MolNFT v1 · #181883 · protein

Crystal structure of the SARS-cov-2(2019-ncov) main protease in complex with compound 50

7M90 · 3C-like proteinase: “Crystal structure of the SARS-cov-2(2019-ncov) main protease in complex with compound 50”. X-ray diffraction, 1 ligand (YTS), 5 pockets (best druggability 0.54). MolNFT v1 #181883 on GenesisL1: 3D structure…

PDB: 7M90
Type: protein
Length: 296 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: YTS
Pockets: 5 · best druggability 0.54

Structure

x-ray diffraction · 1 distinct chain · 22% helix, 29% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	3C-like proteinase (EC 3.4.22.69)	protein	296	22% helix, 29% strand	P0DTD1

Ligands and binding sites

YTS · 5-(3-{3-chloro-5-[2-(3-oxopiperazin-1-yl) ethoxy]phenyl}-2-oxo-2H-[1,3'-bipyridin]-5-yl) pyrimidine-2,4(1H,3H)-dione · ligand · chains A

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

Pockets

5 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	72	0.54	0.86	15	empty
2	186	0.47	0.75	29	YTS
3	99	0.43	0.78	19	empty
4	79	0.37	0.76	16	empty
5	79	0.34	0.75	13	empty

Compared structures

7M90 · Crystal structure of the SARS-cov-2(2019-ncov) main protease in complex with compound 50 · 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 7M90 · PDBe 7M90 · UniProt P0DTD1

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