MolNFT v1 · #117085 · protein
Crystal structure of the er-alpha ligand-binding domain in complex with the cyclofenil derivative 4,4'-{[(3R)-3- METHYLCYCLOHEXYLIDENE]METHANEDIYL}DIPHENOL
5DXR · Estrogen receptor: “Crystal structure of the er-alpha ligand-binding domain in complex with the cyclofenil derivative…”. X-ray diffraction, 1 ligand (5HW), 8 pockets (best druggability 0.83). MolNFT v1 #117085 on GenesisL1: 3D…
- PDB
- 5DXR
- Type
- protein
- Length
- 490 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Estrogen receptor; Nuclear receptor coactivator 2
- UniProt
- P03372, Q15596
- Ligands
- 5HW
- Pockets
- 8 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 68% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Estrogen receptor | protein | 235 | 69% helix, 3% strand | P03372 |
| B | Estrogen receptor | protein | 236 | 65% helix, 3% strand | P03372 |
| C | Nuclear receptor coactivator 2 | protein | 9 | 78% helix, 0% strand | Q15596 |
| D | Nuclear receptor coactivator 2 | protein | 10 | 70% helix, 0% strand | Q15596 |
Ligands and binding sites
- 5HW · 4,4'-{[(3R)-3-methylcyclohexylidene]methanediyl}diphenol · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 182 | 0.83 | 0.97 | 26 | 5HW |
| 2 | 183 | 0.83 | 0.96 | 25 | 5HW |
| 3 | 99 | 0.67 | 0.91 | 20 | empty |
| 4 | 93 | 0.63 | 0.89 | 18 | empty |
| 5 | 247 | 0.62 | 0.81 | 38 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1701 Ų buried · 25 hydrogen bonds · protein-protein
- A–C · 521 Ų buried · 2 hydrogen bonds · protein-protein
- B–D · 477 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 5DXR · 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 B 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
- Every structure of UniProt Q15596
- Elsewhere: RCSB PDB 5DXR · PDBe 5DXR · UniProt P03372 · UniProt Q15596
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