MolNFT v1 · #173298 · protein

Structure of SARS-cov-2 main protease bound to SEN1269 ligand

7AVD · 3C-like proteinase: “Structure of SARS-cov-2 main protease bound to SEN1269 ligand”. X-ray diffraction, 2 ligands (S1W, CL), 5 pockets (best druggability 0.76). MolNFT v1 #173298 on GenesisL1: 3D structure, binding sites and pockets…

PDB: 7AVD
Type: protein
Length: 612 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 3C-like proteinase
EC: 3.4.22.69
UniProt: P0DTD1
Ligands: S1W, CL
Pockets: 5 · best druggability 0.76

Structure

x-ray diffraction · 1 distinct chain · 26% helix, 29% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	3C-like proteinase (EC 3.4.22.69)	protein	306	26% helix, 29% strand	P0DTD1

Ligands and binding sites

S1W · 3-[[5-[3-(dimethylamino)phenoxy]pyrimidin-2-yl]amino]phenol · ligand · chains B
CL · Chloride ion · ion · 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	899	0.76	0.79	78	empty
2	615	0.64	0.74	80	empty
3	216	0.56	0.79	26	S1W
4	200	0.52	0.78	27	empty
5	73	0.32	0.75	16	empty

Interfaces

1 interface between chains.

A–B · 1472 Å² buried · 42 hydrogen bonds · protein-protein

Compared structures

7AVD · Structure of SARS-CoV-2 Main Protease bound to SEN1269 ligand · 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 7AVD · PDBe 7AVD · UniProt P0DTD1

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