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The co-crystal structure of SARS-cov-2 main protease with the peptidomimetic inhibitor (S)-2-cinnamamido-N-((S)-1-oxo-3-((S)-2- oxopyrrolidin-3-YL)PROPAN-2-YL)PENT-4-ynamide
Analyse The co-crystal structure of SARS-cov-2 main protease with the peptidomimetic… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7DHJ
- Type
- protein
- Length
- 303 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3C-like proteinase
- EC
- 3.4.22.69
- UniProt
- P0DTC1
- Ligands
- H6R
- Pockets
- 2 · best druggability 0.50
Structure
x-ray diffraction · 1 distinct chain · 26% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3C-like proteinase (EC 3.4.22.69) | protein | 303 | 26% helix, 29% strand | P0DTC1 |
Ligands and binding sites
- H6R · (2~{S})-~{N}-[(2~{S})-1-oxidanylidene-3-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]propan-2-yl]-2-[[(~{E})-3-phenylprop-2-enoyl]amino]pent-4-ynamide · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 213 | 0.50 | 0.76 | 26 | H6R |
| 2 | 53 | 0.30 | 0.76 | 14 | empty |
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 7DHJ · The co-crystal structure of SARS-CoV-2 main protease with the peptidomimetic inhibitor… · 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 7DHJ · PDBe 7DHJ · UniProt P0DTC1
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