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- PDB-6rsu: TBK1 in complex with Inhibitor compound 35 -

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Basic information

Entry
Database: PDB / ID: 6rsu
TitleTBK1 in complex with Inhibitor compound 35
ComponentsSerine/threonine-protein kinase TBK1
KeywordsIMMUNE SYSTEM / kinase / innate immunity / small molecule inhibitor
Function / homology
Function and homology information


IRF3 mediated activation of type 1 IFN / STAT6-mediated induction of chemokines / positive regulation of xenophagy / serine/threonine protein kinase complex / dendritic cell proliferation / regulation of type I interferon production / IRF3-mediated induction of type I IFN / positive regulation of type I interferon-mediated signaling pathway / Interleukin-37 signaling / cGAS/STING signaling pathway ...IRF3 mediated activation of type 1 IFN / STAT6-mediated induction of chemokines / positive regulation of xenophagy / serine/threonine protein kinase complex / dendritic cell proliferation / regulation of type I interferon production / IRF3-mediated induction of type I IFN / positive regulation of type I interferon-mediated signaling pathway / Interleukin-37 signaling / cGAS/STING signaling pathway / TNFR1-induced proapoptotic signaling / toll-like receptor 4 signaling pathway / TRAF6 mediated IRF7 activation / cytoplasmic pattern recognition receptor signaling pathway / type I interferon-mediated signaling pathway / antiviral innate immune response / positive regulation of macroautophagy / positive regulation of type I interferon production / canonical NF-kappaB signal transduction / positive regulation of interferon-alpha production / positive regulation of autophagy / negative regulation of TORC1 signaling / positive regulation of TORC1 signaling / TICAM1-dependent activation of IRF3/IRF7 / activation of innate immune response / Regulation of innate immune responses to cytosolic DNA / positive regulation of interferon-beta production / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Negative regulators of DDX58/IFIH1 signaling / phosphoprotein binding / Regulation of TNFR1 signaling / peptidyl-threonine phosphorylation / DDX58/IFIH1-mediated induction of interferon-alpha/beta / response to virus / SARS-CoV-1 activates/modulates innate immune responses / positive regulation of peptidyl-serine phosphorylation / TRAF3-dependent IRF activation pathway / peptidyl-serine phosphorylation / protein phosphatase binding / positive regulation of canonical NF-kappaB signal transduction / defense response to virus / Potential therapeutics for SARS / nucleic acid binding / non-specific serine/threonine protein kinase / defense response to Gram-positive bacterium / protein kinase activity / inflammatory response / protein phosphorylation / negative regulation of gene expression / intracellular membrane-bounded organelle / innate immune response / protein serine kinase activity / protein serine/threonine kinase activity / SARS-CoV-2 activates/modulates innate and adaptive immune responses / positive regulation of transcription by RNA polymerase II / nucleoplasm / ATP binding / identical protein binding / cytoplasm / cytosol
Similarity search - Function
Substrate Binding Domain Of Dnak; Chain:A; Domain 2 - #420 / TANK binding kinase 1, ubiquitin-like domain / TANK-binding kinase 1, coiled-coil domain 1 / TANK-binding kinase 1 coiled-coil domain 1 / TANK binding kinase 1 ubiquitin-like domain / Substrate Binding Domain Of Dnak; Chain:A; Domain 2 / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 ...Substrate Binding Domain Of Dnak; Chain:A; Domain 2 - #420 / TANK binding kinase 1, ubiquitin-like domain / TANK-binding kinase 1, coiled-coil domain 1 / TANK-binding kinase 1 coiled-coil domain 1 / TANK binding kinase 1 ubiquitin-like domain / Substrate Binding Domain Of Dnak; Chain:A; Domain 2 / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Roll / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Up-down Bundle / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-KJB / Serine/threonine-protein kinase TBK1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsPanne, D. / Hillig, R.C. / Rengachari, S.
CitationJournal: J.Med.Chem. / Year: 2020
Title: Discovery of BAY-985, a Highly Selective TBK1/IKK epsilon Inhibitor.
Authors: Lefranc, J. / Schulze, V.K. / Hillig, R.C. / Briem, H. / Prinz, F. / Mengel, A. / Heinrich, T. / Balint, J. / Rengachari, S. / Irlbacher, H. / Stockigt, D. / Bomer, U. / Bader, B. / Gradl, S. ...Authors: Lefranc, J. / Schulze, V.K. / Hillig, R.C. / Briem, H. / Prinz, F. / Mengel, A. / Heinrich, T. / Balint, J. / Rengachari, S. / Irlbacher, H. / Stockigt, D. / Bomer, U. / Bader, B. / Gradl, S.N. / Nising, C.F. / von Nussbaum, F. / Mumberg, D. / Panne, D. / Wengner, A.M.
History
DepositionMay 22, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 1, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Serine/threonine-protein kinase TBK1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,7412
Polymers76,1701
Non-polymers5711
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area33520 Å2
Unit cell
Length a, b, c (Å)136.562, 136.562, 87.251
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z

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Components

#1: Protein Serine/threonine-protein kinase TBK1 / NF-kappa-B-activating kinase / T2K / TANK-binding kinase 1


Mass: 76170.055 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TBK1, NAK / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q9UHD2, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-KJB / 3,3,3-tris(fluoranyl)-1-[4-[(1~{R})-1-[2-[[(2~{S})-5-(5-propan-2-yloxypyrimidin-4-yl)-2,3-dihydro-1~{H}-benzimidazol-2-yl]amino]pyridin-4-yl]ethyl]piperazin-1-yl]propan-1-one


Mass: 570.609 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H33F3N8O2 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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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: 3.26 Å3/Da / Density % sol: 62.28 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 100 mM HEPES pH 7.5, 5-8% PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.966 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Dec 11, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.966 Å / Relative weight: 1
ReflectionResolution: 2.74→48.9 Å / Num. obs: 19151 / % possible obs: 99.4 % / Redundancy: 6.7 % / Biso Wilson estimate: 98.98 Å2 / CC1/2: 0.61 / Net I/σ(I): 15.7
Reflection shellResolution: 2.74→2.94 Å / Num. unique obs: 912 / Rrim(I) all: 123

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4IWO

4iwo


Resolution: 2.75→48.9 Å / SU ML: 0.402 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 48.9147
RfactorNum. reflection% reflection
Rfree0.3508 892 4.88 %
Rwork0.2893 --
obs0.2923 18282 73.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 85.74 Å2
Refinement stepCycle: LAST / Resolution: 2.75→48.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5062 0 41 0 5103
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.03525211
X-RAY DIFFRACTIONf_angle_d2.68787041
X-RAY DIFFRACTIONf_chiral_restr0.1832782
X-RAY DIFFRACTIONf_plane_restr0.0217893
X-RAY DIFFRACTIONf_dihedral_angle_d7.30813133
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.75-2.990.5971330.4439721X-RAY DIFFRACTION18.57
2.99-3.140.3998780.41531822X-RAY DIFFRACTION46.4
3.14-3.460.39141970.36832920X-RAY DIFFRACTION75.67
3.46-3.960.41412010.33163903X-RAY DIFFRACTION99.61
3.96-4.990.36811820.26553939X-RAY DIFFRACTION99.95
4.99-48.90.30682010.26794085X-RAY DIFFRACTION99.63

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