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Vim-2 metallo-beta-lactamase in complex with 2-(2-chloro-6- fluorobenzyl)-3-oxoisoindoline-4-carboxylic acid (compound 16)

Analyse Vim-2 metallo-beta-lactamase in complex with 2-(2-chloro-6… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5LE1
Type: protein
Length: 230 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Metallo-beta-lactamase vim-2
UniProt: Q9K2N0
Ligands: 6UW, ZN
Pockets: 1 · best druggability 0.64

Structure

x-ray diffraction · 1 distinct chain · 27% helix, 29% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Metallo-beta-lactamase vim-2	protein	230	27% helix, 29% strand	Q9K2N0

Ligands and binding sites

6UW · 2-[(2-chloranyl-6-fluoranyl-phenyl)methyl]-3-oxidanylidene-1~{H}-isoindole-4-carboxylic acid · ligand · chains A
ZN · Zinc ion · metal · 2 copies · chains A
GOL · Glycerol · additive · 2 copies · chains A
FMT · Formic acid · additive · 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	209	0.64	0.83	30	6UW, GOL

Compared structures

5LE1 · VIM-2 metallo-beta-lactamase in complex with 2-(2-chloro-6-fluorobenzyl)-3-oxoisoindoline… · 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 5LE1 · PDBe 5LE1 · UniProt Q9K2N0

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