Research workbench
Crystal structure of pxr in complex with compound 7
Analyse Crystal structure of pxr in complex with compound 7 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6DUP
- Type
- protein
- Length
- 562 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nuclear receptor subfamily 1 group I member 2
- UniProt
- O75469
- Ligands
- HCJ
- Pockets
- 5 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 61% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nuclear receptor subfamily 1 group I member 2 | protein | 282 | 62% helix, 7% strand | O75469 |
| B | Nuclear receptor subfamily 1 group I member 2 | protein | 280 | 60% helix, 8% strand | O75469 |
Ligands and binding sites
- HCJ · (2S)-2-({[3'-(trifluoromethyl)[1,1'-biphenyl]-4-yl]oxy}methyl)-2,3-dihydro-7H-[1,3]oxazolo[3,2-a]pyrimidin-7-one · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 342 | 0.85 | 0.94 | 41 | empty |
| 2 | 320 | 0.84 | 0.93 | 37 | HCJ |
| 3 | 119 | 0.42 | 0.76 | 20 | empty |
| 4 | 56 | 0.34 | 0.78 | 14 | empty |
| 5 | 69 | 0.33 | 0.76 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 917 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 6DUP · Crystal structure of pxr in complex with compound 7 · 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
- Elsewhere: RCSB PDB 6DUP · PDBe 6DUP · UniProt O75469
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