MolNFT v1 · #181158 · protein
SARS-cov-2 3CLPRO in complex with N-[4-[[2-(benzotriazol-1-YL)ACETYL]- (3-THIENYLMETHYL)AMINO]PHENYL]CYCLOPROPANECARBOXAMIDE
7LME · 3C-like proteinase: “SARS-cov-2 3CLPRO in complex with N-[4-[[2-(benzotriazol-1-YL)ACETYL]…”. X-ray diffraction, 1 ligand (Y6J), 5 pockets (best druggability 0.76). MolNFT v1 #181158 on GenesisL1: 3D structure, binding sites and…
- PDB
- 7LME
- Type
- protein
- Length
- 609 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
- Y6J
- Pockets
- 5 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 26% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3C-like proteinase (EC 3.4.22.69) | protein | 304 | 25% helix, 29% strand | P0DTD1 |
| B | 3C-like proteinase (EC 3.4.22.69) | protein | 305 | 27% helix, 29% strand | P0DTD1 |
Ligands and binding sites
- Y6J · ~{N}-[4-[2-(benzotriazol-1-yl)ethanoyl-(thiophen-3-ylmethyl)amino]phenyl]cyclopropanecarboxamide · 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 904 | 0.76 | 0.79 | 74 | empty |
| 2 | 475 | 0.60 | 0.75 | 77 | empty |
| 3 | 211 | 0.51 | 0.77 | 27 | Y6J |
| 4 | 213 | 0.49 | 0.75 | 29 | empty |
| 5 | 217 | 0.49 | 0.75 | 29 | Y6J |
Interfaces
1 interface between chains.
- A–B · 1588 Ų buried · 44 hydrogen bonds · protein-protein
Compared structures
- 7LME · SARS-CoV-2 3CLPro in complex with N-[4-[[2-(benzotriazol-1-yl)acetyl]-(3-thienylmethyl)ami… · 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 7LME · PDBe 7LME · UniProt P0DTD1
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