MolNFT v1 · #176254 · protein
The co-crystal structure of SARS-cov-2 main protease with peptidomimetic inhibitor (S)-2-cinnamamido-N-((S)-1-oxo-3-((S)-2- oxopiperidin-3-YL)PROPAN-2-YL)HEXANAMIDE
7DGF · 3C-like proteinase: “The co-crystal structure of SARS-cov-2 main protease with peptidomimetic inhibitor…”. X-ray diffraction, 1 ligand (H60), 2 pockets (best druggability 0.55). MolNFT v1 #176254 on GenesisL1: 3D structure, binding…
- PDB
- 7DGF
- 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
- H60
- Pockets
- 2 · best druggability 0.55
Structure
x-ray diffraction · 1 distinct chain · 25% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3C-like proteinase (EC 3.4.22.69) | protein | 303 | 25% helix, 29% strand | P0DTC1 |
Ligands and binding sites
- H60 · (2~{S})-~{N}-[(2~{S})-1-oxidanylidene-3-[(3~{S})-2-oxidanylidenepiperidin-3-yl]propan-2-yl]-2-[[(~{E})-3-phenylprop-2-enoyl]amino]hexanamide · 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 233 | 0.55 | 0.78 | 31 | H60 |
| 2 | 123 | 0.38 | 0.74 | 27 | empty |
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 7DGF · The co-crystal structure of SARS-CoV-2 main protease with 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 7DGF · PDBe 7DGF · UniProt P0DTC1
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