MolNFT v1 · #146285 · protein

Crystal structure of vim-2 complexed with compound 14

6DD1 · Beta-lactamase class B vim-2: “Crystal structure of vim-2 complexed with compound 14”. X-ray diffraction, 2 ligands (M3Q, ZN), 3 pockets (best druggability 0.72). MolNFT v1 #146285 on GenesisL1: 3D structure, binding sites and…

PDB: 6DD1
Type: protein
Length: 462 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Beta-lactamase class B vim-2
UniProt: Q9K2N0
Ligands: M3Q, ZN
Pockets: 3 · best druggability 0.72

Structure

x-ray diffraction · 1 distinct chain · 27% helix, 30% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Beta-lactamase class B vim-2	protein	231	27% helix, 30% strand	Q9K2N0

Ligands and binding sites

M3Q · [(quinolin-8-yl)methyl]phosphonic acid · ligand · 4 copies · chains A, B
ZN · Zinc ion · metal · 6 copies · chains A, B
ACT · Acetate ion · additive · 4 copies · chains A, B

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	665	0.72	0.79	53	ZN, M3Q
2	74	0.42	0.80	17	empty
3	53	0.31	0.77	19	empty

Interfaces

1 interface between chains.

A–B · 553 Å² buried · 10 hydrogen bonds · protein-protein

Compared structures

6DD1 · Crystal structure of VIM-2 complexed with compound 14 · 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 6DD1 · PDBe 6DD1 · UniProt Q9K2N0

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.