MolNFT v1 · #117146 · protein
Crystal structure of the er-alpha ligand-binding domain in complex with the cyclofenil derivative 4,4'-{[(3S)-3-(2-hydroxyethyl) CYCLOHEXYLIDENE]METHANEDIYL}DIPHENOL
5DZI · Estrogen receptor: “Crystal structure of the er-alpha ligand-binding domain in complex with the cyclofenil derivative…”. X-ray diffraction, 1 ligand (5KF), 7 pockets (best druggability 0.84). MolNFT v1 #117146 on GenesisL1: 3D…
- PDB
- 5DZI
- Type
- protein
- Length
- 497 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
- 5KF
- Pockets
- 7 · best druggability 0.84
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 | 239 | 68% helix, 4% strand | P03372 |
| C | Nuclear receptor coactivator 2 | protein | 13 | 54% helix, 0% strand | Q15596 |
| D | Nuclear receptor coactivator 2 | protein | 10 | 70% helix, 0% strand | Q15596 |
Ligands and binding sites
- 5KF · 4,4'-{[(3S)-3-(2-hydroxyethyl)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
7 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 | 0.84 | 0.97 | 24 | 5KF |
| 2 | 185 | 0.84 | 0.97 | 22 | 5KF |
| 3 | 87 | 0.64 | 0.90 | 18 | empty |
| 4 | 90 | 0.63 | 0.89 | 19 | empty |
| 5 | 257 | 0.59 | 0.79 | 36 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1728 Ų buried · 31 hydrogen bonds · protein-protein
- A–C · 602 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 534 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 5DZI · 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 5DZI · PDBe 5DZI · UniProt P03372 · UniProt Q15596
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