Research workbench
1.65 a resolution structure of SARS-cov-2 3CL protease in complex with a deuterated GC376 alpha-ketoamide analog (compound 5)
Analyse 1.65 a resolution structure of SARS-cov-2 3CL protease in complex with a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7K0F
- Type
- protein
- Length
- 596 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3C-like proteinase
- EC
- 3.4.22.69
- UniProt
- P0DTD1
- Ligands
- VR4
- Pockets
- 7 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 26% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3C-like proteinase (EC 3.4.22.69) | protein | 297 | 26% helix, 30% strand | P0DTD1 |
| B | 3C-like proteinase (EC 3.4.22.69) | protein | 299 | 26% helix, 29% strand | P0DTD1 |
Ligands and binding sites
- VR4 · N-{(2S,3R)-4-(benzylamino)-3-hydroxy-4-oxo-1-[(3S)-2-oxopyrrolidin-3-yl]butan-2-yl}-N~2~-[(benzyloxy) carbonyl]-L-leucinamide · ligand · 2 copies · chains A, B
- PG4 · Tetraethylene glycol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1012 | 0.73 | 0.76 | 74 | empty |
| 2 | 206 | 0.53 | 0.77 | 38 | empty |
| 3 | 224 | 0.52 | 0.77 | 31 | VR4 |
| 4 | 181 | 0.51 | 0.78 | 30 | VR4 |
| 5 | 160 | 0.49 | 0.78 | 32 | empty |
Interfaces
1 interface between chains.
- A–B · 861 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 7K0F · 1.65 A resolution structure of SARS-CoV-2 3CL protease in complex with a deuterated GC376… · 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 7K0F · PDBe 7K0F · UniProt P0DTD1
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