MolNFT v1 · #26419 · protein
Crystal structure of SARS-cov mpro in complex with an inhibitor N1
1WOF · 3C-like proteinase: “Crystal structure of SARS-cov mpro in complex with an inhibitor N1”. X-ray diffraction, 1 ligand (I12), 6 pockets (best druggability 0.77). MolNFT v1 #26419 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 1WOF
- Type
- protein
- Length
- 613 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
- I12
- Pockets
- 6 · 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 3.4.24.-) | protein | 309 | 26% helix, 28% strand | P59641 |
| B | 3C-like proteinase (EC 3.4.24.-) | protein | 304 | 25% helix, 30% strand | P59641 |
Ligands and binding sites
- I12 · N-[(5-methylisoxazol-3-yl)carbonyl]-L-alanyl-L-valyl-N~1~-((1S)-4-ethoxy-4-oxo-1-{[(3S)-2-oxopyrrolidin-3-yl]methyl}but-2-enyl)-L-leucinamide · 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, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 868 | 0.77 | 0.81 | 72 | empty |
| 2 | 482 | 0.61 | 0.75 | 72 | empty |
| 3 | 209 | 0.54 | 0.78 | 32 | I12 |
| 4 | 188 | 0.53 | 0.78 | 30 | I12 |
| 5 | 189 | 0.52 | 0.77 | 31 | empty |
Interfaces
1 interface between chains.
- A–B · 1519 Ų buried · 40 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 1WOF · Crystal Structure Of SARS-CoV Mpro in Complex with an Inhibitor N1 · 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 1WOF · PDBe 1WOF · UniProt P59641
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