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MolNFT v1 · #172120 · protein

Crystal structure of SARS COV2 main protease in complex with inhibitor boceprevir

6ZRU: “Crystal structure of SARS COV2 main protease in complex with inhibitor boceprevir”. X-ray diffraction, 1 ligand (U5G), 2 pockets (best druggability 0.55). MolNFT v1 #172120 on GenesisL1: 3D structure, binding sites and pockets in…

PDB
6ZRU
Type
protein
Length
304 residues
Chains
1
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
Main protease
EC
3.4.19.12, 3.4.22.-, 3.4.22.69, 2.7.7.48, 3.6.4.12, 3.6.4.13, 3.1.13.-, 3.1.-.-, 2.1.1.-
UniProt
P0DTD1
Ligands
U5G
Pockets
2 · best druggability 0.55

Structure

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

ChainMoleculeTypeResiduesSecondary structureUniProt
AMain protease (EC 3.4.19.12, 3.4.22.-, 3.4.22.69, 2.7.7.48, 3.6.4.12, 3.6.4.13, 3.1.13.-, 3.1.-.-, 2.1.1.-)protein30426% helix, 29% strandP0DTD1

Ligands and binding sites

  • U5G · boceprevir (bound form) · ligand · chains A
  • DMS · Dimethyl sulfoxide · additive · 2 copies · chains A

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

Pockets

2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
12380.550.7841DMS
21630.490.7721U5G

Modifications

Observed in the structure: 1 covalent (covalent ligand).

Compared structures

  • 6ZRU · Crystal structure of SARS CoV2 main protease in complex with inhibitor Boceprevir · the same entry in another collection · chain A against A, TM-score 1.00

Analyse

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