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Crystal structure of SARS-cov-2 3CL in complex with inhibitor EB56

Analyse Crystal structure of SARS-cov-2 3CL in complex with inhibitor EB56 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7TIX
Type: protein
Length: 302 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: Q56, MG
Pockets: 3 · best druggability 0.57

Structure

x-ray diffraction · 1 distinct chain · 25% helix, 28% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	3C-like proteinase NSP5 (EC 3.4.22.69)	protein	302	25% helix, 28% strand	P0DTC1

Ligands and binding sites

Q56 · N~2~-{[(naphthalen-2-yl)methoxy]carbonyl}-N-{(2S)-1-oxo-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-L-leucinamide · ligand · chains A
MG · Magnesium ion · metal · 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.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	213	0.57	0.79	31	Q56
2	73	0.33	0.75	18	empty
3	50	0.31	0.76	15	empty

Modifications

Observed in the structure: 1 covalent (covalent ligand).

Compared structures

7TIX · Crystal structure of SARS-CoV-2 3CL in complex with inhibitor EB56 · 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 7TIX · PDBe 7TIX · UniProt P0DTC1

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