Research workbench
Structure of SARS-3CL protease complex with a phenyl-beta-alanyl (S, R)-N-decalin type inhibitor
Analyse Structure of SARS-3CL protease complex with a phenyl-beta-alanyl (S… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5C5O
- Type
- protein
- Length
- 600 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3C-like proteinase
- EC
- 3.4.22.69
- UniProt
- P0C6X7
- Ligands
- SDJ
- Pockets
- 6 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 26% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | 3C-like proteinase (EC 3.4.22.69) | protein | 300 | 26% helix, 29% strand | P0C6X7 |
Ligands and binding sites
- SDJ · (2S)-3-(1H-imidazol-5-yl)-2-({[(3S,4aR,8aS)-2-(N-phenyl-beta-alanyl)decahydroisoquinolin-3-yl]methyl}amino)propanal · 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1040 | 0.77 | 0.79 | 79 | empty |
| 2 | 447 | 0.62 | 0.76 | 69 | empty |
| 3 | 233 | 0.53 | 0.77 | 28 | SDJ |
| 4 | 202 | 0.53 | 0.78 | 30 | SDJ |
| 5 | 137 | 0.42 | 0.75 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 1353 Ų buried · 38 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 5C5O · Structure of SARS-3CL protease complex with a phenyl-beta-alanyl (S,R)-N-decalin type… · 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 5C5O · PDBe 5C5O · UniProt P0C6X7
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