Research workbench
Structure of SARS coronavirus main protease in complex with the alpha- ketoamide (S)-N-benzyl-3-((S)-2-cinnamamido-3-phenylpropanamido)-2- oxo-4-((S)-2-oxopyrrolidin-3-YL)BUTANAMIDE
Analyse Structure of SARS coronavirus main protease in complex with the alpha… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5N19
- Type
- protein
- Length
- 306 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- SARS coronavirus main protease
- UniProt
- P0C6X7
- Ligands
- D03
- Pockets
- 2 · best druggability 0.48
Structure
x-ray diffraction · 1 distinct chain · 25% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | SARS coronavirus main protease | protein | 306 | 25% helix, 28% strand | P0C6X7 |
Ligands and binding sites
- D03 · (S)-N-benzyl-3-((S)-2-cinnamamido-3-phenylpropanamido)-2-oxo-4-((S)-2-oxopyrrolidin-3-yl)butanamide · ligand · chains A
- DMS · Dimethyl sulfoxide · additive · 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, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 219 | 0.48 | 0.74 | 28 | D03 |
| 2 | 130 | 0.42 | 0.76 | 24 | empty |
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 5N19 · Structure of SARS coronavirus main protease in complex with the alpha-ketoamide… · 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 P0C6X7
- Elsewhere: RCSB PDB 5N19 · PDBe 5N19 · UniProt P0C6X7
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