MolNFT v1 · #155420 · protein

Complex structure of pedv 3CLPRO with GC376

6L70 · Pedv main protease: “Complex structure of pedv 3CLPRO with GC376”. X-ray diffraction, 1 ligand (K36), 5 pockets (best druggability 0.76). MolNFT v1 #155420 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6L70
Type: protein
Length: 598 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Pedv main protease
UniProt: K4L9I6
Ligands: K36
Pockets: 5 · best druggability 0.76

Structure

x-ray diffraction · 1 distinct chain · 24% helix, 29% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Pedv main protease	protein	299	24% helix, 29% strand	K4L9I6

Ligands and binding sites

K36 · (1S,2S)-2-({N-[(benzyloxy)carbonyl]-L-leucyl}amino)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propane-1-sulfonic acid · ligand · 2 copies · chains A, B

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	905	0.76	0.79	79	empty
2	277	0.62	0.80	43	empty
3	321	0.58	0.77	52	empty
4	214	0.50	0.76	28	K36
5	172	0.49	0.77	28	K36

Interfaces

1 interface between chains.

A–B · 1450 Å² buried · 32 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 covalent (covalent ligand).

Compared structures

6L70 · Complex structure of PEDV 3CLpro with GC376 · 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 K4L9I6
Elsewhere: RCSB PDB 6L70 · PDBe 6L70 · UniProt K4L9I6

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