MolNFT v1 · #180880 · protein
SARS-cov-2 main protease immature form - F2X entry library E06 fragment
7LDX · 3C-like proteinase: “SARS-cov-2 main protease immature form - F2X entry library E06 fragment”. X-ray diffraction, 1 ligand (R9V), 7 pockets (best druggability 0.79). MolNFT v1 #180880 on GenesisL1: 3D structure, binding sites and…
- PDB
- 7LDX
- Type
- protein
- Length
- 603 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
- R9V
- Pockets
- 7 · best druggability 0.79
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 | 304 | 26% helix, 29% strand | P0DTD1 |
| B | 3C-like proteinase (EC 3.4.22.69) | protein | 299 | 25% helix, 31% strand | P0DTD1 |
Ligands and binding sites
- R9V · (3-endo)-8-benzyl-8-azabicyclo[3.2.1]octan-3-ol · ligand · 2 copies · chains A, B
- DMS · Dimethyl sulfoxide · additive · 6 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 3 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 | 1038 | 0.79 | 0.80 | 81 | PEG, DMS |
| 2 | 517 | 0.66 | 0.77 | 62 | DMS |
| 3 | 92 | 0.55 | 0.85 | 21 | DMS |
| 4 | 152 | 0.49 | 0.78 | 23 | empty |
| 5 | 84 | 0.37 | 0.76 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 1285 Ų buried · 26 hydrogen bonds · protein-protein
Compared structures
- 7LDX · SARS-CoV-2 Main protease immature form - F2X Entry Library E06 fragment · 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 7LDX · PDBe 7LDX · UniProt P0DTD1
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