MolNFT v1 · #131310 · protein
Ligand binding to farnesoid-X-receptor
5Q1D · Bile acid receptor: “Ligand binding to farnesoid-X-receptor”. X-ray diffraction, 1 ligand (9ND), 4 pockets (best druggability 0.85). MolNFT v1 #131310 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5Q1D
- Type
- protein
- Length
- 482 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
- 9ND
- Pockets
- 4 · best druggability 0.85
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 | 72% helix, 0% strand | Q96RI1 |
| B | Coactivator peptide src-1 HD3 | protein | 11 | 64% helix, 0% strand | A8K1V4 |
| D | Coactivator peptide src-1 HD3 | protein | 11 | 73% helix, 0% strand | A8K1V4 |
Ligands and binding sites
- 9ND · (2S)-2-[2-(4-chlorophenyl)-5,6-difluoro-1H-benzimidazol-1-yl]-2-cyclohexyl-N-phenylacetamide · ligand · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 357 | 0.85 | 0.93 | 41 | 9ND |
| 2 | 566 | 0.81 | 0.86 | 63 | 9ND |
| 3 | 126 | 0.39 | 0.74 | 21 | empty |
| 4 | 103 | 0.37 | 0.75 | 19 | empty |
Interfaces
3 interfaces between chains.
- C–D · 623 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 575 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 192 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 5Q1D · 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 5Q1D · PDBe 5Q1D · UniProt Q96RI1 · UniProt A8K1V4
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