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
- 5Q15
- Type
- protein
- Length
- 480 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
- 9MP
- Pockets
- 6 · best druggability 0.86
Structure
x-ray diffraction · 4 distinct chains · 72% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Bile acid receptor | protein | 230 | 71% helix, 0% strand | Q96RI1 |
| B | Coactivator peptide src-1 HD3 | protein | 11 | 73% helix, 0% strand | A8K1V4 |
| C | Bile acid receptor | protein | 229 | 72% helix, 0% strand | Q96RI1 |
| D | Coactivator peptide src-1 HD3 | protein | 10 | 80% helix, 0% strand | A8K1V4 |
Ligands and binding sites
- 9MP · (2S)-N,2-dicyclohexyl-2-{5,6-difluoro-2-[(R)-methoxy(phenyl)methyl]-1H-benzimidazol-1-yl}acetamide · 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 331 | 0.86 | 0.96 | 31 | 9MP |
| 2 | 314 | 0.85 | 0.95 | 32 | 9MP |
| 3 | 184 | 0.47 | 0.75 | 28 | empty |
| 4 | 161 | 0.45 | 0.75 | 23 | empty |
| 5 | 111 | 0.39 | 0.75 | 19 | empty |
Interfaces
3 interfaces between chains.
- A–B · 599 Ų buried · 5 hydrogen bonds · protein-protein
- C–D · 595 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 137 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5Q15 · Ligand binding to FARNESOID-X-RECEPTOR · the same entry in another collection · chain C against C, 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 5Q15 · PDBe 5Q15 · UniProt Q96RI1 · UniProt A8K1V4
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