MolNFT v1 · #48979 · protein
4-substituted trinems as broad spectrum-lactamase inhibitors: structure-based design, synthesis and biological activity
2Q9M · Beta-lactamase: “4-substituted trinems as broad spectrum-lactamase inhibitors: structure-based design, synthesis and…”. X-ray diffraction, 1 ligand (LK7), 3 pockets (best druggability 0.66). MolNFT v1 #48979 on GenesisL1: 3D…
- PDB
- 2Q9M
- Type
- protein
- Length
- 359 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-lactamase
- EC
- 3.5.2.6
- UniProt
- P05364
- Ligands
- LK7
- Pockets
- 3 · best druggability 0.66
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-lactamase (EC 3.5.2.6) | protein | 359 | 40% helix, 22% strand | P05364 |
Ligands and binding sites
- LK7 · (1r,4s,7as)-1-(1-formylprop-1-en-1-yl)-4-methoxy-2,4,5,6,7,7A-hexahydro-1H-isoindole-3-carboxylic acid · ligand · chains A
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 | 365 | 0.66 | 0.80 | 44 | LK7 |
| 2 | 82 | 0.32 | 0.74 | 18 | empty |
| 3 | 53 | 0.27 | 0.74 | 16 | empty |
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 2Q9M · 4-Substituted Trinems as Broad Spectrum-Lactamase Inhibitors: Structure-based Design… · the same entry in another collection · chain A against A, TM-score 1.00
- P05364 · AlphaFold monomer V2.0 prediction for beta-lactamase (P05364) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P05364
- Elsewhere: RCSB PDB 2Q9M · PDBe 2Q9M · UniProt P05364
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