MolNFT v1 · #190233 · protein

SARS-cov-2 3CLPRO

7WOH · 3C-like proteinase: “SARS-cov-2 3CLPRO”. X-ray diffraction, 1 ligand (5IW), 5 pockets (best druggability 0.75). MolNFT v1 #190233 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 7WOH
Type: protein
Length: 606 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: 5IW
Pockets: 5 · best druggability 0.75

Structure

x-ray diffraction · 1 distinct chain · 25% helix, 29% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	3C-like proteinase (EC 3.4.22.69)	protein	303	25% helix, 29% strand	P0DTD1

Ligands and binding sites

5IW · (2S)-4-methyl-N-[(2S)-1-oxidanylidene-3-[(3S)-2-oxidanylidenepiperidin-3-yl]propan-2-yl]-2-[[(2S)-3-phenyl-2-[[(E)-3-phenylprop-2-enoyl]amino]propanoyl]amino]pentanamide · 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	557	0.75	0.83	80	empty
2	203	0.63	0.83	32	empty
3	248	0.54	0.77	32	5IW
4	247	0.50	0.75	32	5IW
5	55	0.29	0.75	14	empty

Interfaces

1 interface between chains.

A–B · 639 Å² buried · 11 hydrogen bonds · protein-protein

Modifications

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

Compared structures

7WOH · SARS-CoV-2 3CLpro · 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 7WOH · PDBe 7WOH · UniProt P0DTD1

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