MolNFT v1 · #187046 · protein
Papain-like protease of SARS cov-2 in complex with JUN9-84-3 inhibitor
7RZC · Non-structural protein 3: “Papain-like protease of SARS cov-2 in complex with JUN9-84-3 inhibitor”. X-ray diffraction, 3 ligands (JWX, ZN, CL), 13 pockets (best druggability 0.89). MolNFT v1 #187046 on GenesisL1: 3D structure…
- PDB
- 7RZC
- Type
- protein
- Length
- 940 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.-
- UniProt
- P0DTC1
- Ligands
- JWX, ZN, CL
- Pockets
- 13 · best druggability 0.89
Structure
x-ray diffraction · 2 distinct chains · 26% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Non-structural protein 3 (EC 3.4.19.12, 3.4.22.-) | protein | 314 | 26% helix, 37% strand | P0DTC1 |
| C | Non-structural protein 3 (EC 3.4.19.12, 3.4.22.-) | protein | 312 | 27% helix, 37% strand | P0DTC1 |
Ligands and binding sites
- JWX · (1R)-N-[(1H-indol-3-yl)methyl]-N-methyl-1-(naphthalen-1-yl)ethan-1-amine · ligand · 3 copies · chains A, B, C
- ZN · Zinc ion · metal · 3 copies · chains A, B, C
- CL · Chloride ion · ion · 4 copies · chains A, B, C
- EDO · 1,2-ethanediol · additive · 10 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1088 | 0.89 | 0.90 | 122 | JWX |
| 2 | 441 | 0.77 | 0.86 | 49 | EDO |
| 3 | 256 | 0.64 | 0.82 | 33 | EDO |
| 4 | 121 | 0.52 | 0.81 | 31 | empty |
| 5 | 74 | 0.52 | 0.85 | 21 | empty |
Interfaces
3 interfaces between chains.
- B–C · 1507 Ų buried · 23 hydrogen bonds · protein-protein
- A–C · 472 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 367 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 7RZC · Papain-Like Protease of SARS CoV-2 in complex with Jun9-84-3 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 7RZC · PDBe 7RZC · UniProt P0DTC1
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