Research workbench
Structure guided design and discovery of indazole ethers as highly potent, non-steroidal glucocorticoid receptor modulators
Analyse Structure guided design and discovery of indazole ethers as highly potent… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5G5W
- Type
- protein
- Length
- 260 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glucocorticoid receptor; Nuclear receptor coactivator 2
- UniProt
- P04150, Q15596
- Ligands
- R8C
- Pockets
- 2 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 67% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glucocorticoid receptor | protein | 247 | 68% helix, 4% strand | P04150 |
| B | Nuclear receptor coactivator 2 | protein | 13 | 62% helix, 0% strand | Q15596 |
Ligands and binding sites
- R8C · 2,2,2-trifluoro-N-[(1R,2S)-1-{[1-(4-fluorophenyl)-1H-indazol-5-yl]oxy}-1-phenylpropan-2-yl]acetamide · ligand · chains A
- EDO · 1,2-ethanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 330 | 0.83 | 0.93 | 44 | EDO, R8C |
| 2 | 53 | 0.60 | 0.92 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 651 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 5G5W · Structure guided design and discovery of Indazole ethers as highly potent, non-steroidal… · the same entry in another collection · chain A against A, TM-score 1.00
- P04150 · AlphaFold monomer V2.0 prediction for glucocorticoid receptor (P04150) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 P04150
- Every structure of UniProt Q15596
- Elsewhere: RCSB PDB 5G5W · PDBe 5G5W · UniProt P04150 · UniProt Q15596
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