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
- 5AAU
- Type
- protein
- Length
- 451 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Estrogen receptor
- UniProt
- P03372
- Ligands
- XBR
- Pockets
- 6 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 71% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Estrogen receptor | protein | 229 | 71% helix, 4% strand | P03372 |
| B | Estrogen receptor | protein | 222 | 70% helix, 4% strand | P03372 |
Ligands and binding sites
- XBR · 3-(1-(4-Chlorophenyl)-3,4-dihydro-1H-pyrido(3,4-b)indol-2(9H)-yl)propanoic acid · 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 | 315 | 0.81 | 0.91 | 38 | XBR |
| 2 | 210 | 0.81 | 0.94 | 27 | XBR |
| 3 | 84 | 0.61 | 0.89 | 17 | empty |
| 4 | 259 | 0.54 | 0.76 | 43 | empty |
| 5 | 163 | 0.49 | 0.78 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 1570 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
- 5AAU · 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 0.94
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 5AAU · PDBe 5AAU · UniProt P03372
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