MolNFT v1 · #117106 · protein
Crystal structure of the er-alpha ligand-binding domain in complex with the cyclofenil derivative 4,4'-{[(3S)-3-(methylsulfanyl) CYCLOHEXYLIDENE]METHANEDIYL}DIPHENOL
5DYD · Estrogen receptor: “Crystal structure of the er-alpha ligand-binding domain in complex with the cyclofenil derivative…”. X-ray diffraction, 1 ligand (5K1), 6 pockets (best druggability 0.85). MolNFT v1 #117106 on GenesisL1: 3D…
- PDB
- 5DYD
- Type
- protein
- Length
- 474 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Estrogen receptor; Nuclear receptor coactivator 2
- UniProt
- P03372
- Ligands
- 5K1
- Pockets
- 6 · best druggability 0.85
Structure
x-ray diffraction · 3 distinct chains · 67% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Estrogen receptor | protein | 225 | 69% helix, 4% strand | P03372 |
| B | Estrogen receptor | protein | 231 | 65% helix, 4% strand | P03372 |
| C, D | Nuclear receptor coactivator 2 | protein | 9 | 56% helix, 0% strand | — |
Ligands and binding sites
- 5K1 · 4,4'-{[(3S)-3-(methylsulfanyl)cyclohexylidene]methanediyl}diphenol · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 201 | 0.85 | 0.98 | 25 | 5K1 |
| 2 | 200 | 0.83 | 0.96 | 24 | 5K1 |
| 3 | 89 | 0.64 | 0.89 | 18 | empty |
| 4 | 80 | 0.64 | 0.90 | 16 | empty |
| 5 | 206 | 0.54 | 0.78 | 35 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1697 Ų buried · 25 hydrogen bonds · protein-protein
- A–C · 496 Ų buried · 2 hydrogen bonds · protein-protein
- B–D · 393 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 5DYD · Crystal Structure of the ER-alpha Ligand-binding Domain in Complex with the Cyclofenil… · 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 A against A, TM-score 0.99
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 5DYD · PDBe 5DYD · UniProt P03372
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