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- PDB-9yuf: PKR kinase domain - Dabrafenib complex -

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Basic information

Entry
Database: PDB / ID: 9yuf
TitlePKR kinase domain - Dabrafenib complex
ComponentsInterferon-induced, double-stranded RNA-activated protein kinase
KeywordsTRANSFERASE/INHIBITOR / protein kinase / inhibitor / complex / TRANSFERASE / TRANSFERASE-INHIBITOR complex
Function / homology
Function and homology information


cellular response to amino acid starvation / non-specific protein-tyrosine kinase / non-membrane spanning protein tyrosine kinase activity / double-stranded RNA binding / defense response to virus / non-specific serine/threonine protein kinase / innate immune response / protein serine/threonine kinase activity / perinuclear region of cytoplasm / DNA-templated transcription ...cellular response to amino acid starvation / non-specific protein-tyrosine kinase / non-membrane spanning protein tyrosine kinase activity / double-stranded RNA binding / defense response to virus / non-specific serine/threonine protein kinase / innate immune response / protein serine/threonine kinase activity / perinuclear region of cytoplasm / DNA-templated transcription / ATP binding / nucleus
Similarity search - Function
EIF2AK2, first double-stranded RNA binding domain / EIF2AK2, second double-stranded RNA binding domain / : / Double-stranded RNA binding motif / Double-stranded RNA binding motif / Double stranded RNA-binding domain (dsRBD) profile. / Double-stranded RNA-binding domain / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain ...EIF2AK2, first double-stranded RNA binding domain / EIF2AK2, second double-stranded RNA binding domain / : / Double-stranded RNA binding motif / Double-stranded RNA binding motif / Double stranded RNA-binding domain (dsRBD) profile. / Double-stranded RNA-binding domain / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Dabrafenib / Interferon-induced, double-stranded RNA-activated protein kinase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsYin, J.Z. / Sicheri, F.
Funding support Canada, United States, 6items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)FDN-143277 Canada
Canadian Institutes of Health Research (CIHR)PJT-178026 Canada
Canadian Institutes of Health Research (CIHR)PJT-186218 Canada
Canadian Institutes of Health Research (CIHR)PJT-180338 Canada
Other privateTFRI 1107-04 Canada
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P30 M124165 United States
CitationJournal: J.Med.Chem. / Year: 2026
Title: Structural Transformation of a BRAF Inhibitor into a Selective PKR Inhibitor.
Authors: Yin, J. / Srivastava, S. / Tang, X. / Galbraith, C. / Uchenunu, O. / Miller, J. / Liu, Y. / Crescenzi, I. / Kiyota, T. / Kurinov, I. / Costa-Mattioli, M. / Laufer, R. / Aman, A. / Rottapel, ...Authors: Yin, J. / Srivastava, S. / Tang, X. / Galbraith, C. / Uchenunu, O. / Miller, J. / Liu, Y. / Crescenzi, I. / Kiyota, T. / Kurinov, I. / Costa-Mattioli, M. / Laufer, R. / Aman, A. / Rottapel, R. / Ramnauth, J. / Haakonsen, D.L. / Uehling, D.E. / Sicheri, F.
History
DepositionOct 22, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 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: Interferon-induced, double-stranded RNA-activated protein kinase
B: Interferon-induced, double-stranded RNA-activated protein kinase
C: Interferon-induced, double-stranded RNA-activated protein kinase
D: Interferon-induced, double-stranded RNA-activated protein kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,2808
Polymers130,2024
Non-polymers2,0784
Water00
1
A: Interferon-induced, double-stranded RNA-activated protein kinase
C: Interferon-induced, double-stranded RNA-activated protein kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,1404
Polymers65,1012
Non-polymers1,0392
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Interferon-induced, double-stranded RNA-activated protein kinase
D: Interferon-induced, double-stranded RNA-activated protein kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,1404
Polymers65,1012
Non-polymers1,0392
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)95.330, 95.330, 122.970
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31
Space group name HallP31
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails (eV)
d_1ens_1chain "A"
d_2ens_1chain "B"
d_3ens_1chain "C"
d_4ens_1chain "D"

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ALAALALYSLYSAA256 - 5401 - 272
d_12DRGDRGDRGDRGAE614
d_21ALAALALYSLYSBB256 - 5401 - 272
d_22DRGDRGDRGDRGBF614
d_31ALAALALYSLYSCC256 - 5401 - 272
d_32DRGDRGDRGDRGCG614
d_41ALAALALYSLYSDD256 - 5401 - 272
d_42DRGDRGDRGDRGDH614

NCS oper:
IDCodeMatrixVector
1given(0.501444833537, -0.86518926848, -0.000780145285013), (0.865189615084, 0.501444724867, 0.000343298690025), (9.41813953067E-5, -0.000847118953323, 0.99999963676)-47.6616861986, -27.4008879314, 20.4393216341
2given(0.999999321646, 0.00102076313212, -0.000561025146989), (0.00102016953779, -0.999998920661, -0.00105732268275), (-0.000562103817465, 0.00105674962475, -0.99999928366)0.0676435751353, -110.112466932, -32.5136165215
3given(0.499301822171, 0.866427958893, 0.000531436446547), (0.86642805311, -0.499301932993, 9.21595257192E-5), (0.000345196834786, 0.000414436026611, -0.999999854541)47.7118918008, -82.5143842276, -12.0953320377

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Components

#1: Protein
Interferon-induced, double-stranded RNA-activated protein kinase / Eukaryotic translation initiation factor 2-alpha kinase 2 / Interferon-inducible RNA-dependent ...Eukaryotic translation initiation factor 2-alpha kinase 2 / Interferon-inducible RNA-dependent protein kinase / Protein kinase RNA-activated / Tyrosine-protein kinase EIF2AK2


Mass: 32550.521 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EIF2AK2 / Production host: Escherichia coli (E. coli)
References: UniProt: B7ZKK7, non-specific protein-tyrosine kinase, non-specific serine/threonine protein kinase
#2: Chemical
ChemComp-P06 / Dabrafenib / N-{3-[5-(2-aminopyrimidin-4-yl)-2-tert-butyl-1,3-thiazol-4-yl]-2-fluorophenyl}-2,6-difluorobenzenesulfonamide


Mass: 519.562 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C23H20F3N5O2S2 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

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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: 50.19 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 14% PEG3350, 0.2M sodium fluoride, 0.1M HEPES pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 25, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.5→68.54 Å / Num. obs: 43270 / % possible obs: 99.76 % / Redundancy: 5.3 % / Biso Wilson estimate: 90.49 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.03351 / Rpim(I) all: 0.01614 / Rrim(I) all: 0.03725 / Net I/σ(I): 19.67
Reflection shellResolution: 2.5→2.56 Å / Redundancy: 5.3 % / Rmerge(I) obs: 1.901 / Mean I/σ(I) obs: 0.69 / Num. unique obs: 2856 / CC1/2: 0.348 / CC star: 0.719 / Rpim(I) all: 0.9089 / Rrim(I) all: 2.111 / % possible all: 99.54

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→68.54 Å / SU ML: 0.5372 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 35.0802
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.28 2153 4.99 %
Rwork0.2553 40955 -
obs-43111 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 90.49 Å2
Refinement stepCycle: LAST / Resolution: 2.5→68.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7152 0 140 0 7292
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00157436
X-RAY DIFFRACTIONf_angle_d0.39510168
X-RAY DIFFRACTIONf_chiral_restr0.03881180
X-RAY DIFFRACTIONf_plane_restr0.0031304
X-RAY DIFFRACTIONf_dihedral_angle_d11.79542368
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS0.0545421025884
ens_1d_3AAX-RAY DIFFRACTIONTorsion NCS0.0506440516993
ens_1d_4AAX-RAY DIFFRACTIONTorsion NCS0.0546178324307
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.560.50951380.45682685X-RAY DIFFRACTION99.54
2.56-2.620.4031460.40052761X-RAY DIFFRACTION99.76
2.62-2.690.4071420.36612711X-RAY DIFFRACTION99.96
2.69-2.770.36931450.33072749X-RAY DIFFRACTION99.86
2.77-2.860.34111440.33272738X-RAY DIFFRACTION99.79
2.86-2.960.37611440.32772746X-RAY DIFFRACTION99.86
2.96-3.080.36421430.35972701X-RAY DIFFRACTION99.86
3.08-3.220.38871440.36852736X-RAY DIFFRACTION99.97
3.22-3.390.40931450.3622770X-RAY DIFFRACTION100
3.39-3.610.28461440.29692732X-RAY DIFFRACTION100
3.61-3.880.29281450.28152743X-RAY DIFFRACTION99.76
3.88-4.270.27451420.2372693X-RAY DIFFRACTION99.26
4.28-4.890.22851440.19952725X-RAY DIFFRACTION99.83
4.89-6.160.2821440.23472737X-RAY DIFFRACTION100
6.16-68.540.21341430.2032728X-RAY DIFFRACTION98.9
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)
18.470827576210.808115889275-8.263256467917.00246823722-1.536196898198.481249236720.121697993722-0.944517869658-0.7096120972921.016806132-0.816176791828-0.999945673831-0.184505752041.24571612690.5642370058691.28495272078-0.206487762395-0.2711313325990.6790025632980.1146417032530.98259658588452.8960838259-59.4940461514-3.64721556816
25.615486680140.483854417009-2.409386619580.974638348206-0.3315473763527.148385447480.039892276055-0.04551809484440.04913099827260.499825218903-0.639820382873-0.1153082413880.02539961540710.06833253095180.3578623727480.906121673636-0.0478837649083-0.1281538602630.3836275107810.05376437181390.90847321053849.1050585208-62.3855025485-12.3792827755
39.266755672440.113122635593-1.353825942543.65226870811-0.7367141335463.255234881180.882647262765-0.5107111967430.4826301859970.932355155181-0.336878590857-0.283783947704-0.3788725965710.20766232299-0.5412003205991.20423328337-0.210525299315-0.04316741090810.412048437276-0.005017789410680.77126035409437.9743421969-63.5622928262-6.59524723212
47.06411569711.73603737156-5.195768465865.35696699396-2.731120194848.829922921810.23847642334-0.525253334541-0.6923318759250.458006027906-0.0328620603259-0.3425140355760.170076029914-0.583847107371-0.1654440060671.025042034-0.133579659371-0.211730881610.6382533241290.09602112225980.92739066922324.4384777966-74.1767089682-2.29981542822
56.496453616821.66025325833-2.634146857455.55811781383-3.654411297392.90144758524-0.466492903874-0.6296161105720.4757997349180.9926660468470.04802191437240.0670043499941-0.9406666279050.2385155673710.5642270751710.8952042059260.334466840673-0.2024081999890.946654578408-0.1743827852680.91802700614729.5155878482-12.068799232914.6412623474
63.877790074861.76631746457-0.1112367877787.72032960373-2.762400450914.08910525889-0.15664005924-0.3656003438610.3611819421151.022149943360.5705260183180.182669933752-0.310806350761-0.09613195743850.4356202414590.7507535963460.379015050929-0.02770063436110.867337636579-0.05367047491810.82282996076727.4764974285-26.006154313212.5514528936
74.824457285390.720097456191-0.1016090744388.01791020568-5.224993785867.544299195040.0868263841916-0.385643895935-0.1523016744230.5595909568270.0982278809392-0.794124936720.280010039878-0.1298132541630.08448016304530.846444550.229904664205-0.1820833550040.793212478366-0.1225794262820.85144480216128.7734106833-43.457091769518.2047938935
88.1130525865-1.127214979462.767841130155.01324340662-3.241932057452.851986849540.1466741977860.824884689540.89136951734-1.59640804162-0.823060575398-0.9074168209090.185509540891.20688474620.04558157081131.297553906350.1926633475540.1867790399330.6904467095140.07701959586470.94117970223152.9027280448-50.5598354463-28.9647572711
95.999429456820.5890709595751.585680946251.9503291887-0.3208707955714.48312566932-0.0833732946655-0.289579411502-0.197193811497-0.361881265612-0.232610013575-0.5781458157510.2150345764770.825498551809-0.105120564381.018146307630.1069166512880.1088901983270.344417722450.05393116837650.95216561393649.0942703121-47.6718371953-20.2461314473
108.76777546460.6058505447931.348035456873.12717397528-1.32501305973.777938561570.7526367092750.549521365971-0.727974380618-0.977394535062-0.289534287396-0.1125918194120.280437159550.195670839990.425708618331.239568341970.2086028124670.05520263599570.433811873314-0.02514980508650.81239846063337.9873551394-46.5029306116-26.0011416879
118.18705762137-1.094639758894.670915990915.09280523352-2.165278419248.420165778980.1405103992170.5118216793920.619280325295-0.4781181407860.0578220760183-0.368589001689-0.229441502112-0.3835847736860.05765760563991.012065953130.1268787802920.1799120335880.6061475744440.08828397871360.85599614609924.4342043916-35.9079234555-30.3045463117
125.77286338366-0.001402395579592.968685475057.857682929243.67347077683.93892168301-0.1868392411371.279310588760.62408866302-0.384519828733-0.292946246604-0.339833091235-0.3909680077670.9194159920360.07748956846060.6036578460770.1744760471810.04636903495381.173084914430.2408392973710.92367936948122.4709662247-7.99096669506-6.24006085875
135.47785026282.782328344272.659235212295.673090084750.7661707323673.710636373910.06445782314061.208546430980.197222663456-0.1766381807770.321445178169-0.351612528684-0.04508164707850.4188930833420.2850886799860.4908550394290.2211917747410.04416196470961.099362475620.06375576849370.89032576645811.4025504069-16.7170126819-4.17240485352
147.218596531072.335304075454.081815985375.502366881193.032729885637.28276744738-0.02546805312660.4806809491210.788740308798-0.265094636190.1222600335740.4131598175480.201365342704-0.413026382007-0.05834525768520.6140727981940.1035357280680.008731656999351.044220270180.220637153550.912323102516-4.35685138624-24.3050634291-9.81395817048
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 256 through 285 )AA256 - 2851 - 30
22chain 'A' and (resid 286 through 314 )AA286 - 31431 - 59
33chain 'A' and (resid 315 through 408 )AA315 - 40860 - 134
44chain 'A' and (resid 409 through 540 )AA409 - 540135 - 248
55chain 'B' and (resid 256 through 302 )BC256 - 3021 - 47
66chain 'B' and (resid 303 through 408 )BC303 - 40848 - 134
77chain 'B' and (resid 409 through 540 )BC409 - 540135 - 248
88chain 'C' and (resid 256 through 285 )CE256 - 2851 - 30
99chain 'C' and (resid 286 through 314 )CE286 - 31431 - 59
1010chain 'C' and (resid 315 through 408 )CE315 - 40860 - 134
1111chain 'C' and (resid 409 through 540 )CE409 - 540135 - 248
1212chain 'D' and (resid 256 through 302 )DG256 - 3021 - 47
1313chain 'D' and (resid 303 through 408 )DG303 - 40848 - 134
1414chain 'D' and (resid 409 through 540 )DG409 - 540135 - 248

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