Research workbench
Crystal structure of human ROR gamma LBD in complex with a (quinolinoxymethyl)benzamide inverse agonist
Analyse Crystal structure of human ROR gamma LBD in complex with a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6SLZ
- Type
- protein
- Length
- 436 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.2
- Source
- Homo sapiens
- Molecule
- Nuclear receptor ROR-gamma
- UniProt
- P51449
- Ligands
- LK8
- Pockets
- 7 · best druggability 0.82
Structure
x-ray diffraction · resolution 2.2 · 2 distinct chains · 69% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nuclear receptor ROR-gamma | protein | 218 | 68% helix, 5% strand | P51449 |
| B | Nuclear receptor ROR-gamma | protein | 218 | 70% helix, 5% strand | P51449 |
Ligands and binding sites
- LK8 · (2~{S})-1-[2,4-bis(chloranyl)-3-[[2-methyl-4-(trifluoromethyl)quinolin-8-yl]oxymethyl]phenyl]carbonyl-~{N}-methyl-pyrrolidine-2-carboxamide · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 376 | 0.82 | 0.91 | 37 | LK8 |
| 2 | 426 | 0.82 | 0.89 | 36 | LK8 |
| 3 | 393 | 0.68 | 0.81 | 53 | empty |
| 4 | 132 | 0.45 | 0.77 | 18 | empty |
| 5 | 89 | 0.42 | 0.79 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 1216 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 6SLZ · Crystal structure of human ror gamma lbd in complex with a (QUINOLINOXYMETHYL)BENZAMIDE… · the same entry in another collection · chain A against A, TM-score 1.00
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 P51449
- Elsewhere: RCSB PDB 6SLZ · PDBe 6SLZ · UniProt P51449
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