MolNFT v1 · #14180 · protein
Crystal structure of the human pregane X receptor ligand binding domain in complex with hyperforin, a constituent of st. JOHN'S wort
1M13 · Orphan nuclear receptor pxr: “Crystal structure of the human pregane X receptor ligand binding domain in complex with hyperforin, a…”. X-ray diffraction, 1 ligand (HYF), 2 pockets (best druggability 0.86). MolNFT v1 #14180 on…
- PDB
- 1M13
- Type
- protein
- Length
- 273 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Orphan nuclear receptor pxr
- UniProt
- O75469
- Ligands
- HYF
- Pockets
- 2 · best druggability 0.86
Structure
x-ray diffraction · 1 distinct chain · 61% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Orphan nuclear receptor pxr | protein | 273 | 61% helix, 8% strand | O75469 |
Ligands and binding sites
- HYF · 4-hydroxy-5-isobutyryl-6-methyl-1,3,7-tris-(3-methyl-but-2-enyl)-6-(4-methyl-pent-3-enyl)-bicyclo[3.3.1]non-3-ene-2,9-dione · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 602 | 0.86 | 0.91 | 46 | HYF |
| 2 | 86 | 0.37 | 0.76 | 18 | empty |
Compared structures
- 1M13 · Crystal Structure of the Human Pregane X Receptor Ligand Binding Domain 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 1M13 · PDBe 1M13 · UniProt O75469
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