Research workbench
Structure of E. COLI beta-glucuronidase bound with a novel, potent inhibitor 2-[4-(1,3-benzodioxol-5-YLMETHYL)PIPERAZIN-1-yl]-N-[(1S,2S, 5S)-2,5-DIMETHOXYCYCLOHEXYL]ACETAMIDE
Analyse Structure of E. COLI beta-glucuronidase bound with a novel, potent inhibitor… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4JHZ
- Type
- protein
- Length
- 1,192 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-glucuronidase
- EC
- 3.2.1.31
- UniProt
- P05804
- Ligands
- 1KV
- Pockets
- 17 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 19% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Beta-glucuronidase (EC 3.2.1.31) | protein | 596 | 19% helix, 34% strand | P05804 |
Ligands and binding sites
- 1KV · 2-[4-(1,3-benzodioxol-5-ylmethyl)piperazin-1-yl]-N-[(1S,2S,5S)-2,5-dimethoxycyclohexyl]acetamide · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1133 | 0.85 | 0.86 | 91 | empty |
| 2 | 102 | 0.74 | 0.95 | 21 | empty |
| 3 | 85 | 0.71 | 0.95 | 21 | empty |
| 4 | 51 | 0.69 | 0.97 | 17 | empty |
| 5 | 370 | 0.68 | 0.81 | 33 | 1KV |
Interfaces
1 interface between chains.
- A–B · 1620 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 26 modified (engineered).
Compared structures
- 4JHZ · Structure of E. coli beta-Glucuronidase bound with a novel, potent inhibitor… · the same entry in another collection · chain A against A, TM-score 1.00
- P05804 · AlphaFold monomer V2.0 prediction for beta-glucuronidase (P05804) · 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 P05804
- Elsewhere: RCSB PDB 4JHZ · PDBe 4JHZ · UniProt P05804
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