MolNFT v1 · #173259 · protein
Crystal structure of SARS-cov-2 main protease (NSP5) in complex with compound 3
7AU4 · 3C-like proteinase NSP5: “Crystal structure of SARS-cov-2 main protease (NSP5) in complex with compound 3”. X-ray diffraction, 1 ligand (RY5), 3 pockets (best druggability 0.54). MolNFT v1 #173259 on GenesisL1: 3D structure, binding…
- PDB
- 7AU4
- Type
- protein
- Length
- 305 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3C-like proteinase NSP5
- EC
- 3.4.22.69
- UniProt
- P0DTD1
- Ligands
- RY5
- Pockets
- 3 · best druggability 0.54
Structure
x-ray diffraction · 1 distinct chain · 27% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3C-like proteinase NSP5 (EC 3.4.22.69) | protein | 305 | 27% helix, 29% strand | P0DTD1 |
Ligands and binding sites
- RY5 · (3~{S})-6-chloranyl-3'-(1,2-oxazol-3-ylmethyl)spiro[1, 2-dihydroindene-3,5'-imidazolidine]-2',4'-dione · ligand · chains A
- DMS · Dimethyl sulfoxide · additive · 2 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 | 64 | 0.54 | 0.87 | 17 | DMS |
| 2 | 219 | 0.52 | 0.77 | 28 | RY5 |
| 3 | 160 | 0.47 | 0.76 | 30 | empty |
Compared structures
- 7AU4 · Crystal Structure of SARS-CoV-2 main protease (Nsp5) in complex with compound 3 · 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 7AU4 · PDBe 7AU4 · UniProt P0DTD1
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