MolNFT v1 · #116658 · protein
Crystal structure of the er-alpha ligand-binding domain in complex with a 3-naphthyl-substituted, methyl, cis-diaryl-ethylene compound 4,4'-[2-(naphthalen-2-YL)PROP-1-ene-1,1-DIYL]DIPHENOL
5DKE · Estrogen receptor: “Crystal structure of the er-alpha ligand-binding domain in complex with a 3-naphthyl-substituted, methyl…”. X-ray diffraction, 1 ligand (5C8), 8 pockets (best druggability 0.84). MolNFT v1 #116658 on GenesisL1…
- PDB
- 5DKE
- Type
- protein
- Length
- 476 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Estrogen receptor; Nuclear receptor coactivator 2
- UniProt
- P03372
- Ligands
- 5C8
- Pockets
- 8 · best druggability 0.84
Structure
x-ray diffraction · 3 distinct chains · 66% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Estrogen receptor | protein | 221 | 70% helix, 4% strand | P03372 |
| B | Estrogen receptor | protein | 235 | 61% helix, 4% strand | P03372 |
| C, D | Nuclear receptor coactivator 2 | protein | 10 | 70% helix, 0% strand | — |
Ligands and binding sites
- 5C8 · 4,4'-[2-(naphthalen-2-yl)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, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 191 | 0.84 | 0.97 | 27 | 5C8 |
| 2 | 200 | 0.82 | 0.95 | 26 | 5C8 |
| 3 | 98 | 0.66 | 0.90 | 17 | empty |
| 4 | 100 | 0.64 | 0.89 | 19 | empty |
| 5 | 261 | 0.62 | 0.80 | 34 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1838 Ų buried · 29 hydrogen bonds · protein-protein
- B–D · 511 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 493 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 5DKE · 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 0.98
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 5DKE · PDBe 5DKE · UniProt P03372
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