Research workbench
Crystal structure of lxralpha in complex with tert-butyl benzoate analog, compound 32B
Analyse Crystal structure of lxralpha in complex with tert-butyl benzoate analog… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5AVL
- Type
- protein
- Length
- 239 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Oxysterols receptor lxr-alpha; Nuclear receptor coactivator 1
- EC
- 2.3.1.48
- UniProt
- Q13133, Q15788
- Ligands
- 4KQ
- Pockets
- 3 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 70% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Oxysterols receptor lxr-alpha | protein | 224 | 69% helix, 4% strand | Q13133 |
| B | Nuclear receptor coactivator 1 (EC 2.3.1.48) | protein | 15 | 80% helix, 0% strand | Q15788 |
Ligands and binding sites
- 4KQ · 2-[4-[4-[[2-[(2-methylpropan-2-yl)oxycarbonyl]-3-oxidanyl-4-(trifluoromethyl)phenyl]methoxy]phenyl]phenyl]ethanoic acid · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 264 | 0.80 | 0.91 | 28 | 4KQ |
| 2 | 120 | 0.42 | 0.76 | 20 | empty |
| 3 | 57 | 0.29 | 0.75 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 727 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 5AVL · Crystal structure of LXRalpha in complex with tert-butyl benzoate analog, compound 32b · the same entry in another collection · chain A against A, TM-score 1.00
- Q13133 · AlphaFold monomer V2.0 prediction for oxysterols receptor lxr-alpha (Q13133) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 Q13133
- Every structure of UniProt Q15788
- Elsewhere: RCSB PDB 5AVL · PDBe 5AVL · UniProt Q13133 · UniProt Q15788
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