MolNFT v1 · #31176 · protein
Crystal structure of SARS_COV mpro in complex with an inhibitor N9
2AMD · 3C-like proteinase: “Crystal structure of SARS_COV mpro in complex with an inhibitor N9”. X-ray diffraction, 1 ligand (9IN), 5 pockets (best druggability 0.77). MolNFT v1 #31176 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 2AMD
- Type
- protein
- Length
- 613 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3C-like proteinase
- EC
- 3.4.22.-
- UniProt
- P59641
- Ligands
- 9IN
- Pockets
- 5 · 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.-) | protein | 309 | 25% helix, 28% strand | P59641 |
| B | 3C-like proteinase (EC 3.4.22.-) | protein | 304 | 26% helix, 29% strand | P59641 |
Ligands and binding sites
- 9IN · N-(3-furoyl)-D-valyl-L-valyl-N~1~-((1R,2Z)-4-ethoxy-4-oxo-1-{[(3S)-2-oxopyrrolidin-3-yl]methyl}but-2-enyl)-D-leucinamide · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 834 | 0.77 | 0.80 | 65 | empty |
| 2 | 569 | 0.64 | 0.75 | 88 | empty |
| 3 | 215 | 0.54 | 0.78 | 34 | 9IN |
| 4 | 207 | 0.54 | 0.78 | 28 | 9IN |
| 5 | 182 | 0.50 | 0.77 | 30 | empty |
Interfaces
1 interface between chains.
- A–B · 1522 Ų buried · 32 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 2AMD · Crystal Structure Of SARS_CoV Mpro in Complex with an Inhibitor N9 · 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 2AMD · PDBe 2AMD · UniProt P59641
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