MolNFT v1 · #125091 · protein
Brain penetrant liver X receptor (lxr) modulators based on a 2,4,5,6- TETRAHYDROPYRROLO[3,4-C]PYRAZOLE core
5KYJ · Oxysterols receptor lxr-beta: “Brain penetrant liver X receptor (lxr) modulators based on a 2,4,5,6- TETRAHYDROPYRROLO[3,4-C]PYRAZOLE core”. X-ray diffraction, 1 ligand (6Y8), 12 pockets (best druggability 0.83). MolNFT v1 #125091…
- PDB
- 5KYJ
- Type
- protein
- Length
- 931 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Oxysterols receptor lxr-beta; Retinoic acid receptor rxr-beta
- UniProt
- P55055, P28702
- Ligands
- 6Y8
- Pockets
- 12 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 69% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Oxysterols receptor lxr-beta | protein | 251 | 67% helix, 4% strand | P55055 |
| B | Retinoic acid receptor rxr-beta | protein | 217 | 69% helix, 3% strand | P28702 |
| E | Oxysterols receptor lxr-beta | protein | 245 | 69% helix, 4% strand | P55055 |
| F | Retinoic acid receptor rxr-beta | protein | 218 | 68% helix, 3% strand | P28702 |
Ligands and binding sites
- 6Y8 · (6~{R})-5-(5-fluoranyl-2-methoxy-pyrimidin-4-yl)-2-(3-methylsulfonylphenyl)-6-propan-2-yl-4,6-dihydropyrrolo[3,4-c]pyrazole · ligand · 2 copies · chains A, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 229 | 0.83 | 0.95 | 28 | 6Y8 |
| 2 | 215 | 0.83 | 0.96 | 30 | 6Y8 |
| 3 | 174 | 0.82 | 0.96 | 29 | empty |
| 4 | 205 | 0.80 | 0.94 | 29 | empty |
| 5 | 1112 | 0.76 | 0.79 | 108 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1002 Ų buried · 6 hydrogen bonds · protein-protein
- E–F · 996 Ų buried · 6 hydrogen bonds · protein-protein
- A–E · 231 Ų buried · 0 hydrogen bonds · protein-protein
- A–F · 157 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 5KYJ · Brain penetrant liver X receptor (LXR) modulators based on a… · the same entry in another collection · chain F against F, TM-score 1.00
- P55055 · AlphaFold monomer V2.0 prediction for oxysterols receptor lxr-beta (P55055) · a predicted model of the same protein · chain E against A, TM-score 0.95
- P28702 · AlphaFold monomer V2.0 prediction for retinoic acid receptor rxr-beta (P28702) · a predicted model of the same protein · chain B against A, TM-score 0.95
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
- Every structure of UniProt P28702
- Elsewhere: RCSB PDB 5KYJ · PDBe 5KYJ · UniProt P55055 · UniProt P28702
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.