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- PDB-9na4: IRAK4 in Complex with Compound 18 -

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Basic information

Entry
Database: PDB / ID: 9na4
TitleIRAK4 in Complex with Compound 18
ComponentsInterleukin-1 receptor-associated kinase 4
KeywordsIMMUNE SYSTEM / TRANSFERASE/INHIBITOR / Kinase / Phosphorylated / Signaling Protein / Inhibitor Complex / 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 / extrinsic component of plasma membrane / IRAK4 deficiency (TLR2/4) / MyD88-dependent toll-like receptor signaling pathway / MyD88:MAL(TIRAP) cascade initiated on plasma membrane / toll-like receptor 4 signaling pathway / toll-like receptor signaling pathway / JNK cascade / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / lipopolysaccharide-mediated signaling pathway / positive regulation of smooth muscle cell proliferation / cytokine-mediated signaling pathway / Interleukin-1 signaling / kinase activity / PIP3 activates AKT signaling / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / eukaryotic translation initiation factor 2alpha kinase activity / positive regulation of canonical NF-kappaB signal transduction / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / ribosomal protein S6 kinase activity / histone H3S10 kinase activity / histone H2AXS139 kinase activity / histone H3S28 kinase activity / histone H4S1 kinase activity / histone H2BS14 kinase activity / histone H3T3 kinase activity / histone H2AS121 kinase activity / Rho-dependent protein serine/threonine kinase activity / histone H2BS36 kinase activity / histone H3S57 kinase activity / histone H2AT120 kinase activity / AMP-activated protein kinase activity / histone H2AS1 kinase activity / histone H3T6 kinase activity / histone H3T11 kinase activity / histone H3T45 kinase activity / 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 / cell surface / magnesium ion binding / extracellular space / ATP binding / nucleus / plasma membrane / cytosol / cytoplasm
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: 2.33 Å
AuthorsFerrao, R. / Lansdon, E.B.
Funding support1items
OrganizationGrant numberCountry
Not funded
Citation
Journal: J.Med.Chem. / Year: 2025
Title: Discovery of Edecesertib (GS-5718): A Potent, Selective Inhibitor of IRAK4.
Authors: Ammann, S.E. / Cottell, J.J. / Wright, N.E. / Warr, M.R. / Snyder, C.A. / Bacon, E.M. / Brizgys, G. / Chin, E. / Chou, C. / Conway, A. / Dick, R.A. / Ferrao, R.D. / Garrison, K.L. / Hammond, ...Authors: Ammann, S.E. / Cottell, J.J. / Wright, N.E. / Warr, M.R. / Snyder, C.A. / Bacon, E.M. / Brizgys, G. / Chin, E. / Chou, C. / Conway, A. / Dick, R.A. / Ferrao, R.D. / Garrison, K.L. / Hammond, A. / Lansdon, E.B. / Link, J.O. / Mukherjee, P.K. / Murray, B.P. / Mwangi, J. / Ndukwe, M.S. / Park, G.Y. / Serone, A.P. / Suekawa-Pirrone, K. / Yang, Z.Y. / Zipfel, S.M. / Taylor, J.G.
#1: Journal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams /
Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.
History
DepositionFeb 11, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 28, 2025Provider: 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)138,9568
Polymers136,8624
Non-polymers2,0944
Water2,954164
1
A: Interleukin-1 receptor-associated kinase 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,7392
Polymers34,2161
Non-polymers5241
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)34,7392
Polymers34,2161
Non-polymers5241
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)34,7392
Polymers34,2161
Non-polymers5241
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)34,7392
Polymers34,2161
Non-polymers5241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)88.880, 111.790, 140.830
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z

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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.: 4 / 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-A1BW1 / methyl {[(1S,3s)-3-{[(2P)-2-[(8R)-3-cyanopyrrolo[1,2-b]pyridazin-7-yl]-5-{[(2S)-2-fluoro-3-hydroxy-3-methylbutyl]carbamoyl}pyridin-4-yl]amino}cyclobutyl]methyl}carbamate


Mass: 523.559 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C26H30FN7O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 164 / 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: 2.56 Å3/Da / Density % sol: 51.88 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop
Details: 30% PEG 8000, 0.2 M calcium acetate, 0.1 M MES pH 6.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 7, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.33→49.49 Å / Num. obs: 60240 / % possible obs: 99.6 % / Redundancy: 6.6 % / Biso Wilson estimate: 43.98 Å2 / CC1/2: 0.99 / Net I/σ(I): 9.6
Reflection shellResolution: 2.33→2.41 Å / Num. unique obs: 5850 / CC1/2: 0.63

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.33→49.49 Å / SU ML: 0.3633 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.3481
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2727 1995 3.32 %
Rwork0.2255 58103 -
obs0.2271 60098 99.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 61.95 Å2
Refinement stepCycle: LAST / Resolution: 2.33→49.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8939 0 152 164 9255
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00239251
X-RAY DIFFRACTIONf_angle_d0.555812506
X-RAY DIFFRACTIONf_chiral_restr0.04191404
X-RAY DIFFRACTIONf_plane_restr0.00321585
X-RAY DIFFRACTIONf_dihedral_angle_d12.75341254
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.33-2.390.36751380.33654018X-RAY DIFFRACTION97.88
2.39-2.460.40351400.32264082X-RAY DIFFRACTION99.65
2.46-2.530.37821420.31914110X-RAY DIFFRACTION99.58
2.53-2.610.36651410.31454132X-RAY DIFFRACTION99.95
2.61-2.70.3711420.30714096X-RAY DIFFRACTION99.84
2.7-2.810.33761410.28554121X-RAY DIFFRACTION99.81
2.81-2.940.32991420.27064131X-RAY DIFFRACTION99.72
2.94-3.10.3331430.25714128X-RAY DIFFRACTION99.65
3.1-3.290.25931420.24174154X-RAY DIFFRACTION99.77
3.29-3.540.28051420.2084141X-RAY DIFFRACTION99.88
3.54-3.90.25231440.19674170X-RAY DIFFRACTION99.91
3.9-4.460.20721440.17154223X-RAY DIFFRACTION99.84
4.46-5.620.23661430.18784217X-RAY DIFFRACTION99.59
5.62-49.490.22731510.20084380X-RAY DIFFRACTION98.97
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)
16.33244150681-0.364933380846-0.6914599290764.62448902818-1.097229294795.52091988106-0.346173905621-0.117708445904-1.09769504341-0.217627595522-0.202376876889-0.3568719072011.684970570650.5123942348920.6059305227521.06286438830.1376299425390.1247499346750.5662996576190.09790823135140.66320577454427.44340269667.7712725294924.3777253079
22.40822185776-0.393709392662-0.6508278145422.64204800941-0.1053616845944.25345179165-0.0147553136603-0.153862608814-0.288046106486-0.231804321027-0.0735359096868-0.4288189036650.6953528166590.6691355395690.08509233232760.3812734111950.07756894142720.02669780255110.3928249491010.01107364835870.33919889139628.364673603724.8166229319.0883463596
36.442224438420.37199494092-2.423277887253.30562755823-0.0447588712495.012421454220.2805433422180.8041855364420.281213809386-0.567919382622-0.1747532086820.0712136006229-0.588518792102-0.278267190137-0.08871095477110.4275046004180.09013858884440.04603747029870.416328119920.03813032813390.31899180347520.174847638638.50017641912.5763026491
41.29225529704-1.83097484994-0.6044013160413.86976845638-0.1543251529311.010793172020.312794404822-0.240650605282-1.029174905810.4999193110040.0944509553851-0.05182672259420.9335492610340.588547981657-0.3839092260031.462353145790.482668842256-0.3695536073260.835062906815-0.1162222820360.72084406721434.18861522433.86279830613-28.6813860669
52.969116221390.7032679324241.415496686592.501764440620.3216214398132.357117072290.4945787483910.0147933389898-0.5253101967570.109998412393-0.121263438216-0.08781024773911.083282430370.255347086351-0.338226662850.7075315332580.173200901148-0.1257451360940.470965440861-0.05952462800190.35024762761529.807169736415.1958392225-24.7955464316
69.501231516484.92503734858-1.551764978654.65925727871-0.2594101526482.812261845420.1261139070411.633558980770.913607565882-0.1255001571180.1522223134680.630275712316-0.263892215493-0.486699711458-0.3503665319160.4044426328180.1789353952490.03477762583380.5555567261330.05638919708520.40999017602529.108570809134.0323977021-25.4617957546
71.811027152731.127195551541.765837086374.568958036490.2377831789654.698620904590.215230140986-0.1213282459530.0968216259040.37552424328-0.058520351290.7123343854980.274625926412-0.534541510476-0.1542849641370.3033743476660.07914043666620.04486638103480.408476855219-0.01478045264550.3770757277326.096763475626.3471382307-14.4863676334
89.43291549186-3.341224854483.982893198666.67268509761.571813555042.002222717030.179046550838-1.68446423404-0.8701355259740.56293729906-0.470552619942-0.721958560794-0.1099093333070.7495874545060.2569834793470.70123856168-0.1374737007140.1084471705720.6556134701450.1136369787860.56797968398144.519516537827.6864164654-7.08270848715
94.84263426083.18026145686-0.4472159739848.184791457852.176445511824.109692003461.08829373633-1.717675694891.173197080692.6517064494-0.423745375986-0.1850181024-1.734051764480.368564509597-0.7080810377051.19984488585-0.2256388676210.1643972971150.93549371548-0.1780635195770.66484624908741.985040919341.4587145836-6.82057808829
109.97495702948-0.71903805949-2.352246613363.011131386750.6551295790282.51733656860.7152207434430.6287323565861.10305117493-0.0329985884704-0.4176602846530.41976881928-0.84864683709-0.342404866213-0.3155389080670.5223783807370.09973179059530.03241067822490.417027766536-0.04367747384890.45589336012732.432601291741.3726068044-18.0328018522
113.76422045733-0.7245051441460.4735312920453.19292538785-1.28146148391.663506240370.366222268378-0.02311549610250.842009083785-0.138305087032-0.161294103994-0.0015048220801-0.912210746584-0.358065649662-0.2790605621910.8926426254230.2541868757460.2051383695360.6404624109780.06652604143680.6062547100269.9390684487549.638411898143.88835925
124.13984516496-0.07783025647530.271628482633.40104940284-0.3042227958359.084590234910.05488350198570.04715087634150.1516687084870.4799433542210.1256759982760.167695893132-1.20867640118-0.637805672233-0.291823602670.4693327866660.1326032092640.1391092310710.3530980444990.07434072899920.37020600738711.459646364146.090892957143.4775080232
132.04165310527-3.12205159191-3.408336183492.015693592624.169835460546.473435914670.325658408947-1.13433120873-0.01222891344021.041932943750.164183790865-0.685094522422-0.3859528273780.73994148985-0.4173119937510.722777326591-0.09077980698480.06260459467570.6024616425890.02757105891630.51430473178424.654203963641.61691788151.7518276927
143.503466536660.919530052123-0.7376941123192.60036423927-0.7817753837072.236903660750.1164080385560.3519289717230.137122849614-0.122682029074-0.0822498174407-0.0804557378999-0.0744909067420.11500222425-0.03728913228550.2972658544160.01940253932550.01768995463630.4378513093040.0532327472590.21000298473510.776568141531.067443376343.8641137972
153.089836230620.466509256805-2.352838834144.10792284136-0.3341653991776.45352907704-0.0195289520764-0.2683292637160.02234769023040.342934277208-0.24210426348-0.668401982258-0.1628682104230.629629511860.192010583620.273168800051-0.0338666214132-0.005915212163870.5036891873820.09824739804790.40390902462917.682662516130.172924384655.9814200609
162.036885115030.665711153011.077424014014.9836033383-0.3983050027364.902825795750.21016412244-0.5607044371910.7751640913610.32247717068-0.4066875431490.2344923346660.18537558755-0.6509075964970.06039732454380.371560361408-0.0924363248551-0.05372827042360.586987892186-0.0216011467240.3890443486564.9383067907724.295189403259.0713907389
175.672859921081.74224934912-1.651648475976.85474698558-1.859990483332.79378844550.329621043775-1.54838262722-1.587249529641.63108339972-0.0898511713495-0.1658933377561.47282959853-0.483356329662-0.211942099591.20121510754-0.341763766234-0.1737488491391.025180433740.316361370470.787008966202-0.50392821051513.984779136263.5762047195
187.37062738913-0.6460430788512.725900557932.83085777094-0.2532223023222.519948244190.544929832226-0.0134879837363-0.55094354729-0.00856413455277-0.3217851968220.3049661963230.695395797929-0.352439883818-0.267395848860.380878174502-0.06502870845330.009098419171110.388974267955-0.0122463238450.4356048678781.2028625643913.619770959350.9119159517
196.52649141721-0.4181284253580.5217254197614.597236856120.2058432234179.107323944040.1114191375-0.0792167950117-0.5286057299520.0711575841401-0.372241403195-0.6912244988321.245611215510.92973801710.3460476328070.4795866816860.0562179567030.01159654524960.4096943162230.151234937250.56452732590116.081595150113.570970936553.6156441773
204.909937493580.462373564412-0.7894714918745.61273789579-0.2186590595622.90088094843-0.0541614289833-0.1174467676131.03566563458-0.15163245638-0.09475636511740.590055075916-0.656038048183-0.4920862761650.123868894540.5113136845860.144273818406-0.09927450433330.571619178154-0.1157133265980.55116875349912.835906210644.529872238895.7713054604
213.775778490850.2005635605551.875099352742.521882485090.3293530415324.955761233820.09018816386590.343995335402-0.0559785737411-0.285017374947-0.07897633505720.1003559544280.2184762269580.0128711352089-0.0274958635260.2606230753070.042184758584-0.009178186879070.368970256792-0.01382852808420.26575636245417.647258686722.810170314985.4561825449
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 239 )AA164 - 2391 - 71
22chain 'A' and (resid 240 through 382 )AA240 - 38272 - 206
33chain 'A' and (resid 383 through 459 )AA383 - 459207 - 283
44chain 'B' and (resid 164 through 190 )BC164 - 1901 - 27
55chain 'B' and (resid 191 through 284 )BC191 - 28428 - 113
66chain 'B' and (resid 285 through 304 )BC285 - 304114 - 133
77chain 'B' and (resid 305 through 382 )BC305 - 382134 - 206
88chain 'B' and (resid 383 through 395 )BC383 - 395207 - 219
99chain 'B' and (resid 396 through 413 )BC396 - 413220 - 237
1010chain 'B' and (resid 414 through 459 )BC414 - 459238 - 283
1111chain 'C' and (resid 164 through 197 )CE164 - 1971 - 34
1212chain 'C' and (resid 198 through 222 )CE198 - 22235 - 55
1313chain 'C' and (resid 223 through 239 )CE223 - 23956 - 72
1414chain 'C' and (resid 240 through 304 )CE240 - 30473 - 135
1515chain 'C' and (resid 305 through 365 )CE305 - 365136 - 191
1616chain 'C' and (resid 366 through 395 )CE366 - 395192 - 221
1717chain 'C' and (resid 396 through 413 )CE396 - 413222 - 239
1818chain 'C' and (resid 414 through 436 )CE414 - 436240 - 262
1919chain 'C' and (resid 437 through 459 )CE437 - 459263 - 285
2020chain 'D' and (resid 165 through 269 )DG165 - 2691 - 99
2121chain 'D' and (resid 270 through 459 )DG270 - 459100 - 284

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