MolNFT v1 · #181615 · protein

Structure of SARS-cov-2 3CL protease in complex with inhibitor 21C

7M04 · 3C-like proteinase: “Structure of SARS-cov-2 3CL protease in complex with inhibitor 21C”. X-ray diffraction, 2 ligands (YLV, YM1), 7 pockets (best druggability 0.72). MolNFT v1 #181615 on GenesisL1: 3D structure, binding sites and…

PDB: 7M04
Type: protein
Length: 597 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: YLV, YM1
Pockets: 7 · best druggability 0.72

Structure

x-ray diffraction · 2 distinct chains · 25% helix, 29% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	3C-like proteinase (EC 3.4.22.69)	protein	299	25% helix, 29% strand	P0DTD1
B	3C-like proteinase (EC 3.4.22.69)	protein	298	25% helix, 29% strand	P0DTD1

Ligands and binding sites

YLV · (1R,2S)-1-hydroxy-2-((S)-4-methyl-2-((((perfluorophenyl)methoxy)carbonyl)amino) pentanamido)-3-((R)-2-oxo-2,3-dihydro-1H-pyrrol-3-yl) propane-1-sulfonic acid · ligand · 2 copies · chains A, B
YM1 · (1S,2S)-1-hydroxy-2-((S)-4-methyl-2-((((perfluorophenyl)methoxy)carbonyl)amino) pentanamido)-3-((R)-2-oxo-2,3-dihydro-1H-pyrrol-3-yl) propane-1-sulfonic acid · ligand · 2 copies · chains A, B
PG4 · Tetraethylene glycol · additive · chains B

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

Pockets

7 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	863	0.72	0.77	69	empty
2	211	0.55	0.78	45	empty
3	218	0.52	0.77	27	YLV, YM1
4	179	0.51	0.77	23	YLV, YM1
5	77	0.34	0.75	19	empty

Interfaces

1 interface between chains.

A–B · 1024 Å² buried · 19 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 covalent (covalent ligand).

Compared structures

7M04 · Structure of SARS-CoV-2 3CL protease in complex with inhibitor 21c · 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 7M04 · PDBe 7M04 · UniProt P0DTD1

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