MolNFT v1 · #188870 · protein
Estrogen receptor alpha ligand binding domain in complex with a methylated lasofoxifene derivative with selective estrogen receptor degrader properties
7UJF: “Estrogen receptor alpha ligand binding domain in complex with a methylated lasofoxifene derivative with…”. X-ray diffraction, 1 ligand (R3V), 17 pockets (best druggability 0.81). MolNFT v1 #188870 on GenesisL1: 3D structure, binding…
- PDB
- 7UJF
- Type
- protein
- Length
- 938 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Estrogen receptor
- UniProt
- P03372
- Ligands
- R3V
- Pockets
- 17 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 69% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Estrogen receptor | protein | 235 | 69% helix, 4% strand | P03372 |
| A | Estrogen receptor | protein | 232 | 69% helix, 4% strand | P03372 |
| C | Estrogen receptor | protein | 238 | 69% helix, 4% strand | P03372 |
| D | Estrogen receptor | protein | 233 | 68% 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, A, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 255 | 0.81 | 0.92 | 29 | R3V |
| 2 | 250 | 0.80 | 0.92 | 30 | R3V |
| 3 | 247 | 0.79 | 0.91 | 30 | R3V |
| 4 | 280 | 0.76 | 0.88 | 33 | R3V |
| 5 | 88 | 0.65 | 0.90 | 17 | empty |
Interfaces
3 interfaces between chains.
- C–D · 1556 Ų buried · 21 hydrogen bonds · protein-protein
- B–A · 1547 Ų buried · 20 hydrogen bonds · protein-protein
- B–C · 234 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 7UJF · Estrogen Receptor Alpha Ligand Binding Domain in Complex with a Methylated Lasofoxifene… · 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 A against A, TM-score 0.92
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 7UJF · PDBe 7UJF · UniProt P03372
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