Research workbench
Optimization of a novel binding motif to to (E)-3-(3,5- difluoro-4-((1R,3R)-2-(2-fluoro-2-methylpropyl)-3-methyl-2, 3,4,9-tetrahydro-1H-PYRIDO(3,4-B)INDOL-1-YL)PHENYL)ACRYLIC acid (AZD9496), a potent and orally bioavailable selective estrogen receptor downregulator and antagonist
Analyse Optimization of a novel binding motif to to (E)-3-(3,5… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5AAV
- Type
- protein
- Length
- 441 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Estrogen receptor
- UniProt
- P03372
- Ligands
- GW5
- Pockets
- 7 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 71% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Estrogen receptor | protein | 232 | 69% helix, 4% strand | P03372 |
| B | Estrogen receptor | protein | 209 | 73% helix, 4% strand | P03372 |
Ligands and binding sites
- GW5 · (2E)-3-{4-[(1E)-1,2-diphenylbut-1-enyl]phenyl}acrylic acid · 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, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 236 | 0.77 | 0.90 | 29 | GW5 |
| 2 | 222 | 0.74 | 0.88 | 23 | GW5 |
| 3 | 93 | 0.61 | 0.88 | 19 | empty |
| 4 | 94 | 0.59 | 0.86 | 17 | empty |
| 5 | 289 | 0.55 | 0.76 | 36 | empty |
Interfaces
1 interface between chains.
- A–B · 1381 Ų buried · 21 hydrogen bonds · protein-protein
Compared structures
- 5AAV · Optimization of a novel binding motif to to (E)-3-(3,5-difluoro-4-((1R,3R)-2-(2-fluoro-2-m… · 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 0.95
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 5AAV · PDBe 5AAV · UniProt P03372
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