+Open data
-Basic information
Entry | Database: PDB / ID: 8etr | ||||||
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Title | CryoEM Structure of NLRP3 NACHT domain in complex with G2394 | ||||||
Components | NACHT, LRR and PYD domains-containing protein 3 | ||||||
Keywords | HYDROLASE / NLRP3 / NACHT / inhibitor | ||||||
Function / homology | Function and homology information small molecule sensor activity / detection of biotic stimulus / phosphatidylinositol phosphate binding / cysteine-type endopeptidase activator activity / positive regulation of T-helper 2 cell differentiation / interphase microtubule organizing center / NLRP3 inflammasome complex assembly / positive regulation of T-helper 2 cell cytokine production / NLRP3 inflammasome complex / positive regulation of type 2 immune response ...small molecule sensor activity / detection of biotic stimulus / phosphatidylinositol phosphate binding / cysteine-type endopeptidase activator activity / positive regulation of T-helper 2 cell differentiation / interphase microtubule organizing center / NLRP3 inflammasome complex assembly / positive regulation of T-helper 2 cell cytokine production / NLRP3 inflammasome complex / positive regulation of type 2 immune response / osmosensory signaling pathway / peptidoglycan binding / phosphatidylinositol-4-phosphate binding / negative regulation of non-canonical NF-kappaB signal transduction / microtubule organizing center / negative regulation of interleukin-1 beta production / pattern recognition receptor signaling pathway / negative regulation of NF-kappaB transcription factor activity / pyroptosis / positive regulation of cysteine-type endopeptidase activity involved in apoptotic process / protein maturation / The NLRP3 inflammasome / negative regulation of acute inflammatory response / positive regulation of interleukin-4 production / signaling adaptor activity / Purinergic signaling in leishmaniasis infection / molecular condensate scaffold activity / positive regulation of interleukin-1 beta production / ADP binding / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / protein homooligomerization / defense response / Cytoprotection by HMOX1 / Metalloprotease DUBs / negative regulation of inflammatory response / cellular response to virus / positive regulation of inflammatory response / positive regulation of non-canonical NF-kappaB signal transduction / SARS-CoV-1 activates/modulates innate immune responses / positive regulation of NF-kappaB transcription factor activity / DNA-binding transcription factor binding / cellular response to lipopolysaccharide / sequence-specific DNA binding / molecular adaptor activity / inflammatory response / Golgi membrane / innate immune response / apoptotic process / SARS-CoV-2 activates/modulates innate and adaptive immune responses / endoplasmic reticulum / signal transduction / ATP hydrolysis activity / positive regulation of transcription by RNA polymerase II / mitochondrion / extracellular region / ATP binding / membrane / identical protein binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å | ||||||
Authors | Murray, J.M. / Johnson, M.C. | ||||||
Funding support | 1items
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Citation | Journal: J Med Chem / Year: 2022 Title: Overcoming Preclinical Safety Obstacles to Discover ()--((1,2,3,5,6,7-Hexahydro--indacen-4-yl)carbamoyl)-6-(methylamino)-6,7-dihydro-5-pyrazolo[5,1-][1,3]oxazine-3-sulfonamide (GDC-2394): A ...Title: Overcoming Preclinical Safety Obstacles to Discover ()--((1,2,3,5,6,7-Hexahydro--indacen-4-yl)carbamoyl)-6-(methylamino)-6,7-dihydro-5-pyrazolo[5,1-][1,3]oxazine-3-sulfonamide (GDC-2394): A Potent and Selective NLRP3 Inhibitor. Authors: Christopher McBride / Lynnie Trzoss / Davide Povero / Milos Lazic / Geza Ambrus-Aikelin / Angelina Santini / Rama Pranadinata / Gretchen Bain / Ryan Stansfield / Jeffrey A Stafford / James ...Authors: Christopher McBride / Lynnie Trzoss / Davide Povero / Milos Lazic / Geza Ambrus-Aikelin / Angelina Santini / Rama Pranadinata / Gretchen Bain / Ryan Stansfield / Jeffrey A Stafford / James Veal / Ryan Takahashi / Justin Ly / Shu Chen / Liling Liu / Marika Nespi / Robert Blake / Arna Katewa / Tracy Kleinheinz / Swathi Sujatha-Bhaskar / Nandhini Ramamoorthi / Jessica Sims / Brent McKenzie / Mark Chen / Mark Ultsch / Matthew Johnson / Jeremy Murray / Claudio Ciferri / Steven T Staben / Michael J Townsend / Craig E Stivala / Abstract: Inappropriate activation of the NLRP3 inflammasome has been implicated in multiple inflammatory and autoimmune diseases. Herein, we aimed to develop novel NLRP3 inhibitors that could minimize the ...Inappropriate activation of the NLRP3 inflammasome has been implicated in multiple inflammatory and autoimmune diseases. Herein, we aimed to develop novel NLRP3 inhibitors that could minimize the risk of drug-induced liver injury. Lipophilic ligand efficiency was used as a guiding metric to identify a series of 6,7-dihydro-5H-pyrazolo[5,1-][1,3]oxazinesulfonylureas. A leading compound from this series was advanced into safety studies in cynomolgus monkeys, and renal toxicity, due to compound precipitation, was observed. To overcome this obstacle, we focused on improving the solubility of our compounds, specifically by introducing basic amine substituents into the scaffold. This led to the identification of GDC-2394, a potent and selective NLRP3 inhibitor, with an in vitro and in vivo safety profile suitable for advancement into human clinical trials. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8etr.cif.gz | 170.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8etr.ent.gz | 138.5 KB | Display | PDB format |
PDBx/mmJSON format | 8etr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/et/8etr ftp://data.pdbj.org/pub/pdb/validation_reports/et/8etr | HTTPS FTP |
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-Related structure data
Related structure data | 28596MC M: map data used to model this data C: citing same article (ref.) |
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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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-Components
#1: Protein | Mass: 63380.340 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: NLRP3, C1orf7, CIAS1, NALP3, PYPAF1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q96P20 |
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#2: Chemical | ChemComp-MG / |
#3: Chemical | ChemComp-ADP / |
#4: Chemical | ChemComp-WTN / ( |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: NLRP3 NACHT domain / Type: COMPLEX / Details: NACHT domain only / Entity ID: #1 / Source: RECOMBINANT | |||||||||||||||||||||||||
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Molecular weight | Value: 0.120 MDa / Experimental value: NO | |||||||||||||||||||||||||
Source (natural) | Organism: Homo sapiens (human) | |||||||||||||||||||||||||
Source (recombinant) | Organism: Spodoptera frugiperda (fall armyworm) | |||||||||||||||||||||||||
Buffer solution | pH: 7.5 Details: 0.15M NaCl, 20mM Tris pH 7.5, 10% glycerol, 1mM TCEP, 2.5mM ATP, 2mM MgCl2. | |||||||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 0.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: mono disperse | |||||||||||||||||||||||||
Specimen support | Details: Holey gold grids (UltrAuFoil 25 nm R 1.2/1.3) were glow discharged for 20 seconds using a Solarus plasma cleaner (Gatan, Pleasanton, CA, USA), and grids were blotted and plunge frozen in ...Details: Holey gold grids (UltrAuFoil 25 nm R 1.2/1.3) were glow discharged for 20 seconds using a Solarus plasma cleaner (Gatan, Pleasanton, CA, USA), and grids were blotted and plunge frozen in liquid ethane using a Vitrobot (ThermoFisher Scientific, Waltham, MA), operating at 4C, 100 relative humidity, blot force 7, and with a 4 second blot time. Grid material: GOLD / Grid type: Quantifoil R1.2/1.3 | |||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 3000 nm / Nominal defocus min: 600 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 3 sec. / Electron dose: 64 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 1054244 | ||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 231263 / Algorithm: FOURIER SPACE / Num. of class averages: 2 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: OTHER / Space: REAL |