Download MendeleyX-ray structure of SARS-CoV-2 main protease V186F covalently bound to inhibitor GRL-051-22 at 1.60 A
Beechboard, S.N., Mesecar, A.D., Ghosh, A.K.To be published.
9N9B | pdb_00009n9b
X-ray structure of SARS-CoV-2 main protease V186F covalently bound to inhibitor GRL-051-22 at 1.60 A
- PDB DOI: https://doi.org/10.2210/pdb9N9B/pdb
- Classification: VIRAL PROTEIN, HYDROLASE
- Organism(s): Severe acute respiratory syndrome coronavirus 2
- Expression System: Escherichia coli
- Mutation(s): Yes
- Deposited: 2025-02-10 Released: 2025-11-26
- Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.60 Å
- R-Value Free: 0.185 (Depositor), 0.186 (DCC)
- R-Value Work: 0.136 (Depositor), 0.138 (DCC)
- R-Value Observed: 0.138 (Depositor)
Starting Model: experimental
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This is version 1.0 of the entry. See complete history.
Literature
To be published.
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| 3C-like proteinase nsp5 | 306 | Severe acute respiratory syndrome coronavirus 2 | Mutation(s): 1 Gene Names: rep, 1a-1b EC: 3.4.22.69 |  | |
UniProt | |||||
Find proteins for P0DTD1 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTD1 Go to UniProtKB: P0DTD1 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P0DTD1 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 2 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| A1BFE (Subject of Investigation/LOI) Query on A1BFE | B [auth A] | (3S)-N-{(1Z,2S)-1-imino-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-2-[3-methyl-N-(trifluoroacetyl)-L-valyl]-1,2,3,4-tetrahydroisoquinoline-3-carboxamide C25 H32 F3 N5 O4 PFRRKDXMXGNRNI-DSLXNQLJSA-N |  | ||
| DMS Query on DMS | C [auth A] | DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.60 Å
- R-Value Free: 0.185 (Depositor), 0.186 (DCC)
- R-Value Work: 0.136 (Depositor), 0.138 (DCC)
- R-Value Observed: 0.138 (Depositor)
Space Group: C 1 2 1
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 96.42 | α = 90 |
| b = 82.186 | β = 117.368 |
| c = 54.441 | γ = 90 |
| Software Name | Purpose |
|---|---|
| PHENIX | refinement |
| CrysalisPro | data reduction |
| CrysalisPro | data scaling |
| PHENIX | phasing |
Entry History & Funding Information
Deposition Data
- Released Date: 2025-11-26 Deposition Author(s): Beechboard, S.N., Meadows, M.S., Ghosh, A.K., Mesecar, A.D., Center for Structural Biology of Infectious Diseases (CSBID)
| Funding Organization | Location | Grant Number |
|---|---|---|
| National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) | United States | HHSN272201700060C |
| National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) | United States | 1RO1 AI158649 |
| National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) | United States | GM132024 |
| National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) | United States | S10 OD03050 |
Revision History (Full details and data files)
- Version 1.0: 2025-11-26
Type: Initial release
