Research workbench
Crystal structure of the er-alpha ligand-binding domain in complex with a 4-fluorophenylamino-substituted, methyl triaryl-ethylene derivative 4,4'-(2-{3-[(4-FLUOROPHENYL)AMINO]PHENYL}PROP-1-ene-1,1- DIYL)DIPHENOL
Analyse Crystal structure of the er-alpha ligand-binding domain in complex with a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5DMF
- Type
- protein
- Length
- 491 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
- 5DG
- Pockets
- 8 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 67% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Estrogen receptor | protein | 236 | 67% helix, 4% strand | P03372 |
| B | Estrogen receptor | protein | 233 | 68% helix, 4% strand | P03372 |
| C | Nuclear receptor coactivator 2 | protein | 12 | 58% helix, 0% strand | Q15596 |
| D | Nuclear receptor coactivator 2 | protein | 10 | 50% helix, 0% strand | Q15596 |
Ligands and binding sites
- 5DG · 4,4'-(2-{3-[(4-fluorophenyl)amino]phenyl}prop-1-ene-1,1-diyl)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 | 248 | 0.82 | 0.93 | 34 | 5DG |
| 2 | 237 | 0.80 | 0.93 | 32 | 5DG |
| 3 | 100 | 0.65 | 0.90 | 19 | empty |
| 4 | 93 | 0.63 | 0.89 | 19 | empty |
| 5 | 185 | 0.51 | 0.77 | 28 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1661 Ų buried · 34 hydrogen bonds · protein-protein
- A–C · 618 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 502 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 5DMF · Crystal Structure of the ER-alpha Ligand-binding Domain in complex with a… · 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 5DMF · PDBe 5DMF · UniProt P03372 · UniProt Q15596
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.