MolNFT v1 · #116655 · protein
Crystal structure of the er-alpha ligand-binding domain in complex with a 3-methylphenylamino-substituted ethyl triaryl-ethylene derivative 4,4'-(2-{3-[(3-METHYLPHENYL)AMINO]PHENYL}BUT-1-ene-1,1- DIYL)DIPHENOL
5DKB · Estrogen receptor: “Crystal structure of the er-alpha ligand-binding domain in complex with a 3-methylphenylamino-substituted…”. X-ray diffraction, 1 ligand (5C9), 9 pockets (best druggability 0.78). MolNFT v1 #116655 on GenesisL1…
- PDB
- 5DKB
- Type
- protein
- Length
- 482 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
- 5C9
- Pockets
- 9 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 67% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Estrogen receptor | protein | 230 | 66% helix, 4% strand | P03372 |
| B | Estrogen receptor | protein | 232 | 68% helix, 4% strand | P03372 |
| C, D | Nuclear receptor coactivator 2 | protein | 10 | 70% helix, 0% strand | Q15596 |
Ligands and binding sites
- 5C9 · 4,4'-(2-{3-[(3-methylphenyl)amino]phenyl}but-1-ene-1,1-diyl)diphenol · ligand · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 292 | 0.78 | 0.89 | 33 | 5C9 |
| 2 | 438 | 0.77 | 0.85 | 50 | 5C9 |
| 3 | 75 | 0.66 | 0.92 | 17 | empty |
| 4 | 90 | 0.64 | 0.90 | 20 | empty |
| 5 | 106 | 0.46 | 0.79 | 17 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1713 Ų buried · 35 hydrogen bonds · protein-protein
- B–D · 529 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 521 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 5DKB · 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 5DKB · PDBe 5DKB · UniProt P03372 · UniProt Q15596
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