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Structural analysis of glucocorticoid receptor beta ligand binding domain complexed with glucocorticoid antagonist ru-486: implication of helix 12 in antagonism
Analyse Structural analysis of glucocorticoid receptor beta ligand binding domain… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5UC1
- Type
- protein
- Length
- 410 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glucocorticoid receptor
- Ligands
- CPS, 486, CL
- Pockets
- 6 · best druggability 0.84
Structure
x-ray diffraction · 1 distinct chain · 64% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Glucocorticoid receptor | protein | 205 | 64% helix, 3% strand | — |
Ligands and binding sites
- CPS · 3-[(3-cholamidopropyl)dimethylammonio]-1-propanesulfonate · ligand · 4 copies · chains A, B
- 486 · 11-(4-dimethylamino-phenyl)-17-hydroxy-13-methyl-17-prop-1-ynyl-1,2,6,7,8,11,12,13,14,15,16,17-dodec ahydro-cyclopenta[a]phenanthren-3-one · ligand · 2 copies · chains A, B
- CL · Chloride ion · ion · 4 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 5 copies · chains A, B
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1187 | 0.84 | 0.84 | 75 | 486, CPS |
| 2 | 151 | 0.66 | 0.87 | 19 | EDO |
| 3 | 161 | 0.63 | 0.85 | 22 | EDO |
| 4 | 97 | 0.38 | 0.75 | 13 | CL, CPS |
| 5 | 86 | 0.38 | 0.76 | 15 | CPS, CL |
Interfaces
1 interface between chains.
- A–B · 979 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 5UC1 · Structural Analysis of Glucocorticoid Receptor beta Ligand Binding Domain Complexed with… · 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
- Elsewhere: RCSB PDB 5UC1 · PDBe 5UC1
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