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Crystal Structure of SARS-CoV-2 Main Protease (3CLpro/Mpro) in Complex with Covalent Inhibitor VBY-825 (Partial Occupancy)
Analyse Crystal Structure of SARS-CoV-2 Main Protease (3CLpro/Mpro) in Complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7MNG
- Type
- protein
- Length
- 306 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.7
- Source
- Severe acute respiratory syndrome coronavirus 2
- Molecule
- 3C-like proteinase
- EC
- 3.4.22.69
- UniProt
- P0DTD1
- Ligands
- ZL7
- Pockets
- 3 · best druggability 0.55
Structure
x-ray diffraction · resolution 1.7 · 1 distinct chain · 26% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3C-like proteinase (EC 3.4.22.69) | protein | 306 | 26% helix, 29% strand | P0DTD1 |
Ligands and binding sites
- ZL7 · (2R,3S)-N-cyclopropyl-3-{[(2R)-3-(cyclopropylmethanesulfonyl)-2-{[(1S)-2,2,2-trifluoro-1-(4-fluorophenyl)ethyl]amino}propanoyl]amino}-2-hydroxypentanamide (non-preferred name) · ligand · chains A
- DMS · Dimethyl sulfoxide · additive · 8 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 80 | 0.55 | 0.86 | 16 | DMS |
| 2 | 228 | 0.53 | 0.77 | 27 | ZL7, DMS |
| 3 | 60 | 0.31 | 0.76 | 13 | empty |
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 7MNG · Crystal structure of SARS-cov-2 main protease (3CLPRO/MPRO) in complex with covalent… · 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 7MNG · PDBe 7MNG · UniProt P0DTD1
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