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Crystal structure of estrogen receptor alpha in complex with receptor degrader 16AA
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
- 6DFN
- Type
- protein
- Length
- 901 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Estrogen receptor
- UniProt
- P03372
- Ligands
- G9J, G91, NI
- Pockets
- 12 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 72% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Estrogen receptor | protein | 234 | 70% helix, 4% strand | P03372 |
| B | Estrogen receptor | protein | 218 | 74% helix, 4% strand | P03372 |
| C | Estrogen receptor | protein | 228 | 71% helix, 4% strand | P03372 |
| D | Estrogen receptor | protein | 221 | 71% helix, 4% strand | P03372 |
Ligands and binding sites
- G9J · (2S)-3-(3-hydroxyphenyl)-2-(4-iodophenyl)-4-methyl-2H-1-benzopyran-6-ol · ligand · 4 copies · chains A, B, C, D
- G91 · (8S)-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 · 2 copies · chains B, D
- NI · Nickel (II) ion · metal · chains A, B
- GOL · Glycerol · additive · 3 copies · chains B, A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 265 | 0.82 | 0.93 | 30 | G9J |
| 2 | 262 | 0.81 | 0.92 | 30 | G9J |
| 3 | 271 | 0.80 | 0.91 | 25 | G9J, G91 |
| 4 | 334 | 0.76 | 0.86 | 34 | G91, G9J |
| 5 | 946 | 0.71 | 0.75 | 98 | empty |
Interfaces
5 interfaces between chains.
- C–D · 1524 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 1445 Ų buried · 23 hydrogen bonds · protein-protein
- A–C · 301 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 41 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 11 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6DFN · Crystal structure of estrogen receptor alpha in complex with receptor degrader 16aa · 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 0.95
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 6DFN · PDBe 6DFN · UniProt P03372
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