MolNFT v1 · #186494 · protein
Structure of SARS-cov-2 main protease in complex with a covalent inhibitor
7RFU · 3C-like proteinase: “Structure of SARS-cov-2 main protease in complex with a covalent inhibitor”. X-ray diffraction, 1 ligand (4YG), 3 pockets (best druggability 0.56). MolNFT v1 #186494 on GenesisL1: 3D structure, binding sites and…
- PDB
- 7RFU
- Type
- protein
- Length
- 299 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3C-like proteinase
- EC
- 3.4.22.69
- UniProt
- P0DTD1
- Ligands
- 4YG
- Pockets
- 3 · best druggability 0.56
Structure
x-ray diffraction · 1 distinct chain · 25% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3C-like proteinase (EC 3.4.22.69) | protein | 299 | 25% helix, 28% strand | P0DTD1 |
Ligands and binding sites
- 4YG · (1R,2S,5S)-N-{(1S,2S)-1-(1,3-benzothiazol-2-yl)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-3-[N-(methanesulfonyl)-L-valyl]-6,6-dimethyl-3-azabicyclo[3.1.0]hexane-2-carboxamide · ligand · 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 248 | 0.56 | 0.78 | 28 | 4YG |
| 2 | 75 | 0.37 | 0.77 | 17 | empty |
| 3 | 58 | 0.30 | 0.75 | 15 | empty |
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 7RFU · Structure of SARS-CoV-2 main protease in complex with a covalent inhibitor · 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 7RFU · PDBe 7RFU · UniProt P0DTD1
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