Research workbench
SARS-cov-2 3CL protease (3CL pro) in complex with a novel inhibitor
Analyse SARS-cov-2 3CL protease (3CL pro) in complex with a novel inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6M2N
- Type
- protein
- Length
- 1,223 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3C-like proteinase
- EC
- 3.4.22.69
- UniProt
- P0DTD1
- Ligands
- 3WL
- Pockets
- 16 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 25% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D | 3C-like proteinase (EC 3.4.22.69) | protein | 306 | 25% helix, 29% strand | P0DTD1 |
| C | 3C-like proteinase (EC 3.4.22.69) | protein | 305 | 26% helix, 29% strand | P0DTD1 |
Ligands and binding sites
- 3WL · 5,6,7-trihydroxy-2-phenyl-4H-chromen-4-one · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1010 | 0.77 | 0.79 | 84 | empty |
| 2 | 1023 | 0.77 | 0.79 | 89 | empty |
| 3 | 740 | 0.72 | 0.78 | 60 | empty |
| 4 | 362 | 0.57 | 0.75 | 53 | empty |
| 5 | 270 | 0.54 | 0.76 | 36 | 3WL |
Interfaces
4 interfaces between chains.
- A–C · 1487 Ų buried · 40 hydrogen bonds · protein-protein
- B–D · 1476 Ų buried · 35 hydrogen bonds · protein-protein
- A–D · 112 Ų buried · 0 hydrogen bonds · protein-protein
- C–D · 75 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6M2N · SARS-CoV-2 3CL protease (3CL pro) in complex with a novel inhibitor · 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 6M2N · PDBe 6M2N · UniProt P0DTD1
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