Research workbench
Structure of human pregnane X receptor ligand binding domain bound tethered with src co-activator peptide and compound-3 aka 1,1,1,3,3,3-hexafluoro-2-{4-[1-(4- LUOROBENZENESULFONYL)CYCLOPENTYL]PHENYL}PROPAN-2-ol
Analyse Structure of human pregnane X receptor ligand binding domain bound tethered… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6NX1
- Type
- protein
- Length
- 582 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.27
- Source
- Homo sapiens
- Molecule
- Nuclear receptor subfamily 1 group I member 2,Nuclear receptor coactivator 1 fusion
- EC
- 2.3.1.48
- UniProt
- O75469, Q15788
- Ligands
- L7D
- Pockets
- 8 · best druggability 0.86
Structure
x-ray diffraction · resolution 2.27 · 2 distinct chains · 60% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nuclear receptor subfamily 1 group I member 2,Nuclear receptor coactivator 1 fusion (EC 2.3.1.48) | protein | 288 | 60% helix, 7% strand | O75469, Q15788 |
| B | Nuclear receptor subfamily 1 group I member 2,Nuclear receptor coactivator 1 fusion (EC 2.3.1.48) | protein | 294 | 60% helix, 7% strand | O75469, Q15788 |
Ligands and binding sites
- L7D · 1,1,1,3,3,3-hexafluoro-2-(4-{1-[(4-fluorophenyl) sulfonyl]cyclopentyl}phenyl)propan-2-ol · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 383 | 0.86 | 0.94 | 42 | L7D |
| 2 | 449 | 0.85 | 0.92 | 45 | L7D |
| 3 | 557 | 0.65 | 0.76 | 60 | empty |
| 4 | 247 | 0.54 | 0.76 | 28 | empty |
| 5 | 65 | 0.35 | 0.77 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 447 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 6NX1 · Structure of human pregnane X receptor ligand binding domain bound tethered with src… · the same entry in another collection · chain A against A, TM-score 1.00
- O75469 · AlphaFold monomer V2.0 prediction for nuclear receptor subfamily 1 group I member 2… · a predicted model of the same protein · chain A 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 O75469
- Every structure of UniProt Q15788
- Elsewhere: RCSB PDB 6NX1 · PDBe 6NX1 · UniProt O75469 · UniProt Q15788
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