MolNFT v1 · #133084 · protein

Pandda analysis group deposition of computational designs of SARS-cov- 2 main protease covalent inhibitors -- crystal structure of SARS-cov- 2 main protease in complex with lon-wei-ADC59DF6-2 (mpro-X3110)

5RL0 · 3C-like proteinase: “Pandda analysis group deposition of computational designs of SARS-cov- 2 main protease covalent inhibitors…”. X-ray diffraction, 1 ligand (VEG), 3 pockets (best druggability 0.57). MolNFT v1 #133084 on…

PDB: 5RL0
Type: protein
Length: 304 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: VEG
Pockets: 3 · best druggability 0.57

Structure

x-ray diffraction · 1 distinct chain · 25% helix, 29% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	3C-like proteinase (EC 3.4.22.69)	protein	304	25% helix, 29% strand	P0DTD1

Ligands and binding sites

VEG · ethyl N-[(2R)-2-[(4-tert-butylphenyl)(propanoyl)amino]-2-(pyridin-3-yl)acetyl]-beta-alaninate · ligand · chains A
DMS · Dimethyl sulfoxide · additive · 5 copies · 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	251	0.57	0.78	29	VEG
2	86	0.49	0.82	20	DMS
3	158	0.45	0.75	29	empty

Modifications

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

Compared structures

5RL0 · PanDDA analysis group deposition of computational designs of SARS-CoV-2 main protease… · 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 5RL0 · PDBe 5RL0 · UniProt P0DTD1

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