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Pandda analysis group deposition of computational designs of SARS-cov- 2 main protease covalent inhibitors -- crystal structure of SARS-cov- 2 main protease in complex with lon-wei-ADC59DF6-26 (mpro-X3115)
Analyse Pandda analysis group deposition of computational designs of SARS-cov- 2 main… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5RL2
- Type
- protein
- Length
- 304 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3C-like proteinase
- EC
- 3.4.22.69
- UniProt
- P0DTD1
- Ligands
- VEM
- Pockets
- 4 · best druggability 0.57
Structure
x-ray diffraction · 1 distinct chain · 26% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3C-like proteinase (EC 3.4.22.69) | protein | 304 | 26% helix, 29% strand | P0DTD1 |
Ligands and binding sites
- VEM · N-(4-tert-butylphenyl)-N-[(1R)-2-[(2-methoxyethyl) amino]-2-oxo-1-(pyridin-3-yl)ethyl]propanamide · ligand · chains A
- DMS · Dimethyl sulfoxide · additive · 4 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 238 | 0.57 | 0.79 | 29 | VEM |
| 2 | 83 | 0.49 | 0.83 | 19 | DMS |
| 3 | 75 | 0.31 | 0.74 | 15 | empty |
| 4 | 52 | 0.31 | 0.76 | 16 | empty |
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 5RL2 · PanDDA analysis group deposition of computational designs of SARS-CoV-2 main protease… · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P0DTD1
- Elsewhere: RCSB PDB 5RL2 · PDBe 5RL2 · UniProt P0DTD1
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