Research workbench
Crystal structure of the human pxr-lbd in complex with N-{(2R)-1- [(4S)-4-(4-chlorophenyl)-4-hydroxy-3,3-dimethylpiperidin-1-yl]-3- methyl-1-oxobutan-2-yl}-3-hydroxy-3-methylbutanamide
Analyse Crystal structure of the human pxr-lbd in complex with N-{(2R)-1… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4NY9
- Type
- protein
- Length
- 260 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nuclear receptor subfamily 1 group I member 2
- UniProt
- O75469
- Ligands
- 2Q4
- Pockets
- 4 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 58% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nuclear receptor subfamily 1 group I member 2 | protein | 260 | 58% helix, 8% strand | O75469 |
Ligands and binding sites
- 2Q4 · N-{(2R)-1-[(4S)-4-(4-chlorophenyl)-4-hydroxy-3,3-dimethylpiperidin-1-yl]-3-methyl-1-oxobutan-2-yl}-3-hydroxy-3-methylbutanamide · ligand · chains A
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 484 | 0.85 | 0.91 | 43 | 2Q4 |
| 2 | 105 | 0.40 | 0.76 | 17 | empty |
| 3 | 72 | 0.31 | 0.74 | 16 | empty |
| 4 | 51 | 0.27 | 0.74 | 16 | empty |
Compared structures
- 4NY9 · Crystal Structure Of the Human PXR-LBD In Complex With… · 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 0.99
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 O75469
- Elsewhere: RCSB PDB 4NY9 · PDBe 4NY9 · UniProt O75469
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