Download MendeleySARS-CoV-2 Main Protease in complex with (3R)-3-[(3R)-4-benzyl-3-phenyl-piperidine-1-carbonyl]indan-1-one
Hanoulle, X., Charton, J., Deprez, B.To be published.
9HDJ | pdb_00009hdj
SARS-CoV-2 Main Protease in complex with (3R)-3-[(3R)-4-benzyl-3-phenyl-piperidine-1-carbonyl]indan-1-one
- PDB DOI: https://doi.org/10.2210/pdb9HDJ/pdb
- Classification: VIRAL PROTEIN
- Organism(s): Severe acute respiratory syndrome coronavirus 2
- Expression System: Escherichia coli BL21(DE3)
- Mutation(s): No
- Deposited: 2024-11-12 Released: 2024-11-27
- Funding Organization(s): European Union (EU), Centre National de la Recherche Scientifique (CNRS)
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.05 Å
- R-Value Free: 0.281 (Depositor), 0.282 (DCC)
- R-Value Work: 0.218 (Depositor), 0.216 (DCC)
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): 0 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 | |
| A1IT1 (Subject of Investigation/LOI) Query on A1IT1 | C [auth A], D [auth B] | (3~{R})-3-[(3~{R})-3-phenyl-4-(phenylmethyl)piperazin-1-yl]carbonyl-2,3-dihydroinden-1-one C27 H26 N2 O2 UTDHFZWVCNRNGD-RPBOFIJWSA-N |  | ||
| FMT Query on FMT | E [auth B], F [auth B], G [auth B] | FORMIC ACID C H2 O2 BDAGIHXWWSANSR-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.05 Å
- R-Value Free: 0.281 (Depositor), 0.282 (DCC)
- R-Value Work: 0.218 (Depositor), 0.216 (DCC)
Space Group: P 1 21 1
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 44.883 | α = 90 |
| b = 53.858 | β = 100.269 |
| c = 115.296 | γ = 90 |
| Software Name | Purpose |
|---|---|
| REFMAC | refinement |
| PHENIX | refinement |
| Aimless | data scaling |
| PHASER | phasing |
| MxCuBE | data collection |
| XDS | data reduction |
Entry History & Funding Information
Deposition Data
- Released Date: 2024-11-27 Deposition Author(s): Hanoulle, X., Charton, J., Deprez, B.
| Funding Organization | Location | Grant Number |
|---|---|---|
| European Union (EU) | European Union | REACT-EU 22003061 |
| Centre National de la Recherche Scientifique (CNRS) | France | COVID and ViroCrib programs |
Revision History (Full details and data files)
- Version 1.0: 2024-11-27
Type: Initial release
