MolNFT v1 · #125562 · protein

Vim-2 metallo-beta-lactamase in complex with (S)-1-allyl-2-(3- methoxyphenyl)-3-oxoisoindoline-4-carboxylic acid (compound 42)

5LCH · Metallo-beta-lactamase vim-2: “Vim-2 metallo-beta-lactamase in complex with (S)-1-allyl-2-(3- methoxyphenyl)-3-oxoisoindoline-4-carboxylic…”. X-ray diffraction, 2 ligands (6TU, ZN), 1 pocket (best druggability 0.57). MolNFT v1…

PDB: 5LCH
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: 6TU, ZN
Pockets: 1 · best druggability 0.57

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

6TU · (1~{S})-2-(3-methoxyphenyl)-3-oxidanylidene-1-prop-2-enyl-1~{H}-isoindole-4-carboxylic acid · ligand · chains A
ZN · Zinc ion · metal · 2 copies · 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	210	0.57	0.79	25	6TU

Compared structures

5LCH · VIM-2 metallo-beta-lactamase in complex with (S)-1-allyl-2-(3-methoxyphenyl)-3-oxoisoindol… · 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 5LCH · PDBe 5LCH · UniProt Q9K2N0

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