Research workbench

Discovery of novel, orally efficacious liver X receptor (lxr) beta agonists

Analyse Discovery of novel, orally efficacious liver X receptor (lxr) beta agonists in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5I4V
Type: protein
Length: 938 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Oxysterols receptor lxr-BETA,NUCLEAR receptor coactivator 2; Retinoic acid receptor…
UniProt: P55055, Q15596, P28702
Ligands: 67S
Pockets: 15 · best druggability 0.85

Structure

x-ray diffraction · 4 distinct chains · 70% helix, 3% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Oxysterols receptor lxr-BETA,NUCLEAR receptor coactivator 2	protein	260	68% helix, 4% strand	P55055, Q15596
B	Retinoic acid receptor rxr-BETA,NUCLEAR receptor coactivator 2	protein	215	71% helix, 3% strand	Q15596, P28702
E	Oxysterols receptor lxr-BETA,NUCLEAR receptor coactivator 2	protein	245	72% helix, 4% strand	P55055, Q15596
F	Retinoic acid receptor rxr-BETA,NUCLEAR receptor coactivator 2	protein	218	70% helix, 3% strand	Q15596, P28702

Ligands and binding sites

67S · {2-[(2R)-4-[4-(hydroxymethyl)-3-(methylsulfonyl)phenyl]-2-(propan-2-yl)piperazin-1-yl]-4-(trifluoromethyl)pyrimidin-5-yl}methanol · ligand · 2 copies · chains A, E

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

15 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	283	0.85	0.95	38	67S
2	281	0.84	0.94	35	67S
3	702	0.82	0.86	66	empty
4	216	0.82	0.94	33	empty
5	240	0.79	0.92	32	empty

Interfaces

4 interfaces between chains.

E–F · 1013 Å² buried · 8 hydrogen bonds · protein-protein
A–B · 985 Å² buried · 8 hydrogen bonds · protein-protein
A–E · 796 Å² buried · 7 hydrogen bonds · protein-protein
B–E · 510 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

5I4V · Discovery of novel, orally efficacious Liver X Receptor (LXR) beta agonists · 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 Q15596
Every structure of UniProt P28702
Elsewhere: RCSB PDB 5I4V · PDBe 5I4V · UniProt P55055 · UniProt Q15596 · UniProt P28702

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