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Crystal structure of SARS-cov-2 3CL in complex with inhibitor NK01-14

Analyse Crystal structure of SARS-cov-2 3CL in complex with inhibitor NK01-14 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7TIA
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: XTP, SCN
Pockets: 2 · best druggability 0.51

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

XTP · benzyl [(2S)-3-cyclopropyl-1-({(2S)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}amino)-1-oxopropan-2-yl]carbamate · ligand · chains A
SCN · Thiocyanate ion · ion · 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.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	195	0.51	0.77	27	XTP, SCN
2	74	0.31	0.74	14	empty

Modifications

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

Compared structures

7TIA · Crystal structure of SARS-CoV-2 3CL in complex with inhibitor NK01-14 · the same entry in another collection · chain A against A, TM-score 1.00

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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 7TIA · PDBe 7TIA · UniProt P0DTC1

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