MolNFT v1 · #52711 · protein
RU486 bound to the progesterone receptor in a destabilized agonistic conformation
2W8Y: “RU486 bound to the progesterone receptor in a destabilized agonistic conformation”. X-ray diffraction, 3 ligands (486, NDR, SO4), 9 pockets (best druggability 0.85). MolNFT v1 #52711 on GenesisL1: 3D structure, binding sites and…
- PDB
- 2W8Y
- Type
- protein
- Length
- 500 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Progesterone receptor
- UniProt
- P06401
- Ligands
- 486, NDR, SO4
- Pockets
- 9 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 68% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Progesterone receptor | protein | 250 | 68% helix, 4% strand | P06401 |
Ligands and binding sites
- 486 · 11-(4-dimethylamino-phenyl)-17-hydroxy-13-methyl-17-prop-1-ynyl-1,2,6,7,8,11,12,13,14,15,16,17-dodec ahydro-cyclopenta[a]phenanthren-3-one · ligand · chains A
- NDR · (14beta,17alpha)-17-ethynyl-17-hydroxyestr-4-en-3-one · ligand · chains B
- SO4 · Sulfate ion · ion · chains A
- EDO · 1,2-ethanediol · additive · chains 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, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 247 | 0.85 | 0.97 | 28 | 486 |
| 2 | 201 | 0.85 | 0.97 | 23 | NDR |
| 3 | 299 | 0.70 | 0.83 | 31 | empty |
| 4 | 187 | 0.67 | 0.86 | 25 | empty |
| 5 | 88 | 0.57 | 0.86 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 356 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 2W8Y · RU486 bound to the progesterone receptor in a destabilized agonistic conformation · the same entry in another collection · chain A against A, TM-score 1.00
- P06401 · AlphaFold monomer V2.0 prediction for progesterone receptor (P06401) · 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 P06401
- Elsewhere: RCSB PDB 2W8Y · PDBe 2W8Y · UniProt P06401
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