Research workbench
Benzopyrans as selective estrogen receptor B agonists (serbas). part 2: structure activity relationship studies on the benzopyran scaffold.
Analyse Benzopyrans as selective estrogen receptor B agonists (serbas). part 2… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2POG
- Type
- protein
- Length
- 444 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Estrogen receptor
- UniProt
- P03372
- Ligands
- WST
- Pockets
- 6 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 73% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Estrogen receptor | protein | 233 | 72% helix, 4% strand | P03372 |
| B | Estrogen receptor | protein | 211 | 75% helix, 4% strand | P03372 |
Ligands and binding sites
- WST · (3as,4r,9br)-4-(4-hydroxyphenyl)-1,2,3,3A,4,9B-hexahydrocyclopenta[c]chromen-9-ol · 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 | 216 | 0.81 | 0.93 | 23 | WST |
| 2 | 524 | 0.75 | 0.83 | 61 | WST |
| 3 | 100 | 0.63 | 0.88 | 18 | empty |
| 4 | 90 | 0.62 | 0.89 | 18 | empty |
| 5 | 144 | 0.44 | 0.76 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 1542 Ų buried · 24 hydrogen bonds · protein-protein
Compared structures
- 2POG · Benzopyrans as Selective Estrogen Receptor b Agonists (SERBAs). Part 2: Structure… · the same entry in another collection · chain B against B, 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 0.98
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 2POG · PDBe 2POG · UniProt P03372
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