MolNFT v1 · #31187 · protein
Crystal structure of porcine transmissible gastroenteritis virus mpro in complex with an inhibitor N1
2AMP · 3C-like proteinase: “Crystal structure of porcine transmissible gastroenteritis virus mpro in complex with an inhibitor N1”. X-ray diffraction, 1 ligand (I12), 6 pockets (best druggability 0.79). MolNFT v1 #31187 on GenesisL1: 3D…
- PDB
- 2AMP
- Type
- protein
- Length
- 598 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3C-like proteinase
- EC
- 3.4.22.-
- UniProt
- Q9IW06
- Ligands
- I12
- Pockets
- 6 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 23% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | 3C-like proteinase (EC 3.4.22.-) | protein | 299 | 23% helix, 29% strand | Q9IW06 |
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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1036 | 0.79 | 0.81 | 120 | empty |
| 2 | 451 | 0.66 | 0.79 | 48 | empty |
| 3 | 182 | 0.47 | 0.76 | 29 | I12 |
| 4 | 184 | 0.46 | 0.75 | 28 | I12 |
| 5 | 57 | 0.43 | 0.83 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 1409 Ų buried · 22 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 2AMP · Crystal Structure Of Porcine Transmissible Gastroenteritis Virus Mpro in Complex with an… · 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 Q9IW06
- Elsewhere: RCSB PDB 2AMP · PDBe 2AMP · UniProt Q9IW06
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