Research workbench
Lxrbeta ligand binding domain in comlpex with small molecule inhibitors
Analyse Lxrbeta ligand binding domain in comlpex with small molecule inhibitors in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6S4U
- Type
- protein
- Length
- 703 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Oxysterols receptor lxr-beta
- UniProt
- P55055
- Ligands
- KVK
- Pockets
- 10 · best druggability 0.86
Structure
x-ray diffraction · 3 distinct chains · 69% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Oxysterols receptor lxr-beta | protein | 236 | 69% helix, 4% strand | P55055 |
| B | Oxysterols receptor lxr-beta | protein | 233 | 68% helix, 4% strand | P55055 |
| C | Oxysterols receptor lxr-beta | protein | 234 | 68% helix, 4% strand | P55055 |
Ligands and binding sites
- KVK · 6-[4-[[3-oxidanyl-1,1-bis(oxidanylidene)-5-phenyl-2-propan-2-yl-3~{H}-1,2-thiazol-4-yl]amino]butyl]pyridine-2-sulfonamide · ligand · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 300 | 0.86 | 0.96 | 38 | KVK |
| 2 | 285 | 0.86 | 0.96 | 40 | KVK |
| 3 | 355 | 0.85 | 0.93 | 46 | KVK |
| 4 | 1104 | 0.80 | 0.81 | 94 | empty |
| 5 | 762 | 0.79 | 0.83 | 51 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1046 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 930 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 6S4U · LXRbeta ligand binding domain in comlpex with small molecule inhibitors · the same entry in another collection · chain A against A, TM-score 1.00
- P55055 · AlphaFold monomer V2.0 prediction for oxysterols receptor lxr-beta (P55055) · a predicted model of the same protein · chain B 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 P55055
- Elsewhere: RCSB PDB 6S4U · PDBe 6S4U · UniProt P55055
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