MolNFT v1 · #111356 · protein
HKU4-3CLPRO bound to non-covalent inhibitor 3B
4YOG · 3C-like proteinase: “HKU4-3CLPRO bound to non-covalent inhibitor 3B”. X-ray diffraction, 1 ligand (4F5), 5 pockets (best druggability 0.77). MolNFT v1 #111356 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4YOG
- Type
- protein
- Length
- 612 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3C-like proteinase
- EC
- 3.4.22.-
- UniProt
- P0C6W3
- Ligands
- 4F5
- Pockets
- 5 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 25% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | 3C-like proteinase (EC 3.4.22.-) | protein | 306 | 25% helix, 30% strand | P0C6W3 |
Ligands and binding sites
- 4F5 · N-[4-(acetylamino)phenyl]-2-(1H-benzotriazol-1-yl)-N-[(1R)-2-(tert-butylamino)-2-oxo-1-(thiophen-3-yl)ethyl]acetamide · ligand · 2 copies · chains A, B
- ACT · Acetate ion · additive · 7 copies · 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 | 1037 | 0.77 | 0.79 | 81 | ACT |
| 2 | 921 | 0.74 | 0.77 | 108 | ACT |
| 3 | 263 | 0.51 | 0.75 | 34 | 4F5 |
| 4 | 187 | 0.50 | 0.77 | 27 | 4F5 |
| 5 | 79 | 0.32 | 0.74 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 1305 Ų buried · 32 hydrogen bonds · protein-protein
Compared structures
- 4YOG · HKU4-3CLpro bound to non-covalent inhibitor 3B · 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 P0C6W3
- Elsewhere: RCSB PDB 4YOG · PDBe 4YOG · UniProt P0C6W3
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.