MolNFT v1 · #116672 · protein
Crystal structure of the er-alpha ligand-binding domain in complex with a 2-naphthylamino-substituted, ethyl, triaryl-ethylene derivative 4,4'-{2-[3-(naphthalen-1-YLAMINO)PHENYL]BUT-1-ene-1,1- DIYL}DIPHENOL
5DKS · Estrogen receptor: “Crystal structure of the er-alpha ligand-binding domain in complex with a 2-naphthylamino-substituted, ethyl…”. X-ray diffraction, 1 ligand (5C6), 6 pockets (best druggability 0.86). MolNFT v1 #116672 on…
- PDB
- 5DKS
- Type
- protein
- Length
- 470 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
- 5C6
- Pockets
- 6 · best druggability 0.86
Structure
x-ray diffraction · 3 distinct chains · 64% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Estrogen receptor | protein | 225 | 65% helix, 4% strand | P03372 |
| B | Estrogen receptor | protein | 227 | 64% helix, 4% strand | P03372 |
| C, D | Nuclear receptor coactivator 2 | protein | 9 | 56% helix, 0% strand | Q15596 |
Ligands and binding sites
- 5C6 · 4,4'-{2-[3-(naphthalen-1-ylamino)phenyl]but-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
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 284 | 0.86 | 0.96 | 32 | 5C6 |
| 2 | 462 | 0.79 | 0.87 | 56 | 5C6 |
| 3 | 88 | 0.65 | 0.90 | 16 | empty |
| 4 | 86 | 0.64 | 0.90 | 17 | empty |
| 5 | 131 | 0.42 | 0.75 | 18 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1743 Ų buried · 34 hydrogen bonds · protein-protein
- A–C · 510 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 477 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 5DKS · 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 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
- Every structure of UniProt Q15596
- Elsewhere: RCSB PDB 5DKS · PDBe 5DKS · UniProt P03372 · UniProt Q15596
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.