Research workbench
Vim-2-ox, discovery of novel inhibitor scaffolds against the metallo- beta-lactamase vim-2 by spr based fragment screening
Analyse Vim-2-ox, discovery of novel inhibitor scaffolds against the metallo… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5ACV
- Type
- protein
- Length
- 466 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-lactamase
- EC
- 3.5.2.6
- UniProt
- Q9K2N0
- Ligands
- ZN, CL, OH
- Pockets
- 3 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 27% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Beta-lactamase (EC 3.5.2.6) | protein | 233 | 27% helix, 30% strand | Q9K2N0 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A, B
- CL · Chloride ion · ion · 4 copies · chains A, B
- OH · Hydroxide ion · ion · 2 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.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 709 | 0.74 | 0.80 | 67 | OH |
| 2 | 69 | 0.36 | 0.77 | 18 | empty |
| 3 | 52 | 0.30 | 0.76 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 585 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (oxidation).
Compared structures
- 5ACV · VIM-2-OX, Discovery of novel inhibitor scaffolds against the metallo- beta-lactamase… · 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 5ACV · PDBe 5ACV · UniProt Q9K2N0
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