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A SARS-COV2 major protease non-covalent ligand structure determined to 2.0 a resolution
Analyse A SARS-COV2 major protease non-covalent ligand structure determined to 2.0 a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7PFM
- Type
- protein
- Length
- 610 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Replicase polyprotein 1AB
- UniProt
- P0DTD1
- Ligands
- 7IL
- Pockets
- 6 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 26% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Replicase polyprotein 1AB | protein | 305 | 26% helix, 29% strand | P0DTD1 |
Ligands and binding sites
- 7IL · N-[(1R)-2-(tert-butylamino)-2-oxidanylidene-1-pyridin-3-yl-ethyl]-N-(4-tert-butylphenyl)-1H-imidazole-5-carboxamide · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 893 | 0.75 | 0.79 | 77 | empty |
| 2 | 227 | 0.53 | 0.77 | 29 | 7IL |
| 3 | 309 | 0.52 | 0.74 | 42 | empty |
| 4 | 217 | 0.51 | 0.76 | 26 | 7IL |
| 5 | 151 | 0.44 | 0.75 | 30 | empty |
Interfaces
1 interface between chains.
- A–B · 1643 Ų buried · 44 hydrogen bonds · protein-protein
Compared structures
- 7PFM · A SARS-CoV2 major protease non-covalent ligand structure determined to 2.0 A resolution · 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 7PFM · PDBe 7PFM · UniProt P0DTD1
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