Research workbench
Crystal structure of SARS-cov-2 3CL in complex with inhibitor NK01-63
Analyse Crystal structure of SARS-cov-2 3CL in complex with inhibitor NK01-63 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7TIZ
- Type
- protein
- Length
- 303 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
- P0DTC1
- Ligands
- N63, NA, SCN
- Pockets
- 2 · best druggability 0.53
Structure
x-ray diffraction · 1 distinct chain · 26% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3C-like proteinase NSP5 (EC 3.4.22.69) | protein | 303 | 26% helix, 29% strand | P0DTC1 |
Ligands and binding sites
- N63 · (1S,2S)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]-2-{[N-({[3-(trifluoromethyl)phenyl]methoxy}carbonyl)-L-leucyl]amino}propane-1-sulfonic acid · ligand · chains A
- NA · Sodium ion · metal · chains A
- SCN · Thiocyanate ion · ion · chains A
- EDO · 1,2-ethanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 179 | 0.53 | 0.79 | 28 | N63, SCN |
| 2 | 66 | 0.29 | 0.74 | 14 | empty |
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 7TIZ · Crystal structure of SARS-CoV-2 3CL in complex with inhibitor NK01-63 · 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 7TIZ · PDBe 7TIZ · UniProt P0DTC1
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