MolNFT v1 · #127088 · protein
Vim-2_2B. metallo-beta-lactamase inhibitors by bioisosteric replacement: preparation, activity and binding
5MM9 · Metallo-beta-lactamase vim-17: “Vim-2_2B. metallo-beta-lactamase inhibitors by bioisosteric replacement: preparation, activity and binding”. X-ray diffraction, 3 ligands (8SH, ZN, MG), 2 pockets (best druggability 0.73). MolNFT v1…
- PDB
- 5MM9
- Type
- protein
- Length
- 463 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Metallo-beta-lactamase vim-17
- UniProt
- B5KVR9
- Ligands
- 8SH, ZN, MG
- Pockets
- 2 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 27% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Metallo-beta-lactamase vim-17 | protein | 232 | 27% helix, 29% strand | B5KVR9 |
| B | Metallo-beta-lactamase vim-17 | protein | 231 | 27% helix, 29% strand | B5KVR9 |
Ligands and binding sites
- 8SH · (2~{R})-2-diethoxyphosphoryl-5-phenyl-pentane-1-thiol · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 6 copies · chains A, B
- MG · Magnesium ion · metal · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 606 | 0.73 | 0.80 | 55 | ZN, 8SH |
| 2 | 52 | 0.32 | 0.77 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 578 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 5MM9 · VIM-2_2b. 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 B5KVR9
- Elsewhere: RCSB PDB 5MM9 · PDBe 5MM9 · UniProt B5KVR9
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