MolNFT v1 · #176255 · protein
The co-crystal structure of SARS-cov-2 main protease with (S)-2- cinnamamido-N-((S)-1-oxo-3-((S)-2-oxopyrrolidin-3-YL)PROPAN-2-yl) hexanamide
7DGG · 3C-like proteinase: “The co-crystal structure of SARS-cov-2 main protease with (S)-2…”. X-ray diffraction, 1 ligand (H63), 7 pockets (best druggability 0.72). MolNFT v1 #176255 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 7DGG
- Type
- protein
- Length
- 605 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
- H63
- Pockets
- 7 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 26% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3C-like proteinase (EC 3.4.22.69) | protein | 301 | 27% helix, 30% strand | P0DTC1 |
| B | 3C-like proteinase (EC 3.4.22.69) | protein | 304 | 25% helix, 29% strand | P0DTC1 |
Ligands and binding sites
- H63 · (2~{S})-~{N}-[(2~{S})-1-oxidanylidene-3-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]propan-2-yl]-2-[[(~{E})-3-phenylprop-2-enoyl]amino]hexanamide · ligand · 2 copies · chains A, 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 882 | 0.72 | 0.77 | 58 | empty |
| 2 | 462 | 0.60 | 0.75 | 62 | empty |
| 3 | 207 | 0.52 | 0.77 | 25 | H63 |
| 4 | 179 | 0.50 | 0.77 | 23 | H63 |
| 5 | 157 | 0.44 | 0.75 | 28 | empty |
Interfaces
1 interface between chains.
- A–B · 1277 Ų buried · 26 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 7DGG · The co-crystal structure of SARS-CoV-2 main protease with… · 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 7DGG · PDBe 7DGG · UniProt P0DTC1
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