Research workbench
SARS-cov-2 main protease in a covalent complex with sdz 224015 derivative, compound 5
Analyse SARS-cov-2 main protease in a covalent complex with sdz 224015 derivative… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7AEG
- Type
- protein
- Length
- 308 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3C-like proteinase; N-[(BENZYLOXY)CARBONYL]-L-valyl-N-[(1S)-1-(carboxymethyl)…
- EC
- 3.4.22.69
- UniProt
- P0DTD1
- Ligands
- PHQ, CF0
- Pockets
- 4 · best druggability 0.54
Structure
x-ray diffraction · 2 distinct chains · 26% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3C-like proteinase (EC 3.4.22.69) | protein | 305 | 26% helix, 29% strand | P0DTD1 |
| B | N-[(BENZYLOXY)CARBONYL]-L-valyl-N-[(1S)-1-(carboxymethyl)- 3-fluoro-2-oxopropyl]-L-alaninamide | protein | 3 | 0% helix, 33% strand | — |
Ligands and binding sites
- PHQ · benzyl chlorocarbonate · ligand · chains A, B
- CF0 · Fluoromethane · ion · chains A, B
- DMS · Dimethyl sulfoxide · additive · 5 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 68 | 0.54 | 0.87 | 17 | DMS |
| 2 | 75 | 0.34 | 0.75 | 17 | empty |
| 3 | 86 | 0.33 | 0.74 | 14 | empty |
| 4 | 59 | 0.32 | 0.76 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 312 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 7AEG · SARS-CoV-2 main protease in a covalent complex with SDZ 224015 derivative, compound 5 · 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 P0DTD1
- Elsewhere: RCSB PDB 7AEG · PDBe 7AEG · UniProt P0DTD1
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