MolNFT v1 · #180808 · protein
SARS-cov-2 papain-like protease (plpro) bound to inhibitor XR8-89
7LBR · Non-structural protein 3: “SARS-cov-2 papain-like protease (plpro) bound to inhibitor XR8-89”. X-ray diffraction, 3 ligands (XT7, ZN, SO4), 8 pockets (best druggability 0.49). MolNFT v1 #180808 on GenesisL1: 3D structure, binding…
- PDB
- 7LBR
- Type
- protein
- Length
- 632 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Non-structural protein 3
- EC
- 3.4.19.12
- UniProt
- P0DTC1
- Ligands
- XT7, ZN, SO4
- Pockets
- 8 · best druggability 0.49
Structure
x-ray diffraction · 1 distinct chain · 26% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Non-structural protein 3 (EC 3.4.19.12) | protein | 316 | 26% helix, 36% strand | P0DTC1 |
Ligands and binding sites
- XT7 · 5-[(azetidin-3-yl)amino]-N-[(1R)-1-{3-[5-({[(1S,3R)-3-hydroxycyclopentyl]amino}methyl)thiophen-2-yl]phenyl}ethyl]-2-methylbenzamide · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 4 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 173 | 0.49 | 0.77 | 31 | empty |
| 2 | 151 | 0.44 | 0.76 | 26 | empty |
| 3 | 60 | 0.42 | 0.81 | 12 | empty |
| 4 | 54 | 0.42 | 0.82 | 12 | empty |
| 5 | 90 | 0.41 | 0.78 | 20 | XT7 |
Interfaces
1 interface between chains.
- A–B · 301 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 7LBR · SARS-CoV-2 papain-like protease (PLpro) bound to inhibitor XR8-89 · 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 7LBR · PDBe 7LBR · UniProt P0DTC1
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