+Open data
-Basic information
Entry | Database: PDB / ID: 7szr | ||||||
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Title | NIK bound to inhibitor G02792917 | ||||||
Components | Mitogen-activated protein kinase kinase kinase 14 | ||||||
Keywords | SIGNALING PROTEIN / Kinase / inhibitor / NF-kB inducing kinase | ||||||
Function / homology | Function and homology information CD28 dependent PI3K/Akt signaling / TNF receptor superfamily (TNFSF) members mediating non-canonical NF-kB pathway / Dectin-1 mediated noncanonical NF-kB signaling / NIK-->noncanonical NF-kB signaling / TNFR2 non-canonical NF-kB pathway / mitogen-activated protein kinase kinase kinase / non-canonical NF-kappaB signal transduction / MAP kinase kinase kinase activity / canonical NF-kappaB signal transduction / fibrillar center ...CD28 dependent PI3K/Akt signaling / TNF receptor superfamily (TNFSF) members mediating non-canonical NF-kB pathway / Dectin-1 mediated noncanonical NF-kB signaling / NIK-->noncanonical NF-kB signaling / TNFR2 non-canonical NF-kB pathway / mitogen-activated protein kinase kinase kinase / non-canonical NF-kappaB signal transduction / MAP kinase kinase kinase activity / canonical NF-kappaB signal transduction / fibrillar center / cellular response to mechanical stimulus / defense response to virus / protein kinase activity / immune response / phosphorylation / protein serine kinase activity / intracellular membrane-bounded organelle / protein serine/threonine kinase activity / nucleoplasm / ATP binding / cytosol Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Liau, N.P.D. / Hymowitz, S.G. | ||||||
Funding support | 1items
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Citation | Journal: Bioorg.Med.Chem.Lett. / Year: 2023 Title: Filling a nick in NIK: Extending the half-life of a NIK inhibitor through structure-based drug design. Authors: Crawford, J.J. / Feng, J. / Brightbill, H.D. / Johnson, A.R. / Wright, M. / Kolesnikov, A. / Lee, W. / Castanedo, G.M. / Do, S. / Blaquiere, N. / Staben, S.T. / Chiang, P.C. / Fan, P.W. / ...Authors: Crawford, J.J. / Feng, J. / Brightbill, H.D. / Johnson, A.R. / Wright, M. / Kolesnikov, A. / Lee, W. / Castanedo, G.M. / Do, S. / Blaquiere, N. / Staben, S.T. / Chiang, P.C. / Fan, P.W. / Baumgardner, M. / Wong, S. / Godemann, R. / Grabbe, A. / Wiegel, C. / Sujatha-Bhaskar, S. / Hymowitz, S.G. / Liau, N. / Hsu, P.L. / McEwan, P.A. / Ismaili, M.H.A. / Landry, M.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7szr.cif.gz | 250 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7szr.ent.gz | 204.3 KB | Display | PDB format |
PDBx/mmJSON format | 7szr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sz/7szr ftp://data.pdbj.org/pub/pdb/validation_reports/sz/7szr | HTTPS FTP |
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-Related structure data
Related structure data | 6g4yS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 38801.680 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Map3k14, Nik / Production host: Spodoptera frugiperda (fall armyworm) References: UniProt: Q9WUL6, mitogen-activated protein kinase kinase kinase #2: Chemical | ChemComp-SO4 / #3: Chemical | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.33 Å3/Da / Density % sol: 63.11 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion / pH: 6.2 Details: 100 mM sodium citrate tribasic dihydrate (pH 6.2), 0.5 M ammonium sulfate, 0.9 M lithium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97949 Å |
Detector | Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: May 23, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→48.18 Å / Num. obs: 45790 / % possible obs: 99.82 % / Redundancy: 6.6 % / Biso Wilson estimate: 75.95 Å2 / CC1/2: 0.998 / Rrim(I) all: 0.1121 / Net I/σ(I): 15.26 |
Reflection shell | Resolution: 2.8→2.9 Å / Mean I/σ(I) obs: 1.51 / Num. unique obs: 2374 / CC1/2: 0.78 / Rpim(I) all: 0.524 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6G4Y Resolution: 2.8→48.18 Å / SU ML: 0.5 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 32.42 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 309.81 Å2 / Biso mean: 94.9449 Å2 / Biso min: 36.87 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.8→48.18 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 16
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