MolNFT v1 · #167391 · protein
Estrogen receptor alpha ligand binding domain in complex with lasofoxifene
6VJD: “Estrogen receptor alpha ligand binding domain in complex with lasofoxifene”. X-ray diffraction, 1 ligand (C3D), 16 pockets (best druggability 0.81). MolNFT v1 #167391 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6VJD
- Type
- protein
- Length
- 944 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Estrogen receptor
- UniProt
- P03372
- Ligands
- C3D
- Pockets
- 16 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 67% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Estrogen receptor | protein | 235 | 68% helix, 4% strand | P03372 |
| B | Estrogen receptor | protein | 235 | 66% helix, 4% strand | P03372 |
| C | Estrogen receptor | protein | 239 | 68% helix, 4% strand | P03372 |
| D | Estrogen receptor | protein | 235 | 68% helix, 4% strand | P03372 |
Ligands and binding sites
- C3D · (5R,6S)-6-phenyl-5-[4-(2-pyrrolidin-1-ylethoxy)phenyl]-5,6,7,8-tetrahydronaphthalen-2-ol · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 256 | 0.81 | 0.92 | 31 | C3D |
| 2 | 264 | 0.80 | 0.92 | 35 | C3D |
| 3 | 254 | 0.80 | 0.92 | 32 | C3D |
| 4 | 255 | 0.79 | 0.91 | 32 | C3D |
| 5 | 97 | 0.65 | 0.90 | 19 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1618 Ų buried · 26 hydrogen bonds · protein-protein
- C–D · 1565 Ų buried · 26 hydrogen bonds · protein-protein
- A–C · 236 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6VJD · Estrogen Receptor Alpha Ligand Binding Domain in Complex with 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 B 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 6VJD · PDBe 6VJD · UniProt P03372
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.