Research workbench
Vim-2_10C. metallo-beta-lactamase inhibitors by bioisosteric replacement: preparation, activity and binding
Analyse Vim-2_10C. metallo-beta-lactamase inhibitors by bioisosteric replacement… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5NI0
- Type
- protein
- Length
- 459 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
- 8XW, ZN
- Pockets
- 1 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 27% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-lactamase class B vim-2 | protein | 230 | 27% helix, 29% strand | Q9K2N0 |
| E | Beta-lactamase class B vim-2 | protein | 229 | 27% helix, 29% strand | Q9K2N0 |
Ligands and binding sites
- 8XW · [(2~{R})-1-ethanoylsulfanyl-6-phenyl-hexan-2-yl]phosphonic acid · ligand · 2 copies · chains A, E
- ZN · Zinc ion · metal · 4 copies · chains A, E
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 | 551 | 0.72 | 0.81 | 52 | 8XW |
Interfaces
1 interface between chains.
- A–E · 510 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 5NI0 · VIM-2_10c. Metallo-beta-Lactamase Inhibitors by Bioisosteric Replacement: Preparation… · 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 5NI0 · PDBe 5NI0 · UniProt Q9K2N0
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