Research workbench
Ligand binding to farnesoid-X-receptor
Analyse Ligand binding to farnesoid-X-receptor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5Q16
- Type
- protein
- Length
- 479 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bile acid receptor; Coactivator peptide src-1 HD3
- UniProt
- Q96RI1, A8K1V4
- Ligands
- 9MS
- Pockets
- 6 · best druggability 0.86
Structure
x-ray diffraction · 3 distinct chains · 72% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Bile acid receptor | protein | 230 | 73% helix, 0% strand | Q96RI1 |
| B | Coactivator peptide src-1 HD3 | protein | 10 | 70% helix, 0% strand | A8K1V4 |
| D | Coactivator peptide src-1 HD3 | protein | 9 | 67% helix, 0% strand | A8K1V4 |
Ligands and binding sites
- 9MS · (2S)-2-{2-[(4-chloro-2-methylphenoxy)methyl]-6-fluoro-1H-benzimidazol-1-yl}-N,2-dicyclohexylacetamide · ligand · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 406 | 0.86 | 0.93 | 42 | 9MS |
| 2 | 354 | 0.86 | 0.94 | 39 | 9MS |
| 3 | 238 | 0.53 | 0.77 | 27 | empty |
| 4 | 138 | 0.43 | 0.76 | 20 | empty |
| 5 | 91 | 0.34 | 0.74 | 17 | empty |
Interfaces
3 interfaces between chains.
- A–B · 587 Ų buried · 6 hydrogen bonds · protein-protein
- C–D · 575 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 237 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 5Q16 · Ligand binding to FARNESOID-X-RECEPTOR · 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 Q96RI1
- Every structure of UniProt A8K1V4
- Elsewhere: RCSB PDB 5Q16 · PDBe 5Q16 · UniProt Q96RI1 · UniProt A8K1V4
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