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- PDB-7p2g: Identification of low micromolar SARS-CoV-2 Mpro inhibitors from ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7p2g | ||||||
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Title | Identification of low micromolar SARS-CoV-2 Mpro inhibitors from hits identified by in silico screens | ||||||
![]() | 3C-like proteinase | ||||||
![]() | HYDROLASE / SARS-CoV-2 / Mpro / inhibitor / protease | ||||||
Function / homology | ![]() SARS coronavirus main proteinase / DNA helicase / ubiquitinyl hydrolase 1 / RNA helicase / RNA-directed RNA polymerase Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Rempel, S. / Halazonetis, T.D. | ||||||
![]() | ![]() Title: Non-covalent SARS-CoV-2 M pro inhibitors developed from in silico screen hits. Authors: Rossetti, G.G. / Ossorio, M.A. / Rempel, S. / Kratzel, A. / Dionellis, V.S. / Barriot, S. / Tropia, L. / Gorgulla, C. / Arthanari, H. / Thiel, V. / Mohr, P. / Gamboni, R. / Halazonetis, T.D. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 159 KB | Display | ![]() |
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PDB format | ![]() | 105.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 724.4 KB | Display | ![]() |
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Full document | ![]() | 727.3 KB | Display | |
Data in XML | ![]() | 13.1 KB | Display | |
Data in CIF | ![]() | 16.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6wqfS S: Starting model for refinement |
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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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1 |
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Unit cell |
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Components
#1: Protein | Mass: 33825.547 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: ORF1ab / Production host: ![]() ![]() References: UniProt: A0A7L9RWV7, RNA-directed RNA polymerase, ubiquitinyl hydrolase 1, SARS coronavirus main proteinase, DNA helicase, RNA helicase |
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#2: Chemical | ChemComp-4N0 / ( |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.03 Å3/Da / Density % sol: 39.48 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 0.1 M Tris, 25% (v/v) PEG 3350, 0.2 M lithium chloride |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 16, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→48.53 Å / Num. obs: 31270 / % possible obs: 98.65 % / Redundancy: 3.4 % / Biso Wilson estimate: 74.18 Å2 / CC1/2: 0.983 / CC star: 0.996 / Net I/σ(I): 8.38 |
Reflection shell | Resolution: 2.5→2.59 Å / Redundancy: 3.2 % / Num. unique obs: 912 / CC1/2: 0.208 / CC star: 0.587 / % possible all: 97.33 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6WQF Resolution: 2.5→48.53 Å / Cross valid method: FREE R-VALUE / σ(F): 1.14 / Phase error: 44.4908 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→48.53 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A
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