Research workbench
SARS-cov-2 3CLPRO in complex with 2-(benzotriazol-1-yl)-N-[4-(1H- imidazol-4-YL)PHENYL]-N-(3-THIENYLMETHYL)ACETAMIDE
Analyse SARS-cov-2 3CLPRO in complex with 2-(benzotriazol-1-yl)-N-[4-(1H… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7LMF
- Type
- protein
- Length
- 610 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
- P0DTD1
- Ligands
- Y6G
- Pockets
- 6 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 26% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | 3C-like proteinase (EC 3.4.22.69) | protein | 305 | 26% helix, 29% strand | P0DTD1 |
Ligands and binding sites
- Y6G · 2-(benzotriazol-1-yl)-~{N}-[4-(1~{H}-imidazol-4-yl) phenyl]-~{N}-(thiophen-3-ylmethyl)ethanamide · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 938 | 0.76 | 0.79 | 80 | empty |
| 2 | 232 | 0.54 | 0.77 | 29 | Y6G |
| 3 | 266 | 0.50 | 0.74 | 42 | empty |
| 4 | 217 | 0.50 | 0.75 | 31 | empty |
| 5 | 213 | 0.49 | 0.75 | 30 | empty |
Interfaces
1 interface between chains.
- A–B · 1592 Ų buried · 39 hydrogen bonds · protein-protein
Compared structures
- 7LMF · SARS-CoV-2 3CLPro in complex with 2-(benzotriazol-1-yl)-N-[4-(1H-imidazol-4-yl)phenyl]-N-(… · 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 P0DTD1
- Elsewhere: RCSB PDB 7LMF · PDBe 7LMF · UniProt P0DTD1
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