Research workbench
Estrogen receptor alpha ligand binding domain Y537S mutant in complex with a methylated lasofoxifene derivative that possesses selective estrogen receptor degrader activities
Analyse Estrogen receptor alpha ligand binding domain Y537S mutant in complex with a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7UJW
- Type
- protein
- Length
- 848 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Estrogen receptor
- UniProt
- P03372
- Ligands
- R3V
- Pockets
- 13 · best druggability 0.77
Structure
x-ray diffraction · 4 distinct chains · 70% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Estrogen receptor | protein | 212 | 71% helix, 4% strand | P03372 |
| D | Estrogen receptor | protein | 218 | 68% helix, 4% strand | P03372 |
| C | Estrogen receptor | protein | 208 | 69% helix, 4% strand | P03372 |
| A | Estrogen receptor | protein | 210 | 72% helix, 4% strand | P03372 |
Ligands and binding sites
- R3V · (5R,6S)-5-(4-{2-[(3S)-3-methylpyrrolidin-1-yl]ethoxy}phenyl)-6-phenyl-5,6,7,8-tetrahydronaphthalen-2-ol · ligand · 4 copies · chains B, D, C, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 256 | 0.77 | 0.89 | 31 | R3V |
| 2 | 218 | 0.76 | 0.90 | 24 | R3V |
| 3 | 318 | 0.74 | 0.85 | 36 | R3V |
| 4 | 270 | 0.73 | 0.86 | 29 | R3V |
| 5 | 100 | 0.65 | 0.89 | 18 | empty |
Interfaces
3 interfaces between chains.
- B–C · 1431 Ų buried · 21 hydrogen bonds · protein-protein
- D–A · 433 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 301 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 7UJW · Estrogen Receptor Alpha Ligand Binding Domain Y537S Mutant in Complex with a Methylated… · the same entry in another collection · chain A against A, TM-score 1.00
- P03372 · AlphaFold monomer V2.0 prediction for estrogen receptor (P03372) · a predicted model of the same protein · chain C against A, TM-score 0.96
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 7UJW · PDBe 7UJW · UniProt P03372
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