Research workbench
Crystal structure of SARS-cov-2 3CLPRO in complex with the non- covalent inhibitor wu-04
Analyse Crystal structure of SARS-cov-2 3CLPRO in complex with the non- covalent… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7EN8
- Type
- protein
- Length
- 607 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3C-like proteinase
- EC
- 3.4.22.69
- UniProt
- P0DTC1
- Ligands
- J7R
- Pockets
- 7 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 26% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3C-like proteinase (EC 3.4.22.69) | protein | 306 | 26% helix, 29% strand | P0DTC1 |
| B | 3C-like proteinase (EC 3.4.22.69) | protein | 301 | 26% helix, 30% strand | P0DTC1 |
Ligands and binding sites
- J7R · ~{N}-[(1~{S},2~{R})-2-[[4-bromanyl-2-(methylcarbamoyl)-6-nitro-phenyl]amino]cyclohexyl]isoquinoline-4-carboxamide · ligand · 2 copies · chains A, B
- GOL · Glycerol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 979 | 0.75 | 0.78 | 80 | empty |
| 2 | 439 | 0.57 | 0.74 | 57 | empty |
| 3 | 201 | 0.49 | 0.76 | 29 | J7R |
| 4 | 188 | 0.44 | 0.74 | 27 | J7R |
| 5 | 153 | 0.42 | 0.74 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 1492 Ų buried · 44 hydrogen bonds · protein-protein
Compared structures
- 7EN8 · Crystal structure of SARS-CoV-2 3CLpro in complex with the non-covalent inhibitor WU-04 · 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 7EN8 · PDBe 7EN8 · UniProt P0DTC1
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