MolNFT v1 · #153267 · protein

Metallo-beta-lactamase vim-2 in complex with dual MBL/SBL inhibitor MS01

6J8R · Beta-lactamase class B vim-2: “Metallo-beta-lactamase vim-2 in complex with dual MBL/SBL inhibitor MS01”. X-ray diffraction, 2 ligands (BHU, ZN), 1 pocket (best druggability 0.55). MolNFT v1 #153267 on GenesisL1: 3D structure…

PDB: 6J8R
Type: protein
Length: 231 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Beta-lactamase class B vim-2
UniProt: Q9K2N0
Ligands: BHU, ZN
Pockets: 1 · best druggability 0.55

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Beta-lactamase class B vim-2	protein	231	29% helix, 29% strand	Q9K2N0

Ligands and binding sites

BHU · [[(2S)-2-methyl-3-sulfanyl-propanoyl]amino]methylboronic acid · ligand · chains A
ZN · Zinc ion · metal · 2 copies · chains A
FMT · Formic acid · additive · 7 copies · chains A
GOL · Glycerol · additive · 3 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	150	0.55	0.81	33	ZN, BHU, FMT

Compared structures

6J8R · Metallo-Beta-Lactamase VIM-2 in complex with Dual MBL/SBL Inhibitor MS01 · 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 6J8R · PDBe 6J8R · UniProt Q9K2N0

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