Research workbench
Peptidomimetic nitrile warheads as SARS-cov-2 3CL protease inhibitors
Analyse Peptidomimetic nitrile warheads as SARS-cov-2 3CL protease inhibitors in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7R7H
- Type
- protein
- Length
- 612 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3C-like proteinase
- EC
- 3.4.22.69
- UniProt
- P0DTD1
- Ligands
- 4IT
- Pockets
- 6 · best druggability 0.77
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 | 306 | 26% helix, 29% strand | P0DTD1 |
Ligands and binding sites
- 4IT · N-[(2S)-1-({(1E,2S)-1-imino-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}amino)-4-methyl-1-oxopentan-2-yl]-4-methoxy-1H-indole-2-carboxamide · 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1013 | 0.77 | 0.79 | 91 | empty |
| 2 | 243 | 0.57 | 0.78 | 30 | 4IT |
| 3 | 210 | 0.54 | 0.78 | 27 | 4IT |
| 4 | 164 | 0.43 | 0.74 | 34 | empty |
| 5 | 82 | 0.34 | 0.75 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 1775 Ų buried · 36 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 7R7H · Peptidomimetic nitrile warheads as SARS-CoV-2 3CL protease inhibitors · 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 7R7H · PDBe 7R7H · UniProt P0DTD1
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