Download MendeleyLigand screen against SARS-CoV-2 NSP3 macrodomain
Correy, G.J., Fraser, J.S.To be published.
9D6G | pdb_00009d6g
Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with AVI-3716
- PDB DOI: https://doi.org/10.2210/pdb9D6G/pdb
- Classification: VIRAL PROTEIN
- Organism(s): Severe acute respiratory syndrome coronavirus 2
- Expression System: Escherichia coli BL21(DE3)
- Mutation(s): No
- Deposited: 2024-08-15 Released: 2025-05-21
- Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.00 ?
- R-Value Free: 0.142 (Depositor), 0.150 (DCC)
- R-Value Work: 0.129 (Depositor), 0.142 (DCC)
- R-Value Observed: 0.130 (Depositor)
Starting Model: experimental
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wwPDB Validation 3D Report Full Report
This is version 1.0 of the entry. See complete history.
Literature
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Non-structural protein 3 | 169 | Severe acute respiratory syndrome coronavirus 2 | Mutation(s): 0 Gene Names: rep, 1a-1b EC: 3.4.22 |  | |
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 | |
| A1A2F (Subject of Investigation/LOI) Query on A1A2F | E [auth A] | [(2R,3S)-3-methyl-1-(7H-pyrrolo[2,3-d]pyrimidin-4-yl)piperidin-2-yl]methanol C13 H18 N4 O GXQARUAFSUJAQV-ONGXEEELSA-N |  | ||
| DMS Query on DMS | C [auth A], D [auth A] | DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.00 ?
- R-Value Free: 0.142 (Depositor), 0.150 (DCC)
- R-Value Work: 0.129 (Depositor), 0.142 (DCC)
- R-Value Observed: 0.130 (Depositor)
Space Group: P 43
Unit Cell:
| Length ( ? ) | Angle ( ? ) |
|---|---|
| a = 88.774 | ¦Á = 90 |
| b = 88.774 | ¦Â = 90 |
| c = 39.64 | ¦Ă = 90 |
| Software Name | Purpose |
|---|---|
| PHENIX | refinement |
| XDS | data scaling |
| XDS | data reduction |
| PHASER | phasing |
Entry History & Funding Information
Deposition Data
- Released Date: 2025-05-21 Deposition Author(s): Correy, G.J., Fraser, J.S.
| Funding Organization | Location | Grant Number |
|---|---|---|
| National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) | United States | U19AI171110 |
Revision History (Full details and data files)
- Version 1.0: 2025-05-21
Type: Initial release
