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- PDB-6xhm: Covalent complex of SARS-CoV-2 main protease with N-[(2S)-1-({(2S... -
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Basic information
Entry | Database: PDB / ID: 6xhm | |||||||||
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Title | Covalent complex of SARS-CoV-2 main protease with N-[(2S)-1-({(2S,3S)-3,4-dihydroxy-1-[(3S)-2-oxopyrrolidin-3-yl]butan-2-yl}amino)-4-methyl-1-oxopentan-2-yl]-4-methoxy-1H-indole-2-carboxamide | |||||||||
![]() | 3C-like proteinase | |||||||||
![]() | VIRAL PROTEIN / coronavirus protease 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 | ![]() ![]() ![]() | |||||||||
![]() | Gajiwala, K.S. / Ferre, R.A. / Ryan, K. / Stewart, A.E. | |||||||||
![]() | ![]() Title: Discovery of Ketone-Based Covalent Inhibitors of Coronavirus 3CL Proteases for the Potential Therapeutic Treatment of COVID-19. Authors: Hoffman, R.L. / Kania, R.S. / Brothers, M.A. / Davies, J.F. / Ferre, R.A. / Gajiwala, K.S. / He, M. / Hogan, R.J. / Kozminski, K. / Li, L.Y. / Lockner, J.W. / Lou, J. / Marra, M.T. / ...Authors: Hoffman, R.L. / Kania, R.S. / Brothers, M.A. / Davies, J.F. / Ferre, R.A. / Gajiwala, K.S. / He, M. / Hogan, R.J. / Kozminski, K. / Li, L.Y. / Lockner, J.W. / Lou, J. / Marra, M.T. / Mitchell Jr., L.J. / Murray, B.W. / Nieman, J.A. / Noell, S. / Planken, S.P. / Rowe, T. / Ryan, K. / Smith 3rd, G.J. / Solowiej, J.E. / Steppan, C.M. / Taggart, B. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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PDBx/mmCIF format | ![]() | 142.9 KB | Display | ![]() |
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PDB format | ![]() | 110 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6xhlC ![]() 6xhnC ![]() 6xhoC ![]() 5r8tS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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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 Details: N-[(2S)-1-({(2S,3S)-3,4-dihydroxy-1-[(3S)-2-oxopyrrolidin-3-yl]butan-2-yl}amino)-4-methyl-1-oxopentan-2-yl]-4-methoxy-1H-indole-2-carboxamide Source: (gene. exp.) ![]() ![]() Gene: rep, 1a-1b / Production host: ![]() ![]() References: UniProt: P0DTD1, SARS coronavirus main proteinase #2: Chemical | #3: Chemical | ChemComp-EDO / | #4: 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: 2.3 Å3/Da / Density % sol: 46.49 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion Details: Precipitant: 25.0 %w/v (25.0 uL of stock 50.0 %w/v) PEG 1500, Buffer: 0.1 M (5.0 uL of stock 1.0 M) MMT (pH 4.00) |
-Data collection
Diffraction | Mean temperature: 98 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: May 21, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.406→56.39 Å / Num. obs: 87382 / % possible obs: 75 % / Redundancy: 3.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.047 / Net I/σ(I): 12.3 |
Reflection shell | Resolution: 1.406→1.526 Å / Rmerge(I) obs: 0.721 / Num. unique obs: 4369 / CC1/2: 0.59 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5R8T Resolution: 1.406→56.39 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.954 / SU R Cruickshank DPI: 0.083 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.085 / SU Rfree Blow DPI: 0.08 / SU Rfree Cruickshank DPI: 0.08
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Displacement parameters | Biso mean: 24.33 Å2
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Refine analyze | Luzzati coordinate error obs: 0.21 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.406→56.39 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.41→1.49 Å
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