Research workbench
Crystal structure of SARS-cov mpro in complex with an inhibitor I2
Analyse Crystal structure of SARS-cov mpro in complex with an inhibitor I2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2D2D
- Type
- protein
- Length
- 603 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3C-like proteinase
- EC
- 3.4.24.-
- UniProt
- P59641
- Ligands
- ENB
- Pockets
- 6 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 26% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3C-like proteinase (EC 3.4.24.-) | protein | 301 | 25% helix, 28% strand | P59641 |
| B | 3C-like proteinase (EC 3.4.24.-) | protein | 302 | 26% helix, 30% strand | P59641 |
Ligands and binding sites
- ENB · Ethyl (2E,4S)-4-[((2R)-2-{[N-(tert-butoxycarbonyl)-L-valyl]amino}-2-phenylethanoyl)amino]-5-[(3S)-2-oxopyrrolidin-3-yl]pent-2-enoate · ligand · 2 copies · 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 | 1036 | 0.76 | 0.79 | 91 | empty |
| 2 | 525 | 0.60 | 0.74 | 71 | empty |
| 3 | 179 | 0.51 | 0.78 | 26 | ENB |
| 4 | 182 | 0.45 | 0.74 | 28 | ENB |
| 5 | 96 | 0.41 | 0.77 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 1265 Ų buried · 29 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 2D2D · Crystal Structure Of SARS-CoV Mpro in Complex with an Inhibitor I2 · 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 P59641
- Elsewhere: RCSB PDB 2D2D · PDBe 2D2D · UniProt P59641
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.