Research workbench
Crystal structure of the SARS-cov-2 main protease complexed with N- (pyridin-3-YLMETHYL)THIOFORMAMIDE
Analyse Crystal structure of the SARS-cov-2 main protease complexed with N… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7NTQ
- Type
- protein
- Length
- 305 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
- 35J, NA
- Pockets
- 3 · best druggability 0.52
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 | 305 | 26% helix, 29% strand | P0DTC1 |
Ligands and binding sites
- 35J · N-(pyridin-3-ylmethyl)thioformamide · ligand · chains A
- NA · Sodium ion · metal · 3 copies · chains A
- FMT · Formic acid · additive · 7 copies · chains A
- DMS · Dimethyl sulfoxide · additive · 5 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 66 | 0.52 | 0.86 | 16 | DMS |
| 2 | 193 | 0.50 | 0.77 | 25 | 35J, FMT |
| 3 | 78 | 0.35 | 0.76 | 16 | empty |
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 7NTQ · Crystal structure of the SARS-CoV-2 Main Protease complexed 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 7NTQ · PDBe 7NTQ · UniProt P0DTC1
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