Research workbench
Papain-like protease of SARS cov-2 in complex with JUN9-72-2 inhibitor
Analyse Papain-like protease of SARS cov-2 in complex with JUN9-72-2 inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7SDR
- Type
- protein
- Length
- 939 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Non-structural protein 3
- EC
- 3.4.19.12, 3.4.22.-, 3.4.22.69
- UniProt
- P0DTC1
- Ligands
- JW9, ZN, CL
- Pockets
- 10 · best druggability 0.89
Structure
x-ray diffraction · 2 distinct chains · 26% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Non-structural protein 3 (EC 3.4.19.12, 3.4.22.-, 3.4.22.69) | protein | 314 | 26% helix, 37% strand | P0DTC1 |
| C | Non-structural protein 3 (EC 3.4.19.12, 3.4.22.-, 3.4.22.69) | protein | 311 | 26% helix, 36% strand | P0DTC1 |
Ligands and binding sites
- JW9 · 4-({methyl[(1r)-1-(naphthalen-1-yl)ethyl]amino}methyl) phenol · ligand · 3 copies · chains A, B, C
- ZN · Zinc ion · metal · 3 copies · chains A, B, C
- CL · Chloride ion · ion · chains B
- EDO · 1,2-ethanediol · additive · 5 copies · chains A, B, C
- GOL · Glycerol · additive · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1058 | 0.89 | 0.90 | 110 | JW9 |
| 2 | 444 | 0.76 | 0.85 | 51 | GOL, EDO |
| 3 | 474 | 0.71 | 0.81 | 47 | empty |
| 4 | 95 | 0.46 | 0.80 | 19 | empty |
| 5 | 104 | 0.43 | 0.78 | 25 | JW9 |
Interfaces
3 interfaces between chains.
- B–C · 1604 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 395 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 346 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 7SDR · Papain-Like Protease of SARS CoV-2 in Complex with Jun9-72-2 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 P0DTC1
- Elsewhere: RCSB PDB 7SDR · PDBe 7SDR · UniProt P0DTC1
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