MolNFT v1 · #173043 · protein

Structure of SARS-cov-2 main protease bound to pd 168568.

7AMJ · 3C-like proteinase: “Structure of SARS-cov-2 main protease bound to pd 168568.”. X-ray diffraction, 2 ligands (RMZ, CL), 4 pockets (best druggability 0.52). MolNFT v1 #173043 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 7AMJ
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: RMZ, CL
Pockets: 4 · best druggability 0.52

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

RMZ · (3~{S})-3-[2-[4-(3,4-dimethylphenyl)piperazin-1-yl]ethyl]-2,3-dihydroisoindol-1-one · ligand · chains A
CL · Chloride ion · ion · chains A
DMS · Dimethyl sulfoxide · additive · 7 copies · chains A

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

Pockets

4 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	62	0.52	0.86	15	DMS
2	205	0.50	0.76	26	DMS
3	74	0.36	0.77	19	empty
4	83	0.33	0.74	17	empty

Compared structures

7AMJ · Structure of SARS-CoV-2 Main Protease bound to PD 168568. · 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 7AMJ · PDBe 7AMJ · UniProt P0DTD1

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