Download MendeleySARS-CoV-2 Main Protease in complex with with (1R)-N-(3-chlorophenyl)-N-[4-(2,4-dioxo-1H-pyrimidin-5-yl)phenyl]-3-oxo-indane-1-carboxamide
Hanoulle, X., Charton, J., Deprez, B.To be published.
9HD8 | pdb_00009hd8
SARS-CoV-2 Main Protease in complex with with (1R)-N-(3-chlorophenyl)-N-[4-(2,4-dioxo-1H-pyrimidin-5-yl)phenyl]-3-oxo-indane-1-carboxamide
- PDB DOI: https://doi.org/10.2210/pdb9HD8/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: 1.70 Å
- R-Value Free: 0.221 (Depositor), 0.221 (DCC)
- R-Value Work: 0.171 (Depositor), 0.169 (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 | |
| A1ITV (Subject of Investigation/LOI) Query on A1ITV | B [auth A] | (1~{R})-~{N}-[4-[2,4-bis(oxidanylidene)-1~{H}-pyrimidin-5-yl]phenyl]-~{N}-(3-chlorophenyl)-3-oxidanylidene-1,2-dihydroindene-1-carboxamide C26 H18 Cl N3 O4 WUIFAQSQLPAHRA-OAQYLSRUSA-N |  | ||
| NA Query on NA | C [auth A], D [auth A] | SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.70 Å
- R-Value Free: 0.221 (Depositor), 0.221 (DCC)
- R-Value Work: 0.171 (Depositor), 0.169 (DCC)
Space Group: C 1 2 1
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 114.41 | α = 90 |
| b = 53.825 | β = 100.805 |
| c = 44.64 | γ = 90 |
| Software Name | Purpose |
|---|---|
| REFMAC | refinement |
| MxCuBE | data collection |
| Aimless | data scaling |
| MOLREP | phasing |
| 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
