Research workbench
SARS-cov-2 3CL protease (3CLPRO) in complex with 7-O-methyl- dihydromyricetin
Analyse SARS-cov-2 3CL protease (3CLPRO) in complex with 7-O-methyl- dihydromyricetin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7DPV
- Type
- protein
- Length
- 1,163 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
- P0DTC1
- Ligands
- HF0
- Pockets
- 17 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 24% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | 3C-like proteinase (EC 3.4.22.69) | protein | 299 | 25% helix, 29% strand | P0DTC1 |
| C | 3C-like proteinase (EC 3.4.22.69) | protein | 282 | 23% helix, 31% strand | P0DTC1 |
| D | 3C-like proteinase (EC 3.4.22.69) | protein | 283 | 24% helix, 30% strand | P0DTC1 |
Ligands and binding sites
- HF0 · (2S,3S)-3,5-dihydroxy-7-methoxy-2-(3,4,5-trihydroxyphenyl)chroman-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
17 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 978 | 0.79 | 0.80 | 88 | empty |
| 2 | 716 | 0.73 | 0.79 | 70 | HF0 |
| 3 | 172 | 0.65 | 0.85 | 29 | empty |
| 4 | 242 | 0.59 | 0.80 | 39 | empty |
| 5 | 232 | 0.54 | 0.77 | 45 | empty |
Interfaces
3 interfaces between chains.
- A–C · 1203 Ų buried · 30 hydrogen bonds · protein-protein
- A–D · 532 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 436 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 7DPV · SARS-CoV-2 3CL protease (3CLpro) in complex with 7-O-methyl-dihydromyricetin · 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 P0DTC1
- Elsewhere: RCSB PDB 7DPV · PDBe 7DPV · UniProt P0DTC1
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