MolNFT v1 · #184858 · protein
Crystal structure of the SARS-cov-2 main protease complexed with fragment F01
7P51 · 3C-like proteinase: “Crystal structure of the SARS-cov-2 main protease complexed with fragment F01”. X-ray diffraction, 2 ligands (5P9, NA), 3 pockets (best druggability 0.51). MolNFT v1 #184858 on GenesisL1: 3D structure, binding…
- PDB
- 7P51
- Type
- protein
- Length
- 306 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
- 5P9, NA
- Pockets
- 3 · best druggability 0.51
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 | 306 | 26% helix, 29% strand | P0DTC1 |
Ligands and binding sites
- 5P9 · N-(5-chloropyridin-2-yl)-3-oxo-2,3-dihydro-1H-indene-1-carboxamide · ligand · chains A
- NA · Sodium ion · metal · 2 copies · chains A
- DMS · Dimethyl sulfoxide · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 188 | 0.51 | 0.77 | 26 | 5P9 |
| 2 | 54 | 0.51 | 0.87 | 19 | DMS |
| 3 | 175 | 0.45 | 0.74 | 26 | empty |
Modifications
Observed in the structure: 2 modified (oxidation).
Compared structures
- 7P51 · Crystal structure of the SARS-cov-2 main protease complexed with fragment F01 · 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 7P51 · PDBe 7P51 · UniProt P0DTC1
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