MolNFT v1 · #180078 · protein
The crystal structure of papain-like protease of SARS cov-2, C111S mutant, in complex with PLP_SNYDER494 inhibitor
7KOJ: “The crystal structure of papain-like protease of SARS cov-2, C111S mutant, in complex with PLP_SNYDER494…”. X-ray diffraction, 4 ligands (Y94, ZN, UNX), 3 pockets (best druggability 0.47). MolNFT v1 #180078 on GenesisL1: 3D…
- PDB
- 7KOJ
- Type
- protein
- Length
- 313 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Papain-like protease
- EC
- 3.4.22.-
- UniProt
- P0DTC1
- Ligands
- Y94, ZN, UNX, CL
- Pockets
- 3 · best druggability 0.47
Structure
x-ray diffraction · 1 distinct chain · 26% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Papain-like protease (EC 3.4.22.-) | protein | 313 | 26% helix, 35% strand | P0DTC1 |
Ligands and binding sites
- Y94 · 2-methyl-N-[(1R)-1-(naphthalen-1-yl)ethyl]-5-{[(prop-2-en-1-yl)carbamoyl]amino}benzamide · ligand · chains A
- ZN · Zinc ion · metal · 4 copies · chains A
- UNX · Unknown atom or ion · ion · 12 copies · chains A
- CL · Chloride ion · ion · 3 copies · chains A
- ACT · Acetate ion · additive · 2 copies · chains A
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 50 | 0.47 | 0.85 | 14 | empty |
| 2 | 107 | 0.44 | 0.78 | 23 | empty |
| 3 | 69 | 0.37 | 0.77 | 17 | Y94 |
Compared structures
- 7KOJ · The crystal structure of Papain-Like Protease of SARS CoV-2, C111S mutant, in complex… · 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 7KOJ · PDBe 7KOJ · UniProt P0DTC1
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