MolNFT v2 · #226548 · protein
Crystal structure of MERS 3CL protease in complex with a racemic bicyclo[2.2.1]heptenyl-methyl 2-pyrrolidone inhibitor
9ATI · 3C-like proteinase nsp5: “Crystal structure of MERS 3CL protease in complex with a racemic bicyclo[2.2.1]heptenyl-methyl 2-pyrrolidone…”. X-ray diffraction at 1.6, 2 ligands (A1AGV, A1AGU), 2 pockets (best druggability 0.52). MolNFT…
- PDB
- 9ATI
- Type
- protein
- Length
- 305 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.6
- Source
- Middle East respiratory syndrome-related coronavirus
- Molecule
- 3C-like proteinase nsp5
- EC
- 3.4.22.69
- UniProt
- K9N638
- Ligands
- A1AGV, A1AGU
- Pockets
- 2 · best druggability 0.52
Structure
x-ray diffraction · resolution 1.6 · 1 distinct chain · 23% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3C-like proteinase nsp5 (EC 3.4.22.69) | protein | 305 | 23% helix, 29% strand | K9N638 |
Ligands and binding sites
- A1AGV · (1S,2S)-2-{[N-({[(3S)-1-{[(1R,2R,4R)-bicyclo[2.2.1]hept-5-en-2-yl]methyl}-5-oxopyrrolidin-3-yl]methoxy}carbonyl)-L-leucyl]amino}-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propane-1-sulfonic acid · ligand · chains A
- A1AGU · (1R,2S)-2-{[N-({[(3S)-1-{[(1R,2R,4R)-bicyclo[2.2.1]hept-5-en-2-yl]methyl}-5-oxopyrrolidin-3-yl]methoxy}carbonyl)-L-leucyl]amino}-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propane-1-sulfonic acid · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 240 | 0.52 | 0.76 | 44 | empty |
| 2 | 208 | 0.52 | 0.77 | 27 | A1AGV, A1AGU |
Modifications
Observed in the structure: 2 covalent (covalent ligand).
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 K9N638
- Elsewhere: RCSB PDB 9ATI · PDBe 9ATI · UniProt K9N638
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