MolNFT v1 · #168183 · protein
Structure of pedv main protease bound to potent broad-spectrum non- covalent inhibitor X77
6W81 · Peptidase C30: “Structure of pedv main protease bound to potent broad-spectrum non- covalent inhibitor X77”. X-ray diffraction, 1 ligand (X77), 5 pockets (best druggability 0.77). MolNFT v1 #168183 on GenesisL1: 3D structure…
- PDB
- 6W81
- Type
- protein
- Length
- 602 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peptidase C30
- UniProt
- S0AP56
- Ligands
- X77
- Pockets
- 5 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 24% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Peptidase C30 | protein | 302 | 24% helix, 29% strand | S0AP56 |
| B | Peptidase C30 | protein | 300 | 24% helix, 29% strand | S0AP56 |
Ligands and binding sites
- X77 · N-(4-tert-butylphenyl)-N-[(1R)-2-(cyclohexylamino)-2-oxo-1-(pyridin-3-yl)ethyl]-1H-imidazole-4-carboxamide · ligand · 2 copies · chains A, B
- MLA · Malonic acid · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 901 | 0.77 | 0.80 | 98 | MLA |
| 2 | 360 | 0.64 | 0.79 | 41 | empty |
| 3 | 306 | 0.58 | 0.77 | 47 | empty |
| 4 | 238 | 0.55 | 0.78 | 31 | X77 |
| 5 | 180 | 0.49 | 0.77 | 28 | X77 |
Interfaces
1 interface between chains.
- A–B · 1506 Ų buried · 40 hydrogen bonds · protein-protein
Compared structures
- 6W81 · Structure of PEDV main protease bound to potent broad-spectrum non-covalent inhibitor X77 · 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 S0AP56
- Elsewhere: RCSB PDB 6W81 · PDBe 6W81 · UniProt S0AP56
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