Research workbench
Structure of HKU4 3CLPRO bound to non-covalent inhibitor 1A
Analyse Structure of HKU4 3CLPRO bound to non-covalent inhibitor 1A in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4YOI
- 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
- 4F4
- Pockets
- 7 · 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
- 4F4 · N-{4-[(1H-benzotriazol-1-ylacetyl)(thiophen-3-ylmethyl)amino]phenyl}thiophene-2-carboxamide · ligand · 2 copies · chains A, B
- FMT · Formic acid · additive · 4 copies · chains A, B
- ACT · Acetate ion · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1068 | 0.77 | 0.79 | 73 | ACT, FMT |
| 2 | 456 | 0.64 | 0.77 | 62 | empty |
| 3 | 263 | 0.60 | 0.79 | 34 | empty |
| 4 | 261 | 0.56 | 0.77 | 37 | 4F4 |
| 5 | 187 | 0.53 | 0.78 | 24 | 4F4 |
Interfaces
1 interface between chains.
- A–B · 1284 Ų buried · 32 hydrogen bonds · protein-protein
Compared structures
- 4YOI · Structure of HKU4 3CLpro bound to non-covalent inhibitor 1A · 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 4YOI · PDBe 4YOI · UniProt P0C6W3
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