Research workbench
Crystal structure of SARS-cov-2 main protease in complex with PF07304814
Analyse Crystal structure of SARS-cov-2 main protease in complex with PF07304814 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7VVP
- Type
- protein
- Length
- 592 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
- P0DTD1
- Ligands
- 80I
- Pockets
- 6 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 24% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | 3C-like proteinase (EC 3.4.22.69) | protein | 296 | 24% helix, 29% strand | P0DTD1 |
Ligands and binding sites
- 80I · [(3~{S})-3-[[(2~{S})-2-[(4-methoxy-1~{H}-indol-2-yl) carbonylamino]-4-methyl-pentanoyl]amino]-2-oxidanylidene-4-[(3~{R})-2-oxidanylidene-3,4-dihydropyrrol-3-yl]butyl] dihydrogen phosphate · ligand · chains 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 | 766 | 0.76 | 0.81 | 69 | empty |
| 2 | 684 | 0.66 | 0.75 | 96 | empty |
| 3 | 191 | 0.56 | 0.80 | 29 | empty |
| 4 | 187 | 0.52 | 0.78 | 26 | 80I |
| 5 | 98 | 0.39 | 0.76 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 956 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 7VVP · Crystal structure of SARS-Cov-2 main protease in complex with PF07304814 · the same entry in another collection · chain B against B, 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 7VVP · PDBe 7VVP · UniProt P0DTD1
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.