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Crystal structure of the SARS-cov-2(2019-ncov) main protease in complex with compound 23
Analyse Crystal structure of the SARS-cov-2(2019-ncov) main protease in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7M8P
- Type
- protein
- Length
- 606 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
- YSJ
- Pockets
- 6 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 26% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3C-like proteinase (EC 3.4.22.69) | protein | 301 | 25% helix, 29% strand | P0DTD1 |
| B | 3C-like proteinase (EC 3.4.22.69) | protein | 305 | 27% helix, 29% strand | P0DTD1 |
Ligands and binding sites
- YSJ · 5-(3-{3-chloro-5-[(2-chlorophenyl)methoxy]-4-fluorophenyl}-2-oxo-2H-[1,3'-bipyridin]-5-yl) pyrimidine-2,4(1H,3H)-dione · ligand · 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 | 954 | 0.77 | 0.80 | 80 | empty |
| 2 | 354 | 0.54 | 0.74 | 59 | empty |
| 3 | 233 | 0.51 | 0.75 | 29 | empty |
| 4 | 205 | 0.48 | 0.75 | 25 | empty |
| 5 | 186 | 0.48 | 0.76 | 31 | YSJ |
Interfaces
1 interface between chains.
- A–B · 1454 Ų buried · 38 hydrogen bonds · protein-protein
Compared structures
- 7M8P · Crystal structure of the SARS-cov-2(2019-ncov) main protease in complex with compound 23 · 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 7M8P · PDBe 7M8P · UniProt P0DTD1
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