MolNFT v1 · #169770 · protein
1.70 a resolution structure of SARS-cov-2 3CL protease in complex with inhibitor 7J
6XMK · 3C-like proteinase: “1.70 a resolution structure of SARS-cov-2 3CL protease in complex with inhibitor 7J”. X-ray diffraction, 1 ligand (QYS), 4 pockets (best druggability 0.77). MolNFT v1 #169770 on GenesisL1: 3D structure, binding…
- PDB
- 6XMK
- Type
- protein
- Length
- 600 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
- QYS
- Pockets
- 4 · 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 | 298 | 26% helix, 30% strand | P0DTD1 |
| B | 3C-like proteinase (EC 3.4.22.69) | protein | 302 | 25% helix, 29% strand | P0DTD1 |
Ligands and binding sites
- QYS · (1S,2S)-2-[(N-{[(4,4-difluorocyclohexyl) methoxy]carbonyl}-L-leucyl)amino]-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propane-1-sulfonic acid · ligand · 2 copies · chains A, B
- PG4 · Tetraethylene glycol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 906 | 0.77 | 0.80 | 100 | empty |
| 2 | 203 | 0.54 | 0.78 | 38 | empty |
| 3 | 226 | 0.53 | 0.77 | 29 | QYS |
| 4 | 196 | 0.51 | 0.77 | 25 | QYS |
Interfaces
1 interface between chains.
- A–B · 949 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 6XMK · 1.70 A resolution structure of SARS-CoV-2 3CL protease in complex with inhibitor 7j · 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 6XMK · PDBe 6XMK · UniProt P0DTD1
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