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- PDB-8die: Virtual screening for novel SARS-CoV-2 main protease non-covalent... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8die | ||||||
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Title | Virtual screening for novel SARS-CoV-2 main protease non-covalent and covalent inhibitors | ||||||
![]() | 3C-like proteinase nsp5 | ||||||
![]() | VIRAL PROTEIN / HYDROLASE/INHIBITOR / SARS-CoV2 / MPro / nsp7 / COVID-19 / HYDROLASE-INHIBITOR complex | ||||||
Function / homology | ![]() protein guanylyltransferase activity / RNA endonuclease activity, producing 3'-phosphomonoesters / mRNA guanylyltransferase activity / 5'-3' RNA helicase activity / Lyases; Phosphorus-oxygen lyases / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / Assembly of the SARS-CoV-2 Replication-Transcription Complex (RTC) / Maturation of replicase proteins / ISG15-specific peptidase activity / Transcription of SARS-CoV-2 sgRNAs ...protein guanylyltransferase activity / RNA endonuclease activity, producing 3'-phosphomonoesters / mRNA guanylyltransferase activity / 5'-3' RNA helicase activity / Lyases; Phosphorus-oxygen lyases / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / Assembly of the SARS-CoV-2 Replication-Transcription Complex (RTC) / Maturation of replicase proteins / ISG15-specific peptidase activity / Transcription of SARS-CoV-2 sgRNAs / Translation of Replicase and Assembly of the Replication Transcription Complex / TRAF3-dependent IRF activation pathway / Replication of the SARS-CoV-2 genome / snRNP Assembly / double membrane vesicle viral factory outer membrane / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / 5'-3' DNA helicase activity / SARS coronavirus main proteinase / 3'-5'-RNA exonuclease activity / host cell endoplasmic reticulum-Golgi intermediate compartment / host cell endosome / symbiont-mediated suppression of host toll-like receptor signaling pathway / symbiont-mediated degradation of host mRNA / mRNA guanylyltransferase / symbiont-mediated suppression of host ISG15-protein conjugation / G-quadruplex RNA binding / omega peptidase activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / SARS-CoV-2 modulates host translation machinery / mRNA (guanine-N7)-methyltransferase / host cell Golgi apparatus / methyltransferase cap1 / symbiont-mediated perturbation of host ubiquitin-like protein modification / DNA helicase / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / single-stranded RNA binding / host cell perinuclear region of cytoplasm / host cell endoplasmic reticulum membrane / viral protein processing / lyase activity / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / RNA helicase / induction by virus of host autophagy / copper ion binding / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / DNA-templated transcription / lipid binding / host cell nucleus / SARS-CoV-2 activates/modulates innate and adaptive immune responses / ATP hydrolysis activity / proteolysis / RNA binding / zinc ion binding / ATP binding / membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Singh, I. / Shoichet, B.K. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Large library docking for novel SARS-CoV-2 main protease non-covalent and covalent inhibitors. Authors: Fink, E.A. / Bardine, C. / Gahbauer, S. / Singh, I. / Detomasi, T.C. / White, K. / Gu, S. / Wan, X. / Chen, J. / Ary, B. / Glenn, I. / O'Connell, J. / O'Donnell, H. / Fajtova, P. / Lyu, J. / ...Authors: Fink, E.A. / Bardine, C. / Gahbauer, S. / Singh, I. / Detomasi, T.C. / White, K. / Gu, S. / Wan, X. / Chen, J. / Ary, B. / Glenn, I. / O'Connell, J. / O'Donnell, H. / Fajtova, P. / Lyu, J. / Vigneron, S. / Young, N.J. / Kondratov, I.S. / Alisoltani, A. / Simons, L.M. / Lorenzo-Redondo, R. / Ozer, E.A. / Hultquist, J.F. / O'Donoghue, A.J. / Moroz, Y.S. / Taunton, J. / Renslo, A.R. / Irwin, J.J. / Garcia-Sastre, A. / Shoichet, B.K. / Craik, C.S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 127.8 KB | Display | ![]() |
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PDB format | ![]() | 96.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 8dibC ![]() 8dicC ![]() 8didC ![]() 8difC ![]() 8digC ![]() 8dihC ![]() 8diiC ![]() 7ng3S S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 33825.547 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: rep, 1a-1b Production host: ![]() ![]() References: UniProt: P0DTD1, SARS coronavirus main proteinase #2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.02 Å3/Da / Density % sol: 39 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / Details: 0.1 M MES pH 6.5, 20% PEG 6000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 28, 2021 | ||||||||||||||||||||||||
Radiation | Monochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97946 Å / Relative weight: 1 | ||||||||||||||||||||||||
Reflection | Resolution: 1.9→38.94 Å / Num. obs: 42049 / % possible obs: 98.5 % / Redundancy: 6.8 % / Biso Wilson estimate: 33.31 Å2 / CC1/2: 0.986 / Rmerge(I) obs: 0.46 / Rpim(I) all: 0.188 / Rrim(I) all: 0.498 / Net I/σ(I): 4.5 / Num. measured all: 286886 / Scaling rejects: 53 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 7NG3 Resolution: 1.9→38.638 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 37.12 / 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: 81.1 Å2 / Biso mean: 37.9292 Å2 / Biso min: 19.44 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.9→38.638 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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