MolNFT v1 · #169924 · protein

X-ray structure of SARS-cov-2 main protease bound to grl-024-20 at 1.45 a

6XR3 · 3C-like proteinase: “X-ray structure of SARS-cov-2 main protease bound to grl-024-20 at 1.45 a”. X-ray diffraction, 1 ligand (V7G), 2 pockets (best druggability 0.54). MolNFT v1 #169924 on GenesisL1: 3D structure, binding sites and…

PDB: 6XR3
Type: protein
Length: 305 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 3C-like proteinase
EC: 3.4.22.69
UniProt: P0DTD1
Ligands: V7G
Pockets: 2 · best druggability 0.54

Structure

x-ray diffraction · 1 distinct chain · 26% 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	P0DTD1

Ligands and binding sites

V7G · N-[(2S)-1-({(1S,2S)-1-(1,3-benzothiazol-2-yl)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}amino)-4-methyl-1-oxopentan-2-yl]-4-methoxy-1H-indole-2-carboxamide · ligand · 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	210	0.54	0.78	27	V7G
2	145	0.45	0.76	28	empty

Modifications

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

Compared structures

6XR3 · X-ray Structure of SARS-CoV-2 main protease bound to GRL-024-20 at 1.45 A · 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 6XR3 · PDBe 6XR3 · UniProt P0DTD1

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