Research workbench
Vim-2_1DI-triazole inhibitors with promising inhibitor effects against antibiotic resistance metallo-beta-lactamases
Analyse Vim-2_1DI-triazole inhibitors with promising inhibitor effects against… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6TMB
- Type
- protein
- Length
- 460 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
- 9OB, ZN, CL, OH, IOD
- Pockets
- 1 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 28% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Beta-lactamase class B vim-2 | protein | 230 | 28% helix, 29% strand | Q9K2N0 |
Ligands and binding sites
- 9OB · ~{N}-[[5-[[(phenylmethyl)amino]methyl]-1~{H}-1,2,3-triazol-4-yl]methyl]benzenesulfonamide · ligand · chains A, B
- ZN · Zinc ion · metal · 6 copies · chains A, B
- CL · Chloride ion · ion · 4 copies · chains A, B
- OH · Hydroxide ion · ion · 2 copies · chains A, B
- IOD · Iodide ion · ion · chains A, B
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.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 562 | 0.75 | 0.82 | 53 | ZN, OH, 9OB, IOD |
Interfaces
1 interface between chains.
- A–B · 565 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 6TMB · VIM-2_1di-Triazole inhibitors with promising inhibitor effects against antibiotic… · 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 6TMB · PDBe 6TMB · UniProt Q9K2N0
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.