MolNFT v1 · #113885 · protein
Crystal structure of lxralpha in complex with tert-butyl benzoate analog, compound 4
5AVI · Oxysterols receptor lxr-alpha: “Crystal structure of lxralpha in complex with tert-butyl benzoate analog, compound 4”. X-ray diffraction, 1 ligand (4KM), 4 pockets (best druggability 0.81). MolNFT v1 #113885 on GenesisL1: 3D…
- PDB
- 5AVI
- Type
- protein
- Length
- 484 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
- 4KM
- Pockets
- 4 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 67% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Oxysterols receptor lxr-alpha | protein | 228 | 68% helix, 4% strand | Q13133 |
| B, D | Nuclear receptor coactivator 1 (EC 2.3.1.48) | protein | 15 | 53% helix, 0% strand | Q15788 |
| C | Oxysterols receptor lxr-alpha | protein | 226 | 67% helix, 4% strand | Q13133 |
Ligands and binding sites
- 4KM · tert-butyl 2-[[4-[ethanoyl(methyl)amino]phenoxy]methyl]-5-(trifluoromethyl)benzoate · ligand · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 352 | 0.81 | 0.90 | 42 | 4KM |
| 2 | 344 | 0.81 | 0.90 | 41 | 4KM |
| 3 | 1122 | 0.77 | 0.79 | 102 | empty |
| 4 | 74 | 0.42 | 0.80 | 23 | empty |
Interfaces
3 interfaces between chains.
- A–C · 1296 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 738 Ų buried · 12 hydrogen bonds · protein-protein
- C–D · 731 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 5AVI · Crystal structure of LXRalpha in complex with tert-butyl benzoate analog, compound 4 · 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 C 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 5AVI · PDBe 5AVI · UniProt Q13133 · UniProt Q15788
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