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Vim-2-nat, discovery of novel inhibitor scaffolds against the metallo-beta-lactamase vim-2 by spr based fragment screening

Analyse Vim-2-nat, discovery of novel inhibitor scaffolds against the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5ACU
Type: protein
Length: 230 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Beta-lactamase
EC: 3.5.2.6
UniProt: Q9K2N0
Ligands: ZN, CL, OH
Pockets: 1 · best druggability 0.50

Structure

x-ray diffraction · 1 distinct chain · 26% helix, 27% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Beta-lactamase (EC 3.5.2.6)	protein	230	26% helix, 27% strand	Q9K2N0

Ligands and binding sites

ZN · Zinc ion · metal · 3 copies · chains A
CL · Chloride ion · ion · 2 copies · chains A
OH · Hydroxide ion · ion · chains A

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	124	0.50	0.80	18	OH, ZN

Compared structures

5ACU · VIM-2-NAT, Discovery of novel inhibitor scaffolds against the metallo- beta-lactamase… · 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 Q9K2N0
Elsewhere: RCSB PDB 5ACU · PDBe 5ACU · UniProt Q9K2N0

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