080.264383694938-0.70807142109-0.06112569208520.07952959815580.4218365409610.738329882636-0.5427613130110.214433994190.651582433063-0.053911352440.248637417880.303698113277-0.100583573640.6350246368616.6336905473-19.81318152855.64504677076
57.57327265132-0.644401390040.7058443838055.21744367631-1.546982041598.26262023202-0.000706194645954-0.0732968634305-0.659743696215-0.404918220953-0.059554909828-0.177947777320.5622896931570.006374405276670.04088444333390.308932116258-0.01682567314060.052614021290.283470389125-0.03428032170810.464597555916-12.7844019147-8.5103427798630.7197217061
62.28644149894-0.8514799380260.5370696486233.94028401426-0.3211431785122.1810788916-0.0472840027112-0.321317279607-0.2478563324680.2917615107290.154742789680.5466163461340.145246563476-0.445958813906-0.1172932557610.402584116792-0.02701371484050.1614415499670.2881376017050.02089657635310.415351975001-0.257396055541-13.334844782139.916852118
73.122549079870.53853761979-0.8925196303813.98825114804-1.72671009763.84170942484-0.225419304833-0.289653240535-0.7658718079870.188477913881-0.0985924549638-0.5002488300540.7568380611490.190031198650.3028112942570.4452659778790.008255650799460.1159983658610.2707917866640.1106883785230.56690746595416.1461043117-20.285037894540.9680373028
85.0816838102-1.60105314039-0.3259554939611.120443095610.4651132571656.91523279114-0.117549928844-0.1073950988440.435235594130.238999495410.115803729805-0.0349470055078-0.172649915382-0.2037694180950.01525997201070.6846102133470.04139198515760.1655014910470.3239674950270.05698723286150.5171137024543.996516867-58.312758622919.3323577342
91.67410328211-0.8813979599890.3646327984091.55081047664-0.4729904593220.925261165279-0.0543455158409-0.4566458524510.0584980321370.3391615882440.1163634696470.0629904529606-0.3038997911170.0217072735213-0.05138427999830.765777962629-0.0161104513730.203868724140.2889701104520.0005970517549570.44275696173132.2049007367-53.5008883489.28149847541
102.20456712824-0.263897342751-0.875900988193.02489326065-0.1116696813022.727288652420.307247202114-0.002988625625120.573991113166-0.8665821573630.01807590213420.0566379240945-0.98914632398-0.212861450097-0.3278720503930.8771447780180.07645463432690.1967964685160.305495168886-0.02277860000450.47593847345326.4849022783-46.0916274948-5.78152713602
111.335962207621.2866693674-0.4780153152922.37950566309-1.114649888642.265647633670.2511532514210.2160552524520.5539053845580.1075428519790.2029563591350.362750408024-0.465797948356-0.176272636631-0.4425642300690.6349105889380.02696051387510.1650474699630.2844119615970.09013813762950.505937931548-15.7456681991-60.225986844432.3663608869
125.464851525461.70589682927-0.06597601835744.40586165322-2.286692782352.19941468964-0.1244049261180.4957254479960.771840615945-0.2489045417170.232997969645-0.0278936716305-0.7805179130520.284795957783-0.114400690590.797202246301-0.1103236359510.1653866763360.2777784840250.001020648275250.386291775952-7.0637705208-56.689993780428.763143912
131.02068817250.172084484607-0.08914913818670.5376466760030.9734588941451.917640288450.04160642246950.09377393647020.0524092619533-0.114990469742-0.00347292610434-0.207511379125-0.1118949049870.03775447184-0.04013777933170.475845712254-0.02513930999070.1052262106770.1624312745580.01828846005490.409419889811-0.512389390212-59.602441634940.8852519761
143.284250798910.249806427750.6284541842254.03518543263-0.007007420876641.69983260777-0.03382913668550.2025313325490.46023607993-0.2372260579350.2321042938410.044579630564-0.9288618071570.106002258498-0.1791305008480.759275305664-0.09933136669010.2396196503760.269990903113-0.004955948371640.4559290738393.37608064922-45.838550901243.0021993868
157.237493654071.1430287294-0.736108493976.229755835421.386410254243.181062011640.417509801158-0.8382994216460.2887906218170.5095083652840.0579831752199-0.605427922552-0.7674216810810.932477799824-0.4762629444150.583792901425-0.1273243253560.06743501473960.443062870406-0.04745153294840.41891818122111.9394093563-49.159252741554.9443178188
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 164 through 197 )AA164 - 1971 - 34
22chain 'A' and (resid 198 through 332 )AA198 - 33235 - 161
33chain 'A' and (resid 333 through 365 )AA333 - 365162 - 189
44chain 'A' and (resid 366 through 458 )AA366 - 458190 - 282
55chain 'B' and (resid 164 through 239 )BC164 - 2391 - 71
66chain 'B' and (resid 240 through 365 )BC240 - 36572 - 193
77chain 'B' and (resid 366 through 458 )BC366 - 458194 - 286
88chain 'C' and (resid 164 through 239 )CE164 - 2391 - 67
99chain 'C' and (resid 240 through 365 )CE240 - 36568 - 188
1010chain 'C' and (resid 366 through 458 )CE366 - 458189 - 281
1111chain 'D' and (resid 164 through 197 )DG164 - 1971 - 34
1212chain 'D' and (resid 198 through 239 )DG198 - 23935 - 71
1313chain 'D' and (resid 240 through 304 )DG240 - 30472 - 136
1414chain 'D' and (resid 305 through 404 )DG305 - 404137 - 229
1515chain 'D' and (resid 405 through 457 )DG405 - 457230 - 282

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