Research workbench
Identification of spirooxindole and dibenzoxazepine motifs as potent mineralocorticoid receptor antagonists
Analyse Identification of spirooxindole and dibenzoxazepine motifs as potent… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5HCV
- Type
- protein
- Length
- 697 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mineralocorticoid receptor
- UniProt
- P08235
- Ligands
- 60R, CL
- Pockets
- 13 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 70% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Mineralocorticoid receptor | protein | 236 | 71% helix, 6% strand | P08235 |
| B | Mineralocorticoid receptor | protein | 232 | 70% helix, 5% strand | P08235 |
| C | Mineralocorticoid receptor | protein | 229 | 70% helix, 5% strand | P08235 |
Ligands and binding sites
- 60R · 6-[(~{E})-(3-fluoranyl-6~{H}-benzo[c][1]benzoxepin-11-ylidene)methyl]-4~{H}-1,4-benzoxazin-3-one · ligand · 3 copies · chains A, B, C
- CL · Chloride ion · ion · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 184 | 0.83 | 0.97 | 25 | 60R |
| 2 | 306 | 0.81 | 0.91 | 44 | 60R |
| 3 | 311 | 0.81 | 0.91 | 45 | 60R, CL |
| 4 | 539 | 0.67 | 0.77 | 37 | empty |
| 5 | 147 | 0.61 | 0.84 | 29 | empty |
Interfaces
3 interfaces between chains.
- B–C · 501 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 393 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 354 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 5HCV · Identification of Spirooxindole and Dibenzoxazepine Motifs as Potent Mineralocorticoid… · the same entry in another collection · chain A against A, TM-score 1.00
- P08235 · AlphaFold monomer V2.0 prediction for mineralocorticoid receptor (P08235) · a predicted model of the same protein · chain C 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 P08235
- Elsewhere: RCSB PDB 5HCV · PDBe 5HCV · UniProt P08235
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.