Research workbench
X-ray structure of benzisoxazole urea synthetic agonist bound to the lxr-alpha
Analyse X-ray structure of benzisoxazole urea synthetic agonist bound to the lxr-alpha in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3IPU
- Type
- protein
- Length
- 503 residues
- Chains
- 4
- 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
- O40, SO4
- Pockets
- 6 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 70% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Oxysterols receptor lxr-alpha | protein | 238 | 70% helix, 3% strand | Q13133 |
| B | Oxysterols receptor lxr-alpha | protein | 235 | 71% helix, 3% strand | Q13133 |
| C, D | Nuclear receptor coactivator 1 (EC 2.3.1.48) | protein | 15 | 53% helix, 0% strand | Q15788 |
Ligands and binding sites
- O40 · 4-{[methyl(3-{[7-propyl-3-(trifluoromethyl)-1,2-benzisoxazol-6-yl]oxy}propyl)carbamoyl]amino}benzoic acid · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains B, D, A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 379 | 0.81 | 0.89 | 47 | O40 |
| 2 | 318 | 0.80 | 0.90 | 35 | O40 |
| 3 | 1126 | 0.78 | 0.80 | 104 | empty |
| 4 | 63 | 0.46 | 0.83 | 17 | empty |
| 5 | 145 | 0.44 | 0.76 | 28 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1204 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 713 Ų buried · 11 hydrogen bonds · protein-protein
- B–D · 712 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 3IPU · X-ray structure of benzisoxazole urea synthetic agonist bound to the LXR-alpha · 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 B against A, TM-score 0.97
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 3IPU · PDBe 3IPU · UniProt Q13133 · UniProt Q15788
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