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| Discovery of N-(benzo[1,2,3]triazol-1-yl)-N-(benzyl)acetamido)phenyl) carboxamides as severe acute respiratory syndrome coronavirus (SARS-CoV) 3CLpro inhibitors: identification of ML300 and non-covalent nanomolar inhibitors with an induced-fit binding |
| This entry was created with PDB-REDO version 8.07 using the deposited PDB model version 1.3 |
| From original header | |||||||
|---|---|---|---|---|---|---|---|
| Spacegroup | C 1 2 1 | a: 118.824 Å | b: 56.244 Å | c: 56.244 Å | α: 90.00° | β: 111.13° | γ: 90.00° |
| Resolution | 1.60 Å | Reflections | 41353 | Test set | 2081 (5.0%) | ||
| R | 0.1699 | R-free | 0.2123 | ||||
| According to PDB-REDO | |||||||
| Resolution | 1.60 Å | Reflections | 41353 | Test set | 2081 (5.0%) | ||
| Twin | false | Radiation damage | 42 | ||||
| PDB-REDO files | |||||||
| Re-refined and rebuilt structure | Re-refined (only) structure |
All files
(compressed) |
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| Links | |||||||
| PDBe | RCSB PDB | 3D bionotes | Proteopedia | ||||
| Original | PDB-REDO | |
|---|---|---|
| Crystallographic refinement | ||
| R | 0.1935 | 0.1584 |
| R-free | 0.2269 | 0.1967 |
| Bond length RMS Z-score | 1.070 | 0.731 |
| Bond angle RMS Z-score | 0.838 | 0.816 |
| Model quality | ||
| Ramachandran plot normality | -0.388 73 | -0.568 68 |
| Rotamer normality | -0.913 74 | -0.509 82 |
| Coarse packing | 0.061 52 | 0.017 50 |
| Fine packing | -1.865 18 | -1.660 25 |
| Bump severity | 0.001 90 | 0.007 65 |
| Hydrogen bond satisfaction | 0.889 37 | 0.899 49 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 10 |
| Side chains flipped | 0 |
| Waters removed | 124 |
| Peptides flipped | 0 |
| Chiralities fixed | 0 |
| Residues fitting density better | 50 |
| Residues fitting density worse | 0 |