MolNFT v1 · #189589 · protein
Crystal structure of SARS-cov-2 main protease in complex with PF07321332 in spacegroup P212121
7VLQ · 3C-like proteinase: “Crystal structure of SARS-cov-2 main protease in complex with PF07321332 in spacegroup P212121”. X-ray diffraction, 1 ligand (4WI), 5 pockets (best druggability 0.74). MolNFT v1 #189589 on GenesisL1: 3D…
- PDB
- 7VLQ
- Type
- protein
- Length
- 596 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
- P0DTC1
- Ligands
- 4WI
- Pockets
- 5 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 26% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3C-like proteinase (EC 3.4.22.69) | protein | 296 | 26% helix, 30% strand | P0DTC1 |
| B | 3C-like proteinase (EC 3.4.22.69) | protein | 300 | 27% helix, 30% strand | P0DTC1 |
Ligands and binding sites
- 4WI · (1R,2S,5S)-N-{(1E,2S)-1-imino-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-6,6-dimethyl-3-[3-methyl-N-(trifluoroacetyl)-L-valyl]-3-azabicyclo[3.1.0]hexane-2-carboxamide · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 848 | 0.74 | 0.79 | 72 | empty |
| 2 | 476 | 0.61 | 0.75 | 86 | empty |
| 3 | 196 | 0.52 | 0.78 | 28 | 4WI |
| 4 | 214 | 0.52 | 0.77 | 30 | 4WI |
| 5 | 84 | 0.36 | 0.76 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 971 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 7VLQ · Crystal structure of SARS-Cov-2 main protease in complex with PF07321332 in spacegroup… · 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 P0DTC1
- Elsewhere: RCSB PDB 7VLQ · PDBe 7VLQ · UniProt P0DTC1
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