MolNFT v1 · #183515 · protein
Crystal structure of SARS COV2 main protease in complex with FSP007
7NT1 · 3C-like proteinase: “Crystal structure of SARS COV2 main protease in complex with FSP007”. X-ray diffraction, 1 ligand (UQW), 7 pockets (best druggability 0.76). MolNFT v1 #183515 on GenesisL1: 3D structure, binding sites and…
- PDB
- 7NT1
- 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
- P0DTC1
- Ligands
- UQW
- Pockets
- 7 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 25% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3C-like proteinase (EC 3.4.22.69) | protein | 305 | 26% helix, 29% strand | P0DTC1 |
| B | 3C-like proteinase (EC 3.4.22.69) | protein | 304 | 24% helix, 29% strand | P0DTC1 |
Ligands and binding sites
- UQW · [(2R)-1-[2-(1H-indol-3-yl)ethylamino]-1-oxidanylidene-butan-2-yl] prop-2-enoate · ligand · chains A, B
- DMS · Dimethyl sulfoxide · additive · 6 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 949 | 0.76 | 0.79 | 84 | empty |
| 2 | 373 | 0.65 | 0.79 | 53 | DMS |
| 3 | 209 | 0.52 | 0.77 | 30 | empty |
| 4 | 210 | 0.51 | 0.77 | 28 | UQW |
| 5 | 201 | 0.49 | 0.76 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 1497 Ų buried · 31 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 7NT1 · Crystal structure of SARS CoV2 main protease in complex with FSP007 · 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 7NT1 · PDBe 7NT1 · UniProt P0DTC1
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