MolNFT v1 · #117746 · protein
Crystal structure of the er-alpha ligand-binding domain in complex with the cyclofenil derivative 4,4'-[(4AR,8AR)-octahydronaphthalen- 2(1H)-YLIDENEMETHANEDIYL]DIPHENOL
5EHJ · Estrogen receptor: “Crystal structure of the er-alpha ligand-binding domain in complex with the cyclofenil derivative…”. X-ray diffraction, 1 ligand (5K5), 7 pockets (best druggability 0.84). MolNFT v1 #117746 on GenesisL1: 3D…
- PDB
- 5EHJ
- Type
- protein
- Length
- 482 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Estrogen receptor; NCOA2
- UniProt
- P03372
- Ligands
- 5K5
- Pockets
- 7 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 67% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Estrogen receptor | protein | 229 | 69% helix, 4% strand | P03372 |
| B | Estrogen receptor | protein | 234 | 66% helix, 3% strand | P03372 |
| C | NCOA2 | protein | 9 | 78% helix, 0% strand | — |
| D | NCOA2 | protein | 10 | 50% helix, 0% strand | — |
Ligands and binding sites
- 5K5 · 4,4'-[(4aR,8aR)-octahydronaphthalen-2(1H)-ylidenemethanediyl]diphenol · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 285 | 0.84 | 0.95 | 36 | 5K5 |
| 2 | 315 | 0.80 | 0.90 | 37 | 5K5 |
| 3 | 83 | 0.66 | 0.91 | 17 | empty |
| 4 | 82 | 0.63 | 0.90 | 17 | empty |
| 5 | 153 | 0.47 | 0.77 | 23 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1656 Ų buried · 29 hydrogen bonds · protein-protein
- A–D · 531 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 530 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 5EHJ · 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 0.98
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 5EHJ · PDBe 5EHJ · UniProt P03372
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