Research workbench
Crystal structure of estrogen receptor alpha in complex with receptor degrader 16AB
Analyse Crystal structure of estrogen receptor alpha in complex with receptor degrader… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6DF6
- Type
- protein
- Length
- 919 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Estrogen receptor
- UniProt
- P03372
- Ligands
- G8Y
- Pockets
- 15 · best druggability 0.79
Structure
x-ray diffraction · 4 distinct chains · 70% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Estrogen receptor | protein | 235 | 70% helix, 4% strand | P03372 |
| B | Estrogen receptor | protein | 220 | 71% helix, 4% strand | P03372 |
| C | Estrogen receptor | protein | 233 | 70% helix, 4% strand | P03372 |
| D | Estrogen receptor | protein | 231 | 70% helix, 4% strand | P03372 |
Ligands and binding sites
- G8Y · (8R)-8-(4-{2-[3-(fluoromethyl)azetidin-1-yl]ethoxy}phenyl)-1,8-dihydro-2H-[1]benzopyrano[4,3-d][1]benzoxepine-5,11-diol · ligand · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · 2 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 335 | 0.79 | 0.88 | 28 | G8Y |
| 2 | 276 | 0.79 | 0.90 | 32 | G8Y |
| 3 | 288 | 0.78 | 0.89 | 29 | G8Y |
| 4 | 255 | 0.76 | 0.89 | 29 | G8Y |
| 5 | 99 | 0.65 | 0.90 | 20 | empty |
Interfaces
3 interfaces between chains.
- C–D · 1587 Ų buried · 23 hydrogen bonds · protein-protein
- A–B · 1460 Ų buried · 24 hydrogen bonds · protein-protein
- A–C · 307 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 6DF6 · Crystal structure of estrogen receptor alpha in complex with receptor degrader 16ab · the same entry in another collection · chain D against D, TM-score 1.00
- P03372 · AlphaFold monomer V2.0 prediction for estrogen receptor (P03372) · a predicted model of the same protein · chain B against A, TM-score 0.94
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 P03372
- Elsewhere: RCSB PDB 6DF6 · PDBe 6DF6 · UniProt P03372
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.